From 58bf829bfe6e6a29459e646ac8a7cd2df563b78c Mon Sep 17 00:00:00 2001 From: Leon Kuchenbecker Date: Tue, 2 Feb 2021 10:32:52 +0100 Subject: [PATCH 01/25] Version bump 3.0.0rc2 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 78323b62..c34a040b 100644 --- a/setup.py +++ b/setup.py @@ -43,7 +43,7 @@ name='epytope', # Version: - version='3.0.0rc1', + version='3.0.0rc2', description='A Framework for Epitope Detection and Vaccine Design', long_description=readme, From db7130c63d4137bc18176822db679b500ed2896f Mon Sep 17 00:00:00 2001 From: Leon Kuchenbecker Date: Tue, 2 Feb 2021 10:38:53 +0100 Subject: [PATCH 02/25] Fix master / main branch naming in GH action --- .github/workflows/python-test-conda-external.yml | 4 ++-- .github/workflows/python-test-conda.yml | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/python-test-conda-external.yml b/.github/workflows/python-test-conda-external.yml index 3efc74d2..d574d876 100644 --- a/.github/workflows/python-test-conda-external.yml +++ b/.github/workflows/python-test-conda-external.yml @@ -2,9 +2,9 @@ name: Unit tests external tools on: push: - branches: [ master, develop ] + branches: [ main, develop ] pull_request: - branches: [ master, develop ] + branches: [ main, develop ] jobs: tests-external: diff --git a/.github/workflows/python-test-conda.yml b/.github/workflows/python-test-conda.yml index 89cc8c82..74f2106f 100644 --- a/.github/workflows/python-test-conda.yml +++ b/.github/workflows/python-test-conda.yml @@ -2,9 +2,9 @@ name: Unit tests without external tools on: push: - branches: [ master, develop ] + branches: [ main, develop ] pull_request: - branches: [ master, develop ] + branches: [ main, develop ] jobs: tests: From 5817e3e51a091f78d203801018b1f16d818d10a6 Mon Sep 17 00:00:00 2001 From: Leon Kuchenbecker Date: Tue, 2 Feb 2021 10:30:44 +0100 Subject: [PATCH 03/25] Fix typos in README file --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 6f048683..9f24e79d 100644 --- a/README.md +++ b/README.md @@ -35,7 +35,7 @@ Dependencies - PickPocket (http://www.cbs.dtu.dk/services/software.php) - Integer Linear Programming Solver (recommended CBC: https://projects.coin-or.org/Cbc) -Please pay attanention to the different licensings of the third party tools. +Please pay attention to the different licensing of third party tools. Getting Started --------------- From 12fb912b54f618b3870ba72d46ad53d122db2681 Mon Sep 17 00:00:00 2001 From: Leon Kuchenbecker Date: Fri, 5 Feb 2021 10:20:36 +0100 Subject: [PATCH 04/25] Add pypi GH action --- .github/workflows/pypi-publish.yml | 48 ++++++++++++++++++++++++++++++ README.rst | 23 -------------- setup.py | 14 ++++----- 3 files changed, 53 insertions(+), 32 deletions(-) create mode 100644 .github/workflows/pypi-publish.yml delete mode 100644 README.rst diff --git a/.github/workflows/pypi-publish.yml b/.github/workflows/pypi-publish.yml new file mode 100644 index 00000000..b6b3d7c1 --- /dev/null +++ b/.github/workflows/pypi-publish.yml @@ -0,0 +1,48 @@ +name: PyPI + +on: + push: + tags: + - v*.*.* + +jobs: + pypi-publish: + name: Publish tagged release on PyPI + runs-on: ubuntu-18.04 + steps: + - uses: actions/checkout@master + - name: Install utilities + run: sudo apt-get install -y mmv + - name: Set up Python 3.7 + uses: actions/setup-python@v1 + with: + python-version: 3.7 + - name: Install pypa/build + run: >- + python -m + pip install + build + --user + - name: Build a binary wheel and a source tarball + run: >- + python -m + build + --sdist + --wheel + --outdir dist/ + . + - name: Create timestamp + run: echo timestamp=$(date +%s) >> $GITHUB_ENV + - name: Rename built files to include timestamp + run: | + mmv -v dist/'*.*.*-*' dist/'#1.#2.#3-'$timestamp'-#4' + mmv -v dist/'*.tar.gz' dist/'#1-'$timestamp.tar.gz + - name: Publish distribution package to PyPI (test) + uses: pypa/gh-action-pypi-publish@master + with: + password: ${{ secrets.TEST_PYPI_API_TOKEN }} + repository_url: https://test.pypi.org/legacy/ + - name: Publish distribution package to PyPI (production) + uses: pypa/gh-action-pypi-publish@master + with: + password: ${{ secrets.PYPI_API_TOKEN }} diff --git a/README.rst b/README.rst deleted file mode 100644 index 172511c5..00000000 --- a/README.rst +++ /dev/null @@ -1,23 +0,0 @@ -epytope - An Immunoinformatics Framework for Python -------------------------------------------------- -Copyright 2014 by Benjamin Schuber, Mathias Walzer, Philipp Brachvogel, Andras Szolek, Christopher Mohr, and Oliver Kohlbacher - - -Epytope is a framework for T-cell epitope detection, and vaccine design. It offers consistent, easy, and simultaneous access to well established prediction methods of computational immunology. Epytope can handle polymorphic proteins and offers analysis tools to select, assemble, and design linker sequences for string-of-beads epitope-based vaccines. It is implemented in Python in a modular way and can easily be extended by user defined methods. - - -Copyright ----------- -epytope is released under the three clause BSD licence. - -Installation ------------- - -use the following commands: - - $ pip install git+https://github.com/KohlbacherLab/epytope - -Getting Started ---------------- - -Users and developers should start by reading our [wiki](https://github.com/KohlbacherLab/epytope/wiki) and [IPython tutorials](https://github.com/KohlbacherLab/epytope/tree/master/epytope/tutorials). diff --git a/setup.py b/setup.py index c34a040b..b81b622f 100644 --- a/setup.py +++ b/setup.py @@ -6,10 +6,6 @@ here = path.abspath(path.dirname(__file__)) -# Get the long description from the relevant file -with open(path.join(here, 'README.rst'), encoding='utf-8') as f: - readme = f.read() - #d2s_src_dir = path.join(path.join('epytope', 'Distance2Self'), 'src') #d2s_module = Extension('epytope.d2s', # define_macros=[('MAJOR_VERSION', '1'), @@ -89,11 +85,11 @@ # have to be included in MANIFEST.in as well. #include_package_data=True, package_data={ - 'epytope.Data.examples': ['*.*'], - 'epytope.Data.svms.svmtap': ['*'], - 'epytope.Data.svms.svmhc': ['*'], - 'epytope.Data.svms.unitope': ['*'], - #'epytope.Distance2Self': ['src/*'], #does not get installed, because the src folder is no package folder - compiles ok + 'epytope.Data.examples': ['*.*'], + 'epytope.Data.svms.svmtap': ['*'], + 'epytope.Data.svms.svmhc': ['*'], + 'epytope.Data.svms.unitope': ['*'], + #'epytope.Distance2Self': ['src/*'], #does not get installed, because the src folder is no package folder - compiles ok }, #package_data is a lie: http://stackoverflow.com/questions/7522250/how-to-include-package-data-with-setuptools-distribute From 428ddf27ea1660426e1eac6ed7260fd0bbdff10f Mon Sep 17 00:00:00 2001 From: Leon Kuchenbecker Date: Fri, 5 Feb 2021 12:48:14 +0100 Subject: [PATCH 05/25] Fix PyPI linting errors --- README.md | 2 +- setup.py | 13 ++++++++++--- 2 files changed, 11 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 9f24e79d..77c2ade9 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ [![Anaconda-Server Badge](https://anaconda.org/bioconda/fred2/badges/installer/conda.svg)](https://conda.anaconda.org/bioconda) epytope - An Immunoinformatics Framework for Python -------------------------------------------------- +--------------------------------------------------- Copyright 2014 by Benjamin Schuber, Mathias Walzer, Philipp Brachvogel, Andras Szolek, Christopher Mohr, and Oliver Kohlbacher diff --git a/setup.py b/setup.py index b81b622f..30316987 100644 --- a/setup.py +++ b/setup.py @@ -35,6 +35,12 @@ # and there is a bug in patternmatching http://bugs.python.org/issue19286 # install unclear for data_files +# Read the contents of the README.md file for use as long_description +from os import path +this_directory = path.abspath(path.dirname(__file__)) +with open(path.join(this_directory, 'README.md'), encoding='utf-8') as f: + long_description = f.read() + setup( name='epytope', @@ -42,7 +48,8 @@ version='3.0.0rc2', description='A Framework for Epitope Detection and Vaccine Design', - long_description=readme, + long_description=long_description, + long_description_content_type='text/markdown', # The project's main homepage. url='https://github.com/KohlbacherLab/epytope', @@ -63,8 +70,8 @@ 'Development Status :: 4 - Beta', # Indicate who your project is intended for - 'Intended Audience :: Biologists, Pharmacologist, Developer', - 'Topic :: Immunoinformatics :: Prediction Tools', + 'Intended Audience :: Science/Research', + 'Topic :: Scientific/Engineering :: Medical Science Apps.', # The license as you wish (should match "license" above) 'License :: OSI Approved :: BSD License', From 3e009c6a178079e9101adaa68bc42a4aa7de7857 Mon Sep 17 00:00:00 2001 From: Leon Kuchenbecker Date: Fri, 5 Feb 2021 17:41:28 +0100 Subject: [PATCH 06/25] Reduce version to 3.0.0rc1 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 30316987..831e84a3 100644 --- a/setup.py +++ b/setup.py @@ -45,7 +45,7 @@ name='epytope', # Version: - version='3.0.0rc2', + version='3.0.0rc1', description='A Framework for Epitope Detection and Vaccine Design', long_description=long_description, From 87536a02adf0b3bbf8dcdebd030981af2cb43699 Mon Sep 17 00:00:00 2001 From: Leon Kuchenbecker Date: Fri, 5 Feb 2021 21:09:51 +0100 Subject: [PATCH 07/25] Add a changelog --- CHANGELOG.md | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 CHANGELOG.md diff --git a/CHANGELOG.md b/CHANGELOG.md new file mode 100644 index 00000000..4e064037 --- /dev/null +++ b/CHANGELOG.md @@ -0,0 +1,24 @@ +# epytope: Changelog + +The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) +and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). + +## v3.0.0dev - [date] + +Initial release of epytope. Epytope is the successor project of FRED-2, which was renamed to a more versioning friendly base name. + +### `Added` + +- [#1](https://github.com/KohlbacherLab/epytope/pull/1) - Switch CI/CD from Travis to GitHub Actions +- [#6](https://github.com/KohlbacherLab/epytope/pull/6) - Add CI for external tools +- [#9](https://github.com/KohlbacherLab/epytope/pull/9) - Initial Python 2 to Python 3 conversion based on 2to3conv +- [#11](https://github.com/KohlbacherLab/epytope/pull/11) - Fix python version matrix in CI, remove versions that fail +- [#16](https://github.com/KohlbacherLab/epytope/pull/16) - Fix epitope prediction 2to3 bugs and tests +- [#17](https://github.com/KohlbacherLab/epytope/pull/17) - Fix Invalid subprocess handling and mhcflurry polluting stdout +- [#18](https://github.com/KohlbacherLab/epytope/pull/18) - Fix external (NetMHC tool family) epitope prediction error and tempfile handling +- [#20](https://github.com/KohlbacherLab/epytope/pull/20) - Use logging module rather than print calls across the library +- [#23](https://github.com/KohlbacherLab/epytope/pull/23) - Rename the package from FRED-2 to epytope +- [#24](https://github.com/KohlbacherLab/epytope/pull/24) - Add keras dependency +- [#25](https://github.com/KohlbacherLab/epytope/pull/25) - Refactor CI to use more pip and less conda +- [#26](https://github.com/KohlbacherLab/epytope/pull/26) - Add a license file +- [#31](https://github.com/KohlbacherLab/epytope/pull/31) - Add deployment to PyPI From 23d34c3725428107cd092a7e65bb42059c3954e5 Mon Sep 17 00:00:00 2001 From: Leon Kuchenbecker Date: Fri, 5 Feb 2021 21:12:22 +0100 Subject: [PATCH 08/25] Install changelog with package --- setup.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/setup.py b/setup.py index 831e84a3..f7800e0d 100644 --- a/setup.py +++ b/setup.py @@ -99,6 +99,10 @@ #'epytope.Distance2Self': ['src/*'], #does not get installed, because the src folder is no package folder - compiles ok }, + data_files = [ + ('docs', ['CHANGELOG.md']), + ], + #package_data is a lie: http://stackoverflow.com/questions/7522250/how-to-include-package-data-with-setuptools-distribute # 'package_data' is used to also install non package data files From 6bf305e86dcc693f9d2d3bd3196547968a9c086b Mon Sep 17 00:00:00 2001 From: Leon Kuchenbecker Date: Fri, 5 Feb 2021 21:23:41 +0100 Subject: [PATCH 09/25] Change PyPI CD trigger to published release --- .github/workflows/pypi-publish.yml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/.github/workflows/pypi-publish.yml b/.github/workflows/pypi-publish.yml index b6b3d7c1..827a434f 100644 --- a/.github/workflows/pypi-publish.yml +++ b/.github/workflows/pypi-publish.yml @@ -1,9 +1,8 @@ name: PyPI on: - push: - tags: - - v*.*.* + release: + types: [published] jobs: pypi-publish: From 65fd57a77a4ad5a35e9b1f2e5ddb242ae3ccd05f Mon Sep 17 00:00:00 2001 From: Jonas Scheid <43858870+jonasscheid@users.noreply.github.com> Date: Mon, 13 Dec 2021 13:58:44 +0100 Subject: [PATCH 10/25] Add rank metric #15 (#42) * Push all changes made on fork * Set Setuptools version also for external yml * Fixed erroneous variable names in matrix files * deleted A_2601_9 matrix for now. Caused troubles * Add A2601_9 syf matrix for debugging * Fixed bug in test caused by addition of A*26:01 matrix * Change solver from cbc to glpk to investigate if macOS dependant env problems in github actions can be solved * Corrected after review * Adjust tutorials to new structure * Change filter_result as discussed * Adjusted filter method and tutorials according to #12 * Fixed a bug occuring for netMHCfamily tools when peptide input has multiple lengths * remove logging * Alter filter_result method as discussed --- .../workflows/python-test-conda-external.yml | 2 +- .github/workflows/python-test-conda.yml | 4 +- epytope/Core/Result.py | 113 ++- epytope/Data/pssms/syfpeithi/mat/A_0101_10.py | 2 +- epytope/Data/pssms/syfpeithi/mat/A_0101_11.py | 2 +- epytope/Data/pssms/syfpeithi/mat/A_0101_12.py | 1 + epytope/Data/pssms/syfpeithi/mat/A_0101_13.py | 1 + epytope/Data/pssms/syfpeithi/mat/A_0101_9.py | 2 +- epytope/Data/pssms/syfpeithi/mat/A_0201_10.py | 2 +- 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epytope/Data/pssms/syfpeithi/mat/H2_Db_10.py create mode 100644 epytope/Data/pssms/syfpeithi/mat/H2_Db_9.py create mode 100644 epytope/Data/pssms/syfpeithi/mat/H2_Kb_8.py create mode 100644 epytope/Data/pssms/syfpeithi/mat/H2_Kd_10.py create mode 100644 epytope/Data/pssms/syfpeithi/mat/H2_Kd_9.py create mode 100644 epytope/Data/pssms/syfpeithi/mat/H2_Ld_9.py diff --git a/.github/workflows/python-test-conda-external.yml b/.github/workflows/python-test-conda-external.yml index d574d876..fbc3b89c 100644 --- a/.github/workflows/python-test-conda-external.yml +++ b/.github/workflows/python-test-conda-external.yml @@ -40,7 +40,7 @@ jobs: echo "PATH=$PATH" - name: Set up Python ${{ matrix.python-version }} run: | - $CONDA/bin/conda create -p /tmp/condaenv python==${{ matrix.python-version }}'.*' + $CONDA/bin/conda create -p /tmp/condaenv python==${{ matrix.python-version }}'.*' setuptools"==52.0" - name: Activate conda environment run: | echo "/tmp/condaenv/bin" >> $GITHUB_PATH diff --git a/.github/workflows/python-test-conda.yml b/.github/workflows/python-test-conda.yml index 74f2106f..cadb590d 100644 --- a/.github/workflows/python-test-conda.yml +++ b/.github/workflows/python-test-conda.yml @@ -22,7 +22,7 @@ jobs: echo "CONDA_PKGS_DIRS=/tmp/condapkgs" >> $GITHUB_ENV - name: Set up Python ${{ matrix.python-version }} run: | - $CONDA/bin/conda create -p /tmp/condaenv python==${{ matrix.python-version }}'.*' + $CONDA/bin/conda create -p /tmp/condaenv python==${{ matrix.python-version }}'.*' setuptools"==52.0" - name: Activate conda environment run: | echo "/tmp/condaenv/bin" >> $GITHUB_PATH @@ -31,6 +31,6 @@ jobs: run: | pip install . - name: Install Test dependencies - run: conda install -p /tmp/condaenv -c conda-forge -c bioconda nose nose-exclude coincbc + run: conda install -p /tmp/condaenv -c conda-forge -c bioconda nose nose-exclude glpk - name: Run Tests run: nosetests --exclude-dir=epytope/test/external epytope diff --git a/epytope/Core/Result.py b/epytope/Core/Result.py index a7657697..4b738438 100644 --- a/epytope/Core/Result.py +++ b/epytope/Core/Result.py @@ -11,7 +11,13 @@ import abc import numpy +from numpy.lib.arraysetops import isin import pandas +from epytope.Core.Allele import Allele +from epytope.Core.Peptide import Peptide +from copy import deepcopy +from sys import exit +import logging class AResult(pandas.DataFrame, metaclass=abc.ABCMeta): @@ -27,8 +33,7 @@ def filter_result(self, expressions): """ Filter result based on a list of expressions - :param list((str,comparator,float)) expressions: A list of triples consisting of (method_name, comparator, - threshold) + :param list((str,comparator,float)) expressions: A list of triples consisting of (method_name, comparator,threshold) :return: A new filtered AResult object :rtype: :class:`~epytope.Core.Result.AResult` """ @@ -56,46 +61,55 @@ class EpitopePredictionResult(AResult): EpitopePredictionResult - +--------------+-------------+-------------+-------------+-------------+ - | Peptide Obj | Method Name | Allele1 Obj | Allele2 Obj | Allele3 Obj | - +==============+=============+=============+=============+=============+ - | Peptide1 | Method 1 | 0.324 | 0.56 | 0.013 | - + +-------------+-------------+-------------+-------------+ - | | Method 2 | 20 | 15 | 23 | - +--------------+-------------+-------------+-------------+-------------+ - | Peptide2 | Method 1 | 0.50 | 0.36 | 0.98 | - + +-------------+-------------+-------------+-------------+ - | | Method 2 | 26 | 10 | 50 | - +--------------+-------------+-------------+-------------+-------------+ + +----------------+-------------------------------+-------------------------------+ + | Allele | Allele Obj 1 | Allele Obj 2 | + +- - - - - - - - +- - - - - - - -+- - - - - - - -+- - - - - - - -+- - - - - - - -+ + | Method | Method 1 | Method 2 | Method 1 | Method 2 | + +- - - - - - - - +- - - -+- - - -+- - - -+- - - -+- - - -+- - - -+- - - -+- - - -+ + | ScoreType | Score | Rank | Score | Rank | Score | Rank | Score | Rank | + +- - - - - - - - +- - - -+- - - -+- - - -+- - - -+- - - -+- - - -+- - - -+- - - -+ + | Peptides | | | | | | | | | + +================+=======+=======+=======+=======+=======+=======+=======+=======+ + | Peptide Obj 1 | 0.03 | 57.4 | 0.05 | 51.1 | 0.08 | 49.4 | 0.73 | 3.12 | + +----------------+-------+-------+-------+-------+-------+-------+-------+-------+ + | Peptide Obj 2 | 0.32 | 13.2 | 0.31 | 14.1 | 0.25 | 22.1 | 0.11 | 69.1 | + +----------------+-------+-------+-------+-------+-------+-------+-------+-------+ """ - def filter_result(self, expressions): + def filter_result(self, expressions, scoretype='Score'): """ Filters a result data frame based on a specified expression consisting of a list of triple with - (method_name, comparator, threshold). The expression is applied to each row. If any of the columns fulfill - the criteria the row remains. + (method_name, comparator, threshold) and a str of the methods scoretype to be filtered. + The expression is applied to each row. If any of the columns fulfill the criteria the row remains. + + :param list((str,comparator,float)) expression: A list of triples consisting of (method_name, comparator, threshold) + :param str scoretype: Indicates which scoretype of the specified method should be filtered - :param list((str,comparator,float)) expressions: A list of triples consisting of (method_name, comparator, - threshold) :return: Filtered result object :rtype: :class:`~epytope.Core.Result.EpitopePredictionResult` """ if isinstance(expressions, tuple): expressions = [expressions] + + df = deepcopy(self) + methods = list(set(df.columns.get_level_values(1))) + scoretypes = list(set(df.columns.get_level_values(2))) + if scoretype not in scoretypes: + raise ValueError("Specified ScoreType {} does not match ScoreTypes of data frame {}.".format(scoretype, scoretypes)) + + for expr in expressions: + method, comp, thr = expr + if method not in methods: + raise ValueError("Specified method {} does not match methods of data frame {}.".format(method, methods)) + else: + filt = comp(df.xs(method, axis = 1, level = 1).xs(scoretype, axis = 1, level = 1), thr).values + # Only keep rows which contain values fulfilling the comparators logic in the specified method + keep_row = [bool.any() for bool in filt] + df = df.loc[keep_row] - #builde logical expression - masks = list(map(list, [comp(self.loc[(slice(None), method), :], thr).any(axis=1) - for method, comp, thr in expressions])) - if len(masks) > 1: - masks = numpy.logical_and(*masks) - else: - masks = masks[0] - - #apply to all rows - idx = [f for f in masks - for _ in range(len(self.index.levels[1]))] - return EpitopePredictionResult(self.loc[idx, :]) + return EpitopePredictionResult(df) + def merge_results(self, others): """ @@ -110,20 +124,33 @@ def merge_results(self, others): if type(others) == type(self): others = [others] + + # Concatenates self and to be merged dataframe(s) + for other in others: + df = pandas.concat([df, other], axis=1) - for i in range(len(others)): - df1a, df2a = df.align(others[i]) - zero1 = df1a == 0 - zero2 = df2a == 0 - df1a = df1a.fillna(0) - df2a = df2a.fillna(0) - df = df1a+df2a - true_zero = zero1 | zero2 - false_zero = df == 0 - zero = true_zero & false_zero - nans = ~true_zero & false_zero - df[zero] = 0 - df[nans] = numpy.NaN + # Merge result of multiple predictors in others per allele + df_merged = pandas.concat([group[1] for group in df.groupby(level=[0,1], axis=1)], axis=1) + + return EpitopePredictionResult(df_merged) + + def from_dict(d, peps, method): + """ + Create EpitopePredictionResult object from dictionary holding scores for alleles, peptides and a specified method + """ + scoreType = numpy.asarray([list(m.keys()) for m in [metrics for a, metrics in d.items()]]).flatten() + alleles = numpy.asarray([numpy.repeat(a, len(set(scoreType))) for a in d]).flatten() + + meth = numpy.repeat(method, len(scoreType)) + multi_cols = pandas.MultiIndex.from_arrays([alleles, meth, scoreType], names=["Allele", "Method", "ScoreType"]) + df = pandas.DataFrame(float(0),index=pandas.Index(peps), columns=multi_cols) + df.index.name = 'Peptides' + # Fill DataFrame + for allele, metrics in d.items(): + for metric, pep_scores in metrics.items(): + for pep, score in pep_scores.items(): + df[allele][method][metric][pep] = score + return EpitopePredictionResult(df) diff --git a/epytope/Data/pssms/syfpeithi/mat/A_0101_10.py b/epytope/Data/pssms/syfpeithi/mat/A_0101_10.py index 70d6e2b9..65d28350 100644 --- a/epytope/Data/pssms/syfpeithi/mat/A_0101_10.py +++ b/epytope/Data/pssms/syfpeithi/mat/A_0101_10.py @@ -1 +1 @@ -A_0101_10 = {0: {'A': 1, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 1, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 1, 'X': 0}, 1: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 1, 'N': 0, 'Q': 0, 'P': 0, 'S': 4, 'R': 0, 'T': 6, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 2: {'A': 0, 'C': 0, 'E': 8, 'D': 10, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 3: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 1, 'M': 0, 'L': 1, 'N': 0, 'Q': 0, 'P': 1, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 1, 'Y': 0, 'X': 0}, 4: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 5: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 6: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 1, 'M': 0, 'L': 2, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 1, 'T': 1, 'W': 0, 'V': 0, 'Y': 1, 'X': 0}, 7: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 3, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 8: {'A': 0, 'C': 0, 'E': 1, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 1, 'M': 0, 'L': 1, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 1, 'T': 0, 'W': 0, 'V': 1, 'Y': 0, 'X': 0}, 9: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 15, 'X': 0}} \ No newline at end of file +A_0101_10 = {0: {'A': 1, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 1, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 1}, 1: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 1, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 4, 'T': 6, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 2: {'A': 0, 'C': 0, 'D': 10, 'E': 8, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 3: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 1, 'L': 1, 'M': 0, 'N': 0, 'P': 1, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 1, 'W': 0, 'X': 0, 'Y': 0}, 4: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 5: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 6: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 1, 'L': 2, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 1, 'S': 0, 'T': 1, 'V': 0, 'W': 0, 'X': 0, 'Y': 1}, 7: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 3, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 8: {'A': 0, 'C': 0, 'D': 0, 'E': 1, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 1, 'L': 1, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 1, 'S': 0, 'T': 0, 'V': 1, 'W': 0, 'X': 0, 'Y': 0}, 9: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 15}} \ No newline at end of file diff --git a/epytope/Data/pssms/syfpeithi/mat/A_0101_11.py b/epytope/Data/pssms/syfpeithi/mat/A_0101_11.py index 0be66a85..d458adbb 100644 --- a/epytope/Data/pssms/syfpeithi/mat/A_0101_11.py +++ b/epytope/Data/pssms/syfpeithi/mat/A_0101_11.py @@ -1 +1 @@ -A_0101_11 = {0: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 1, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 1, 'X': 0}, 1: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 1, 'N': 0, 'Q': 0, 'P': 0, 'S': 4, 'R': 0, 'T': 6, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 2: {'A': 0, 'C': 0, 'E': 8, 'D': 10, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 3: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 1, 'M': 0, 'L': 1, 'N': 0, 'Q': 0, 'P': 1, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 1, 'Y': 0, 'X': 0}, 4: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 5: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 6: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 7: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 1, 'M': 0, 'L': 2, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 1, 'T': 1, 'W': 0, 'V': 0, 'Y': 1, 'X': 0}, 8: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 3, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 9: {'A': 0, 'C': 0, 'E': 1, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 1, 'M': 0, 'L': 1, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 1, 'T': 0, 'W': 0, 'V': 1, 'Y': 0, 'X': 0}, 10: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 15, 'X': 0}} \ No newline at end of file +A_0101_11 = {0: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 1, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 1}, 1: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 1, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 4, 'T': 6, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 2: {'A': 0, 'C': 0, 'D': 10, 'E': 8, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 3: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 1, 'L': 1, 'M': 0, 'N': 0, 'P': 1, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 1, 'W': 0, 'X': 0, 'Y': 0}, 4: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 5: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 6: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 7: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 1, 'L': 2, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 1, 'S': 0, 'T': 1, 'V': 0, 'W': 0, 'X': 0, 'Y': 1}, 8: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 3, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 9: {'A': 0, 'C': 0, 'D': 0, 'E': 1, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 1, 'L': 1, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 1, 'S': 0, 'T': 0, 'V': 1, 'W': 0, 'X': 0, 'Y': 0}, 10: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 15}} \ No newline at end of file diff --git a/epytope/Data/pssms/syfpeithi/mat/A_0101_12.py b/epytope/Data/pssms/syfpeithi/mat/A_0101_12.py new file mode 100644 index 00000000..308a5027 --- /dev/null +++ b/epytope/Data/pssms/syfpeithi/mat/A_0101_12.py @@ -0,0 +1 @@ +A_0101_12 = {0: {'A': 1, 'C': 0, 'D': 0, 'E': 0, 'F': 1, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 2, 'T': 0, 'V': 1, 'W': 0, 'X': 0, 'Y': 2}, 1: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 1, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 4, 'T': 6, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 2: {'A': 0, 'C': 0, 'D': 10, 'E': 10, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 3: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 4: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 5: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 6: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 7: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 8: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 9: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 4, 'K': 0, 'L': 6, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 10: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 2, 'L': 2, 'M': 1, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 1, 'W': 0, 'X': 0, 'Y': 0}, 11: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 15}} \ No newline at end of file diff --git a/epytope/Data/pssms/syfpeithi/mat/A_0101_13.py b/epytope/Data/pssms/syfpeithi/mat/A_0101_13.py new file mode 100644 index 00000000..7e585453 --- /dev/null +++ b/epytope/Data/pssms/syfpeithi/mat/A_0101_13.py @@ -0,0 +1 @@ +A_0101_13 = {0: {'A': 1, 'C': 0, 'D': 0, 'E': 0, 'F': 1, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 2, 'T': 0, 'V': 1, 'W': 0, 'X': 0, 'Y': 2}, 1: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 1, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 4, 'T': 6, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 2: {'A': 0, 'C': 0, 'D': 10, 'E': 10, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 3: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 4: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 5: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 6: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 7: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 8: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 9: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 10: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 4, 'K': 0, 'L': 6, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 11: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 2, 'L': 2, 'M': 1, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 1, 'W': 0, 'X': 0, 'Y': 0}, 12: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 15}} \ No newline at end of file diff --git a/epytope/Data/pssms/syfpeithi/mat/A_0101_9.py b/epytope/Data/pssms/syfpeithi/mat/A_0101_9.py index e35e400c..48ff943a 100644 --- a/epytope/Data/pssms/syfpeithi/mat/A_0101_9.py +++ b/epytope/Data/pssms/syfpeithi/mat/A_0101_9.py @@ -1 +1 @@ -A_0101_9 = {0: {'A': 1, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 1, 'N': 0, 'Q': 0, 'P': 0, 'S': 1, 'R': 0, 'T': 0, 'W': 0, 'V': 1, 'Y': 1, 'X': 0}, 1: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 1, 'N': 0, 'Q': 0, 'P': 0, 'S': 4, 'R': 0, 'T': 6, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 2: {'A': 0, 'C': 0, 'E': 8, 'D': 10, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 3: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 1, 'P': 1, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 4: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 1, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 1, 'N': 0, 'Q': 1, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 5: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 2, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 1, 'T': 0, 'W': 0, 'V': 1, 'Y': 0, 'X': 0}, 6: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 3, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 7: {'A': 0, 'C': 0, 'E': 1, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 1, 'M': 0, 'L': 1, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 1, 'T': 0, 'W': 0, 'V': 1, 'Y': 0, 'X': 0}, 8: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 15, 'X': 0}} \ No newline at end of file +A_0101_9 = {0: {'A': 1, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 1, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 1, 'T': 0, 'V': 1, 'W': 0, 'X': 0, 'Y': 1}, 1: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 1, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 4, 'T': 6, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 2: {'A': 0, 'C': 0, 'D': 10, 'E': 8, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 3: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 1, 'Q': 1, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 4: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 1, 'H': 0, 'I': 0, 'K': 0, 'L': 1, 'M': 0, 'N': 0, 'P': 0, 'Q': 1, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 5: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 2, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 1, 'S': 0, 'T': 0, 'V': 1, 'W': 0, 'X': 0, 'Y': 0}, 6: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 3, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 7: {'A': 0, 'C': 0, 'D': 0, 'E': 1, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 1, 'L': 1, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 1, 'S': 0, 'T': 0, 'V': 1, 'W': 0, 'X': 0, 'Y': 0}, 8: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 15}} \ No newline at end of file diff --git a/epytope/Data/pssms/syfpeithi/mat/A_0201_10.py b/epytope/Data/pssms/syfpeithi/mat/A_0201_10.py index 4ff8e852..13fa7e3b 100644 --- a/epytope/Data/pssms/syfpeithi/mat/A_0201_10.py +++ b/epytope/Data/pssms/syfpeithi/mat/A_0201_10.py @@ -1 +1 @@ -A_0201_10 = {0: {'A': 2, 'C': 0, 'E': -3, 'D': -1, 'G': 1, 'F': 1, 'I': 2, 'H': 0, 'K': 1, 'M': 0, 'L': 2, 'N': 0, 'Q': 0, 'P': -3, 'S': 2, 'R': 0, 'T': 0, 'W': 0, 'V': 1, 'Y': 2, 'X': 0}, 1: {'A': 4, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 8, 'H': 0, 'K': 0, 'M': 8, 'L': 10, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 4, 'W': 0, 'V': 4, 'Y': 0, 'X': 0}, 2: {'A': 2, 'C': 0, 'E': -1, 'D': 0, 'G': 0, 'F': 1, 'I': 2, 'H': 0, 'K': -1, 'M': 1, 'L': 2, 'N': 1, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': -1, 'W': 1, 'V': 0, 'Y': 1, 'X': 0}, 3: {'A': 0, 'C': 0, 'E': 2, 'D': 1, 'G': 2, 'F': -1, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 2, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': -1, 'X': 0}, 4: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 5: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 6: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 4, 'H': 0, 'K': 0, 'M': 0, 'L': 4, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 4, 'Y': 0, 'X': 0}, 7: {'A': 2, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 1, 'K': -1, 'M': 0, 'L': 1, 'N': 1, 'Q': 0, 'P': 1, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 2, 'Y': 1, 'X': 0}, 8: {'A': 1, 'C': 0, 'E': 2, 'D': 0, 'G': 1, 'F': 0, 'I': 0, 'H': 0, 'K': 2, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 2, 'R': 0, 'T': 2, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 9: {'A': 4, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 8, 'H': 0, 'K': 0, 'M': 4, 'L': 10, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 4, 'W': 0, 'V': 10, 'Y': 0, 'X': 0}} \ No newline at end of file +A_0201_10 = {0: {'A': 2, 'C': 0, 'D': -1, 'E': -3, 'F': 1, 'G': 1, 'H': 0, 'I': 2, 'K': 1, 'L': 2, 'M': 0, 'N': 0, 'P': -3, 'Q': 0, 'R': 0, 'S': 2, 'T': 0, 'V': 1, 'W': 0, 'X': 0, 'Y': 2}, 1: {'A': 4, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 8, 'K': 0, 'L': 10, 'M': 8, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 4, 'V': 4, 'W': 0, 'X': 0, 'Y': 0}, 2: {'A': 2, 'C': 0, 'D': 0, 'E': -1, 'F': 1, 'G': 0, 'H': 0, 'I': 2, 'K': -1, 'L': 2, 'M': 1, 'N': 1, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': -1, 'V': 0, 'W': 1, 'X': 0, 'Y': 1}, 3: {'A': 0, 'C': 0, 'D': 1, 'E': 2, 'F': -1, 'G': 2, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 2, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': -1}, 4: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 5: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 6: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 4, 'K': 0, 'L': 4, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 4, 'W': 0, 'X': 0, 'Y': 0}, 7: {'A': 2, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 1, 'I': 0, 'K': -1, 'L': 1, 'M': 0, 'N': 1, 'P': 1, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 2, 'W': 0, 'X': 0, 'Y': 1}, 8: {'A': 1, 'C': 0, 'D': 0, 'E': 2, 'F': 0, 'G': 1, 'H': 0, 'I': 0, 'K': 2, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 2, 'T': 2, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 9: {'A': 4, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 8, 'K': 0, 'L': 10, 'M': 4, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 4, 'V': 10, 'W': 0, 'X': 0, 'Y': 0}} \ No newline at end of file diff --git a/epytope/Data/pssms/syfpeithi/mat/A_0201_11.py b/epytope/Data/pssms/syfpeithi/mat/A_0201_11.py new file mode 100644 index 00000000..b7ca1600 --- /dev/null +++ b/epytope/Data/pssms/syfpeithi/mat/A_0201_11.py @@ -0,0 +1 @@ +A_0201_11 = {0: {'A': 2, 'C': 0, 'D': -1, 'E': -3, 'F': 1, 'G': 1, 'H': 0, 'I': 2, 'K': 1, 'L': 2, 'M': 0, 'N': 0, 'P': -3, 'Q': 0, 'R': 0, 'S': 2, 'T': 0, 'V': 1, 'W': 0, 'X': 0, 'Y': 2}, 1: {'A': 4, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 8, 'K': 0, 'L': 10, 'M': 8, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 4, 'V': 4, 'W': 0, 'X': 0, 'Y': 0}, 2: {'A': 2, 'C': 0, 'D': 0, 'E': -1, 'F': 1, 'G': 0, 'H': 0, 'I': 2, 'K': -1, 'L': 2, 'M': 1, 'N': 1, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': -1, 'V': 0, 'W': 1, 'X': 0, 'Y': 1}, 3: {'A': 0, 'C': 0, 'D': 1, 'E': 2, 'F': -1, 'G': 2, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 2, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': -1}, 4: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 5: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 6: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 7: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 4, 'K': 0, 'L': 4, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 4, 'W': 0, 'X': 0, 'Y': 0}, 8: {'A': 2, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 1, 'I': 0, 'K': -1, 'L': 1, 'M': 0, 'N': 1, 'P': 1, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 2, 'W': 0, 'X': 0, 'Y': 1}, 9: {'A': 1, 'C': 0, 'D': 0, 'E': 2, 'F': 0, 'G': 1, 'H': 0, 'I': 0, 'K': 2, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 2, 'T': 2, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 10: {'A': 4, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 8, 'K': 0, 'L': 10, 'M': 4, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 4, 'V': 10, 'W': 0, 'X': 0, 'Y': 0}} \ No newline at end of file diff --git a/epytope/Data/pssms/syfpeithi/mat/A_0201_9.py b/epytope/Data/pssms/syfpeithi/mat/A_0201_9.py index 8962269a..82d21086 100644 --- a/epytope/Data/pssms/syfpeithi/mat/A_0201_9.py +++ b/epytope/Data/pssms/syfpeithi/mat/A_0201_9.py @@ -1 +1 @@ -A_0201_9 = {0: {'A': 2, 'C': 0, 'E': -3, 'D': -1, 'G': 1, 'F': 1, 'I': 2, 'H': 0, 'K': 1, 'M': 0, 'L': 2, 'N': 0, 'Q': 0, 'P': -3, 'S': 2, 'R': 0, 'T': 0, 'W': 0, 'V': 1, 'Y': 2, 'X': 0}, 1: {'A': 4, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 8, 'H': 0, 'K': 0, 'M': 8, 'L': 10, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 4, 'W': 0, 'V': 4, 'Y': 0, 'X': 0}, 2: {'A': 2, 'C': 0, 'E': -1, 'D': 0, 'G': 0, 'F': 1, 'I': 2, 'H': 0, 'K': -1, 'M': 1, 'L': 2, 'N': 1, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': -1, 'W': 1, 'V': 0, 'Y': 1, 'X': 0}, 3: {'A': 0, 'C': 0, 'E': 2, 'D': 1, 'G': 2, 'F': -1, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 2, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': -1, 'X': 0}, 4: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 2, 'F': 1, 'I': 0, 'H': 0, 'K': 1, 'M': 0, 'L': 1, 'N': 0, 'Q': 0, 'P': 1, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 1, 'X': 0}, 5: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 4, 'H': 0, 'K': 0, 'M': 0, 'L': 4, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 2, 'W': 0, 'V': 4, 'Y': 0, 'X': 0}, 6: {'A': 2, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 1, 'K': -1, 'M': 0, 'L': 1, 'N': 1, 'Q': 0, 'P': 1, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 2, 'Y': 1, 'X': 0}, 7: {'A': 1, 'C': 0, 'E': 2, 'D': 0, 'G': 1, 'F': 0, 'I': 0, 'H': 0, 'K': 2, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 2, 'R': 0, 'T': 2, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 8: {'A': 4, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 8, 'H': 0, 'K': 0, 'M': 4, 'L': 10, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 4, 'W': 0, 'V': 10, 'Y': 0, 'X': 0}} \ No newline at end of file +A_0201_9 = {0: {'A': 2, 'C': 0, 'D': -1, 'E': -3, 'F': 1, 'G': 1, 'H': 0, 'I': 2, 'K': 1, 'L': 2, 'M': 0, 'N': 0, 'P': -3, 'Q': 0, 'R': 0, 'S': 2, 'T': 0, 'V': 1, 'W': 0, 'X': 0, 'Y': 2}, 1: {'A': 4, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 8, 'K': 0, 'L': 10, 'M': 8, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 4, 'V': 4, 'W': 0, 'X': 0, 'Y': 0}, 2: {'A': 2, 'C': 0, 'D': 0, 'E': -1, 'F': 1, 'G': 0, 'H': 0, 'I': 2, 'K': -1, 'L': 2, 'M': 1, 'N': 1, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': -1, 'V': 0, 'W': 1, 'X': 0, 'Y': 1}, 3: {'A': 0, 'C': 0, 'D': 1, 'E': 2, 'F': -1, 'G': 2, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 2, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': -1}, 4: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 1, 'G': 2, 'H': 0, 'I': 0, 'K': 1, 'L': 1, 'M': 0, 'N': 0, 'P': 1, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 1}, 5: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 4, 'K': 0, 'L': 4, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 2, 'V': 4, 'W': 0, 'X': 0, 'Y': 0}, 6: {'A': 2, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 1, 'I': 0, 'K': -1, 'L': 1, 'M': 0, 'N': 1, 'P': 1, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 2, 'W': 0, 'X': 0, 'Y': 1}, 7: {'A': 1, 'C': 0, 'D': 0, 'E': 2, 'F': 0, 'G': 1, 'H': 0, 'I': 0, 'K': 2, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 2, 'T': 2, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 8: {'A': 4, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 8, 'K': 0, 'L': 10, 'M': 4, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 4, 'V': 10, 'W': 0, 'X': 0, 'Y': 0}} \ No newline at end of file diff --git a/epytope/Data/pssms/syfpeithi/mat/A_0300_9.py b/epytope/Data/pssms/syfpeithi/mat/A_0300_9.py new file mode 100644 index 00000000..3f3d87a3 --- /dev/null +++ b/epytope/Data/pssms/syfpeithi/mat/A_0300_9.py @@ -0,0 +1 @@ +A_0300_9 = {0: {'A': 4, 'C': 0, 'D': 4, 'E': 4, 'F': 0, 'G': 4, 'H': 0, 'I': 0, 'K': 4, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 4, 'S': 4, 'T': 4, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 1: {'A': 10, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 10, 'K': 0, 'L': 10, 'M': 10, 'N': 0, 'P': 0, 'Q': 10, 'R': 0, 'S': 10, 'T': 10, 'V': 10, 'W': 0, 'Y': 0, 'X': 0}, 2: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 3: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 4: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 5: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 6: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 7: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 8: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 10, 'G': 0, 'H': 10, 'I': 0, 'K': 10, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 10, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 10, 'X': 0}} \ No newline at end of file diff --git a/epytope/Data/pssms/syfpeithi/mat/A_0301_10.py b/epytope/Data/pssms/syfpeithi/mat/A_0301_10.py index a785205d..4af52a99 100644 --- a/epytope/Data/pssms/syfpeithi/mat/A_0301_10.py +++ b/epytope/Data/pssms/syfpeithi/mat/A_0301_10.py @@ -1 +1 @@ -A_0301_10 = {0: {'A': 3, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 2, 'H': 0, 'K': 3, 'M': 0, 'L': 0, 'N': 0, 'Q': 2, 'P': 0, 'S': 1, 'R': 4, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 1: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 8, 'H': 0, 'K': 0, 'M': 0, 'L': 10, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 10, 'Y': 0, 'X': 0}, 2: {'A': 1, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 3, 'H': 0, 'K': 1, 'M': 0, 'L': 2, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 3, 'T': 0, 'W': 0, 'V': 0, 'Y': 4, 'X': 0}, 3: {'A': 2, 'C': 0, 'E': 1, 'D': 1, 'G': 2, 'F': 0, 'I': 1, 'H': 0, 'K': 0, 'M': 0, 'L': 1, 'N': 1, 'Q': 0, 'P': 3, 'S': 0, 'R': 3, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 4: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 5: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 6: {'A': 3, 'C': 0, 'E': 0, 'D': 0, 'G': 3, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 1, 'S': 0, 'R': 1, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 7: {'A': 3, 'C': 0, 'E': 0, 'D': 0, 'G': 1, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 1, 'L': 3, 'N': 0, 'Q': 0, 'P': 0, 'S': 3, 'R': 0, 'T': 1, 'W': 0, 'V': 4, 'Y': 0, 'X': 0}, 8: {'A': 1, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 1, 'L': 0, 'N': 0, 'Q': 3, 'P': 0, 'S': 2, 'R': 0, 'T': 4, 'W': 1, 'V': 4, 'Y': 0, 'X': 0}, 9: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 4, 'I': 0, 'H': 4, 'K': 10, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 4, 'T': 0, 'W': 0, 'V': 0, 'Y': 6, 'X': 0}} \ No newline at end of file +A_0301_10 = {0: {'A': 1, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 4, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 4, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 1: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 10, 'K': 0, 'L': 10, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 10, 'V': 10, 'W': 0, 'Y': 0, 'X': 0}, 2: {'A': 1, 'C': 0, 'D': 0, 'E': 0, 'F': 1, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 1, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 1, 'X': 0}, 3: {'A': 0, 'C': 0, 'D': 1, 'E': 1, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 1, 'Q': 0, 'R': 0, 'S': 1, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 4: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 1, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 1, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 5: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 1, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 1, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 1, 'W': 0, 'Y': 0, 'X': 0}, 6: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 1, 'K': 0, 'L': 1, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 7: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 1, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 1, 'T': 1, 'V': 1, 'W': 0, 'Y': 0, 'X': 0}, 8: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 1, 'L': 1, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 9: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 10, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}} \ No newline at end of file diff --git a/epytope/Data/pssms/syfpeithi/mat/A_0301_11.py b/epytope/Data/pssms/syfpeithi/mat/A_0301_11.py new file mode 100644 index 00000000..02996f0f --- /dev/null +++ b/epytope/Data/pssms/syfpeithi/mat/A_0301_11.py @@ -0,0 +1 @@ +A_0301_11 = {0: {'A': 1, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 4, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 4, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 1: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 10, 'K': 0, 'L': 10, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 10, 'V': 10, 'W': 0, 'Y': 0, 'X': 0}, 2: {'A': 1, 'C': 0, 'D': 0, 'E': 0, 'F': 1, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 1, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 1, 'X': 0}, 3: {'A': 0, 'C': 0, 'D': 1, 'E': 1, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 1, 'Q': 0, 'R': 0, 'S': 1, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 4: {'A': 1, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 1, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 1, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 5: {'A': 0, 'C': 0, 'D': 1, 'E': 1, 'F': 0, 'G': 0, 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at end of file diff --git a/epytope/Data/pssms/syfpeithi/mat/A_0301_9.py b/epytope/Data/pssms/syfpeithi/mat/A_0301_9.py index d649c02b..1ff6ff30 100644 --- a/epytope/Data/pssms/syfpeithi/mat/A_0301_9.py +++ b/epytope/Data/pssms/syfpeithi/mat/A_0301_9.py @@ -1 +1 @@ -A_0301_9 = {0: {'A': 3, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 2, 'H': 0, 'K': 3, 'M': 0, 'L': 0, 'N': 0, 'Q': 2, 'P': 0, 'S': 1, 'R': 4, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 1: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 8, 'H': 0, 'K': 0, 'M': 0, 'L': 10, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 10, 'Y': 0, 'X': 0}, 2: {'A': 1, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 3, 'H': 0, 'K': 1, 'M': 0, 'L': 2, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 3, 'T': 0, 'W': 0, 'V': 0, 'Y': 4, 'X': 0}, 3: {'A': 2, 'C': 0, 'E': 1, 'D': 1, 'G': 2, 'F': 0, 'I': 1, 'H': 0, 'K': 0, 'M': 0, 'L': 1, 'N': 1, 'Q': 0, 'P': 3, 'S': 0, 'R': 3, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 4: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 2, 'F': 0, 'I': 0, 'H': 0, 'K': 1, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 2, 'T': 0, 'W': 0, 'V': 1, 'Y': 0, 'X': 0}, 5: {'A': 3, 'C': 0, 'E': 0, 'D': 0, 'G': 3, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 1, 'S': 0, 'R': 1, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 6: {'A': 3, 'C': 0, 'E': 0, 'D': 0, 'G': 1, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 1, 'L': 3, 'N': 0, 'Q': 0, 'P': 0, 'S': 3, 'R': 0, 'T': 1, 'W': 0, 'V': 4, 'Y': 0, 'X': 0}, 7: {'A': 1, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 1, 'L': 0, 'N': 0, 'Q': 3, 'P': 0, 'S': 2, 'R': 0, 'T': 4, 'W': 1, 'V': 4, 'Y': 0, 'X': 0}, 8: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 4, 'I': 0, 'H': 4, 'K': 10, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 4, 'T': 0, 'W': 0, 'V': 0, 'Y': 6, 'X': 0}} \ No newline at end of file +A_0301_9 = {0: {'A': 1, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 4, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 4, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 1: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 10, 'K': 0, 'L': 10, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 10, 'V': 10, 'W': 0, 'Y': 0, 'X': 0}, 2: {'A': 1, 'C': 0, 'D': 0, 'E': 0, 'F': 1, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 1, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 1, 'X': 0}, 3: {'A': 0, 'C': 0, 'D': 1, 'E': 1, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 1, 'Q': 0, 'R': 0, 'S': 1, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 4: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 1, 'L': 0, 'M': 0, 'N': 0, 'P': 1, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 5: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 1, 'K': 0, 'L': 1, 'M': 0, 'N': 0, 'P': 1, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 1, 'W': 0, 'Y': 0, 'X': 0}, 6: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 1, 'K': 0, 'L': 2, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 7: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 1, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 1, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 8: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 6, 'I': 0, 'K': 10, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 6, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 6, 'X': 0}} \ No newline at end of file diff --git a/epytope/Data/pssms/syfpeithi/mat/A_1101_10.py b/epytope/Data/pssms/syfpeithi/mat/A_1101_10.py index 1351279c..26bda92a 100644 --- a/epytope/Data/pssms/syfpeithi/mat/A_1101_10.py +++ b/epytope/Data/pssms/syfpeithi/mat/A_1101_10.py @@ -1 +1 @@ -A_1101_10 = {0: {'A': 3, 'C': 0, 'E': 0, 'D': 0, 'G': 3, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 3, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 1: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 6, 'H': 0, 'K': 0, 'M': 6, 'L': 6, 'N': 0, 'Q': 0, 'P': 0, 'S': 10, 'R': 0, 'T': 10, 'W': 0, 'V': 10, 'Y': 0, 'X': 0}, 2: {'A': 1, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 1, 'I': 1, 'H': 0, 'K': 0, 'M': 0, 'L': 1, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 3: {'A': 1, 'C': 0, 'E': 0, 'D': 2, 'G': 1, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 1, 'S': 1, 'R': 0, 'T': 1, 'W': 0, 'V': 1, 'Y': 0, 'X': 0}, 4: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 5: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 6: {'A': 1, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 1, 'I': 1, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 1, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 1, 'Y': 0, 'X': 0}, 7: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 4, 'H': 0, 'K': 0, 'M': 0, 'L': 4, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 4, 'Y': 0, 'X': 0}, 8: {'A': 0, 'C': 0, 'E': 1, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 2, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 1, 'Y': 0, 'X': 0}, 9: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 10, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 8, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}} \ No newline at end of file +A_1101_10 = {0: {'A': 3, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 3, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 3, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 1: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 6, 'K': 0, 'L': 6, 'M': 6, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 10, 'T': 10, 'V': 10, 'W': 0, 'X': 0, 'Y': 0}, 2: {'A': 1, 'C': 0, 'D': 0, 'E': 0, 'F': 1, 'G': 0, 'H': 0, 'I': 1, 'K': 0, 'L': 1, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 3: {'A': 1, 'C': 0, 'D': 2, 'E': 0, 'F': 0, 'G': 1, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 1, 'Q': 0, 'R': 0, 'S': 1, 'T': 1, 'V': 1, 'W': 0, 'X': 0, 'Y': 0}, 4: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 5: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 6: {'A': 1, 'C': 0, 'D': 0, 'E': 0, 'F': 1, 'G': 0, 'H': 0, 'I': 1, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 1, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 1, 'W': 0, 'X': 0, 'Y': 0}, 7: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 4, 'K': 0, 'L': 4, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 4, 'W': 0, 'X': 0, 'Y': 0}, 8: {'A': 0, 'C': 0, 'D': 0, 'E': 1, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 2, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 1, 'W': 0, 'X': 0, 'Y': 0}, 9: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 10, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 8, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}} \ No newline at end of file diff --git a/epytope/Data/pssms/syfpeithi/mat/A_1101_11.py b/epytope/Data/pssms/syfpeithi/mat/A_1101_11.py new file mode 100644 index 00000000..550b8beb --- /dev/null +++ b/epytope/Data/pssms/syfpeithi/mat/A_1101_11.py @@ -0,0 +1 @@ +A_1101_11 = {0: {'A': 3, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 3, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 3, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 1: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 6, 'K': 0, 'L': 6, 'M': 6, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 10, 'T': 10, 'V': 10, 'W': 0, 'X': 0, 'Y': 0}, 2: {'A': 1, 'C': 0, 'D': 0, 'E': 0, 'F': 1, 'G': 0, 'H': 0, 'I': 1, 'K': 0, 'L': 1, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 3: {'A': 1, 'C': 0, 'D': 2, 'E': 0, 'F': 0, 'G': 1, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 1, 'Q': 0, 'R': 0, 'S': 1, 'T': 1, 'V': 1, 'W': 0, 'X': 0, 'Y': 0}, 4: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 5: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 6: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 7: {'A': 1, 'C': 0, 'D': 0, 'E': 0, 'F': 1, 'G': 0, 'H': 0, 'I': 1, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 1, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 1, 'W': 0, 'X': 0, 'Y': 0}, 8: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 4, 'K': 0, 'L': 4, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 4, 'W': 0, 'X': 0, 'Y': 0}, 9: {'A': 0, 'C': 0, 'D': 0, 'E': 1, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 2, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 1, 'W': 0, 'X': 0, 'Y': 0}, 10: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 10, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 8, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}} \ No newline at end of file diff --git a/epytope/Data/pssms/syfpeithi/mat/A_1101_9.py b/epytope/Data/pssms/syfpeithi/mat/A_1101_9.py index 7f23b8e0..d7d30a9d 100644 --- a/epytope/Data/pssms/syfpeithi/mat/A_1101_9.py +++ b/epytope/Data/pssms/syfpeithi/mat/A_1101_9.py @@ -1 +1 @@ -A_1101_9 = {0: {'A': 3, 'C': 0, 'E': 0, 'D': 0, 'G': 3, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 3, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 1: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 6, 'H': 0, 'K': 0, 'M': 6, 'L': 6, 'N': 0, 'Q': 0, 'P': 0, 'S': 10, 'R': 0, 'T': 10, 'W': 0, 'V': 10, 'Y': 0, 'X': 0}, 2: {'A': 1, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 1, 'I': 1, 'H': 0, 'K': 0, 'M': 0, 'L': 1, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 3: {'A': 1, 'C': 0, 'E': 0, 'D': 2, 'G': 1, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 1, 'S': 1, 'R': 0, 'T': 1, 'W': 0, 'V': 1, 'Y': 0, 'X': 0}, 4: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 1, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 5: {'A': 1, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 1, 'I': 1, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 1, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 1, 'Y': 0, 'X': 0}, 6: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 4, 'H': 0, 'K': 0, 'M': 0, 'L': 4, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 4, 'Y': 0, 'X': 0}, 7: {'A': 0, 'C': 0, 'E': 1, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 2, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 1, 'Y': 0, 'X': 0}, 8: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 10, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 8, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}} \ No newline at end of file +A_1101_9 = {0: {'A': 3, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 3, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 3, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 1: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 6, 'K': 0, 'L': 6, 'M': 6, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 10, 'T': 10, 'V': 10, 'W': 0, 'X': 0, 'Y': 0}, 2: {'A': 1, 'C': 0, 'D': 0, 'E': 0, 'F': 1, 'G': 0, 'H': 0, 'I': 1, 'K': 0, 'L': 1, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 3: {'A': 1, 'C': 0, 'D': 2, 'E': 0, 'F': 0, 'G': 1, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 1, 'Q': 0, 'R': 0, 'S': 1, 'T': 1, 'V': 1, 'W': 0, 'X': 0, 'Y': 0}, 4: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 1, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 5: {'A': 1, 'C': 0, 'D': 0, 'E': 0, 'F': 1, 'G': 0, 'H': 0, 'I': 1, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 1, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 1, 'W': 0, 'X': 0, 'Y': 0}, 6: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 4, 'K': 0, 'L': 4, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 4, 'W': 0, 'X': 0, 'Y': 0}, 7: {'A': 0, 'C': 0, 'D': 0, 'E': 1, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 2, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 1, 'W': 0, 'X': 0, 'Y': 0}, 8: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 10, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 8, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}} \ No newline at end of file diff --git a/epytope/Data/pssms/syfpeithi/mat/A_2402_10.py b/epytope/Data/pssms/syfpeithi/mat/A_2402_10.py index 1862ceae..e2ffd8ea 100644 --- a/epytope/Data/pssms/syfpeithi/mat/A_2402_10.py +++ b/epytope/Data/pssms/syfpeithi/mat/A_2402_10.py @@ -1 +1 @@ -A_2402_10 = {0: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 1, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 1, 'W': 0, 'V': 2, 'Y': 0, 'X': 0}, 1: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 6, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 10, 'X': 0}, 2: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 2, 'H': -1, 'K': -1, 'M': 0, 'L': 2, 'N': 0, 'Q': 0, 'P': 2, 'S': 0, 'R': -1, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 3: {'A': 0, 'C': 0, 'E': 2, 'D': 1, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 1, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 1, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 4: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 5: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 6: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 1, 'I': 1, 'H': 1, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 1, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 1, 'Y': 0, 'X': 0}, 7: {'A': 0, 'C': 0, 'E': 1, 'D': 0, 'G': 0, 'F': 1, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 8: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 1, 'K': 2, 'M': 0, 'L': 2, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 9: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 10, 'I': 10, 'H': 0, 'K': 0, 'M': 0, 'L': 10, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}} \ No newline at end of file +A_2402_10 = {0: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 1, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 1, 'V': 2, 'W': 0, 'X': 0, 'Y': 0}, 1: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 6, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 10}, 2: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': -1, 'I': 2, 'K': -1, 'L': 2, 'M': 0, 'N': 0, 'P': 2, 'Q': 0, 'R': -1, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 3: {'A': 0, 'C': 0, 'D': 1, 'E': 2, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 1, 'L': 0, 'M': 0, 'N': 0, 'P': 1, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 4: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 5: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 6: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 1, 'G': 0, 'H': 1, 'I': 1, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 1, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 1, 'W': 0, 'X': 0, 'Y': 0}, 7: {'A': 0, 'C': 0, 'D': 0, 'E': 1, 'F': 1, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 8: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 1, 'I': 0, 'K': 2, 'L': 2, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 9: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 10, 'G': 0, 'H': 0, 'I': 10, 'K': 0, 'L': 10, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}} \ No newline at end of file diff --git a/epytope/Data/pssms/syfpeithi/mat/A_2402_11.py b/epytope/Data/pssms/syfpeithi/mat/A_2402_11.py new file mode 100644 index 00000000..59f24cfd --- /dev/null +++ b/epytope/Data/pssms/syfpeithi/mat/A_2402_11.py @@ -0,0 +1 @@ +A_2402_11 = {0: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 1, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 1, 'V': 2, 'W': 0, 'X': 0, 'Y': 0}, 1: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 6, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 10}, 2: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': -1, 'I': 2, 'K': -1, 'L': 2, 'M': 0, 'N': 0, 'P': 2, 'Q': 0, 'R': -1, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 3: {'A': 0, 'C': 0, 'D': 1, 'E': 2, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 1, 'L': 0, 'M': 0, 'N': 0, 'P': 1, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 4: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 5: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 6: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 7: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 1, 'G': 0, 'H': 1, 'I': 1, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 1, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 1, 'W': 0, 'X': 0, 'Y': 0}, 8: {'A': 0, 'C': 0, 'D': 0, 'E': 1, 'F': 1, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 9: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 1, 'I': 0, 'K': 2, 'L': 2, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 10: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 10, 'G': 0, 'H': 0, 'I': 10, 'K': 0, 'L': 10, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}} \ No newline at end of file diff --git a/epytope/Data/pssms/syfpeithi/mat/A_2402_9.py b/epytope/Data/pssms/syfpeithi/mat/A_2402_9.py index 6e7455a0..67e89516 100644 --- a/epytope/Data/pssms/syfpeithi/mat/A_2402_9.py +++ b/epytope/Data/pssms/syfpeithi/mat/A_2402_9.py @@ -1 +1 @@ -A_2402_9 = {0: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 1, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 1, 'W': 0, 'V': 2, 'Y': 0, 'X': 0}, 1: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 6, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 10, 'X': 0}, 2: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 2, 'H': -1, 'K': -1, 'M': 0, 'L': 2, 'N': 0, 'Q': 0, 'P': 2, 'S': 0, 'R': -1, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 3: {'A': 0, 'C': 0, 'E': 2, 'D': 1, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 1, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 1, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 4: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 1, 'H': 1, 'K': 1, 'M': 0, 'L': 0, 'N': 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--git a/epytope/Data/pssms/syfpeithi/mat/A_6801_11.py b/epytope/Data/pssms/syfpeithi/mat/A_6801_11.py new file mode 100644 index 00000000..ccfd54c6 --- /dev/null +++ b/epytope/Data/pssms/syfpeithi/mat/A_6801_11.py @@ -0,0 +1 @@ +A_6801_11 = {0: {'A': 0, 'C': 0, 'D': 4, 'E': 4, 'F': -1, 'G': 0, 'H': -1, 'I': 0, 'K': -1, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': -1, 'S': 0, 'T': 1, 'V': 0, 'W': -1, 'X': 0, 'Y': -1}, 1: {'A': 6, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 6, 'K': 0, 'L': 4, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 4, 'T': 8, 'V': 8, 'W': 0, 'X': 0, 'Y': 0}, 2: {'A': 1, 'C': 0, 'D': -1, 'E': -1, 'F': 0, 'G': 0, 'H': -1, 'I': 1, 'K': -1, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': -1, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 3: {'A': 0, 'C': 0, 'D': 1, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 4: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 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'V': 0, 'Y': 0, 'X': 0}} \ No newline at end of file +A_6801_9 = {0: {'A': 0, 'C': 0, 'D': 4, 'E': 4, 'F': -1, 'G': 0, 'H': -1, 'I': 0, 'K': -1, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': -1, 'S': 0, 'T': 1, 'V': 0, 'W': -1, 'X': 0, 'Y': -1}, 1: {'A': 6, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 6, 'K': 0, 'L': 4, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 4, 'T': 8, 'V': 8, 'W': 0, 'X': 0, 'Y': 0}, 2: {'A': 1, 'C': 0, 'D': -1, 'E': -1, 'F': 0, 'G': 0, 'H': -1, 'I': 1, 'K': -1, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': -1, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 3: {'A': 0, 'C': 0, 'D': 1, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 4: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 2, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 5: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 4, 'K': 0, 'L': 4, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 4, 'W': 0, 'X': 0, 'Y': 0}, 6: {'A': 4, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 4, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 4, 'V': 4, 'W': 0, 'X': 0, 'Y': 0}, 7: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 1, 'I': 0, 'K': 1, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 1, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 8: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 8, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 10, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}} \ No newline at end of file diff --git a/epytope/Data/pssms/syfpeithi/mat/B_0702_10.py b/epytope/Data/pssms/syfpeithi/mat/B_0702_10.py index 19665fa5..8ab4378d 100644 --- a/epytope/Data/pssms/syfpeithi/mat/B_0702_10.py +++ b/epytope/Data/pssms/syfpeithi/mat/B_0702_10.py @@ -1 +1 @@ -B_0702_10 = {0: {'A': 2, 'C': 0, 'E': 1, 'D': 0, 'G': 0, 'F': 0, 'I': 1, 'H': 0, 'K': 1, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 1, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 1: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 10, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 2: {'A': 1, 'C': 0, 'E': 0, 'D': 1, 'G': 1, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 1, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 2, 'R': 2, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 3: {'A': 1, 'C': 0, 'E': 0, 'D': 0, 'G': 2, 'F': 0, 'I': 0, 'H': 0, 'K': 1, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 1, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 4: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 5: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 6: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 1, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 1, 'T': 1, 'W': 0, 'V': 1, 'Y': 0, 'X': 0}, 7: {'A': 1, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 2, 'N': 0, 'Q': 0, 'P': 1, 'S': 0, 'R': 0, 'T': 1, 'W': 0, 'V': 2, 'Y': 0, 'X': 0}, 8: {'A': 1, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 1, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 1, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 1, 'Y': 0, 'X': 0}, 9: {'A': 6, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 6, 'I': 6, 'H': 0, 'K': 0, 'M': 6, 'L': 10, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 6, 'W': 0, 'V': 6, 'Y': 0, 'X': 0}} \ No newline at end of file +B_0702_10 = {0: {'A': 2, 'C': 0, 'D': 0, 'E': 1, 'F': 0, 'G': 0, 'H': 0, 'I': 1, 'K': 1, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 1, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 1: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 10, 'Q': 0, 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0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 1, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 1: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 10, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 2: {'A': 1, 'C': 0, 'E': 0, 'D': 1, 'G': 1, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 1, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 2, 'R': 2, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 3: {'A': 1, 'C': 0, 'E': 0, 'D': 0, 'G': 2, 'F': 0, 'I': 0, 'H': 0, 'K': 1, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 1, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 4: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 3, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 5: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 1, 'F': 1, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 1, 'T': 1, 'W': 0, 'V': 1, 'Y': 0, 'X': 0}, 6: {'A': 1, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 2, 'N': 0, 'Q': 0, 'P': 1, 'S': 0, 'R': 0, 'T': 1, 'W': 0, 'V': 2, 'Y': 0, 'X': 0}, 7: {'A': 1, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 1, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 1, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 1, 'Y': 0, 'X': 0}, 8: {'A': 6, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 6, 'I': 6, 'H': 0, 'K': 0, 'M': 6, 'L': 10, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 6, 'W': 0, 'V': 6, 'Y': 0, 'X': 0}} \ No newline at end of file +B_0702_9 = {0: {'A': 2, 'C': 0, 'D': 0, 'E': 1, 'F': 0, 'G': 0, 'H': 0, 'I': 1, 'K': 1, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 1, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 1: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 10, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 2: {'A': 1, 'C': 0, 'D': 1, 'E': 0, 'F': 0, 'G': 1, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 1, 'N': 0, 'P': 0, 'Q': 0, 'R': 2, 'S': 2, 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'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 6, 'V': 6, 'W': 0, 'X': 0, 'Y': 0}} \ No newline at end of file diff --git a/epytope/Data/pssms/syfpeithi/mat/B_0801_8.py b/epytope/Data/pssms/syfpeithi/mat/B_0801_8.py index a989c449..f3634029 100644 --- a/epytope/Data/pssms/syfpeithi/mat/B_0801_8.py +++ b/epytope/Data/pssms/syfpeithi/mat/B_0801_8.py @@ -1 +1 @@ -B_0801_8 = {0: {'A': 0, 'C': 0, 'E': 2, 'D': 0, 'G': 1, 'F': 1, 'I': 1, 'H': 1, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 2, 'R': 0, 'T': 0, 'W': 0, 'V': 1, 'Y': 0, 'X': 0}, 1: {'A': 4, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 4, 'H': 0, 'K': 0, 'M': 0, 'L': 6, 'N': 0, 'Q': 0, 'P': 6, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 2: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 10, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 6, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 3: {'A': 0, 'C': 0, 'E': 2, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 1, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 1, 'Y': 1, 'X': 0}, 4: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 10, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 8, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 5: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 6: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 7: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 6, 'I': 6, 'H': 0, 'K': 0, 'M': 0, 'L': 10, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}} \ No newline at end of file +B_0801_8 = {0: {'A': 0, 'C': 0, 'D': 0, 'E': 2, 'F': 1, 'G': 1, 'H': 1, 'I': 1, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 2, 'T': 0, 'V': 1, 'W': 0, 'X': 0, 'Y': 0}, 1: {'A': 4, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 4, 'K': 0, 'L': 6, 'M': 0, 'N': 0, 'P': 6, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 2: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 10, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 6, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 3: {'A': 0, 'C': 0, 'D': 0, 'E': 2, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 1, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 1, 'W': 0, 'X': 0, 'Y': 1}, 4: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 10, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 8, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 5: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 6: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 7: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 6, 'G': 0, 'H': 0, 'I': 6, 'K': 0, 'L': 10, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}} \ No newline at end of file diff --git a/epytope/Data/pssms/syfpeithi/mat/B_0801_9.py b/epytope/Data/pssms/syfpeithi/mat/B_0801_9.py index bb542f38..216a1eea 100644 --- a/epytope/Data/pssms/syfpeithi/mat/B_0801_9.py +++ b/epytope/Data/pssms/syfpeithi/mat/B_0801_9.py @@ -1 +1 @@ -B_0801_9 = {0: {'A': 0, 'C': 0, 'E': 2, 'D': 0, 'G': 1, 'F': 1, 'I': 1, 'H': 1, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 2, 'R': 0, 'T': 0, 'W': 0, 'V': 1, 'Y': 0, 'X': 0}, 1: {'A': 4, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 4, 'H': 0, 'K': 0, 'M': 0, 'L': 6, 'N': 0, 'Q': 0, 'P': 6, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 2: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 10, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 6, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 3: 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0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}} \ No newline at end of file +B_0801_9 = {0: {'A': 0, 'C': 0, 'D': 0, 'E': 2, 'F': 1, 'G': 1, 'H': 1, 'I': 1, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 2, 'T': 0, 'V': 1, 'W': 0, 'X': 0, 'Y': 0}, 1: {'A': 4, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 4, 'K': 0, 'L': 6, 'M': 0, 'N': 0, 'P': 6, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 2: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 10, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 6, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 3: {'A': 0, 'C': 0, 'D': 0, 'E': 2, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 1, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 1, 'W': 0, 'X': 0, 'Y': 1}, 4: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 10, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 8, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 5: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 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0, 'V': 6, 'W': 0, 'X': 0, 'Y': 0}} \ No newline at end of file diff --git a/epytope/Data/pssms/syfpeithi/mat/B_1501_10.py b/epytope/Data/pssms/syfpeithi/mat/B_1501_10.py index d72f3b39..ff5400f4 100644 --- a/epytope/Data/pssms/syfpeithi/mat/B_1501_10.py +++ b/epytope/Data/pssms/syfpeithi/mat/B_1501_10.py @@ -1 +1 @@ -B_1501_10 = {0: {'A': 1, 'C': 0, 'E': -1, 'D': -1, 'G': 0, 'F': 0, 'I': 1, 'H': 0, 'K': 2, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 2, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 1: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 10, 'N': 0, 'Q': 10, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 8, 'Y': 0, 'X': 0}, 2: {'A': 0, 'C': 0, 'E': -1, 'D': -1, 'G': 0, 'F': 1, 'I': 1, 'H': 0, 'K': -1, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 1, 'T': 0, 'W': 0, 'V': 0, 'Y': 1, 'X': 0}, 3: {'A': 0, 'C': 0, 'E': 1, 'D': 1, 'G': 1, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 2, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 4: {'A': 0, 'C': 0, 'E': 1, 'D': 1, 'G': 1, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 2, 'V': 1, 'Y': 0, 'X': 0}, 5: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 2, 'F': 0, 'I': 1, 'H': 0, 'K': 0, 'M': 0, 'L': 1, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 1, 'W': 0, 'V': 1, 'Y': 0, 'X': 0}, 6: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 1, 'N': 0, 'Q': 0, 'P': 1, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 7: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 1, 'W': 0, 'V': 2, 'Y': 0, 'X': 0}, 8: {'A': 1, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 1, 'R': 0, 'T': 1, 'W': 0, 'V': 1, 'Y': 0, 'X': 0}, 9: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 8, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 10, 'X': 0}} \ No newline at end of file +B_1501_10 = {0: {'A': 1, 'C': 0, 'D': -1, 'E': -1, 'F': 0, 'G': 0, 'H': 0, 'I': 1, 'K': 2, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 2, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 1: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 10, 'M': 0, 'N': 0, 'P': 0, 'Q': 10, 'R': 0, 'S': 0, 'T': 0, 'V': 8, 'W': 0, 'X': 0, 'Y': 0}, 2: {'A': 0, 'C': 0, 'D': -1, 'E': -1, 'F': 1, 'G': 0, 'H': 0, 'I': 1, 'K': -1, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 1, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 1}, 3: {'A': 0, 'C': 0, 'D': 1, 'E': 1, 'F': 0, 'G': 1, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 2, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 4: {'A': 0, 'C': 0, 'D': 1, 'E': 1, 'F': 0, 'G': 1, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 1, 'W': 2, 'X': 0, 'Y': 0}, 5: {'A': 0, 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ebdbd277..a2f6880b 100644 --- a/epytope/Data/pssms/syfpeithi/mat/B_1501_9.py +++ b/epytope/Data/pssms/syfpeithi/mat/B_1501_9.py @@ -1 +1 @@ -B_1501_9 = {0: {'A': 1, 'C': 0, 'E': -1, 'D': -1, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 1, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 1, 'T': 0, 'W': 0, 'V': 1, 'Y': 0, 'X': 0}, 1: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 6, 'H': 0, 'K': 0, 'M': 0, 'L': 10, 'N': 0, 'Q': 10, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 8, 'Y': 0, 'X': 0}, 2: {'A': 0, 'C': 0, 'E': -1, 'D': -1, 'G': 0, 'F': 1, 'I': 1, 'H': 0, 'K': 1, 'M': 0, 'L': -1, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 1, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 3: {'A': 0, 'C': 0, 'E': 1, 'D': 1, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 1, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 4: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 1, 'F': 0, 'I': 1, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 1, 'Y': 0, 'X': 0}, 5: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 1, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 1, 'W': 0, 'V': 1, 'Y': 0, 'X': 0}, 6: {'A': 0, 'C': 0, 'E': 1, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 1, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 1, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 7: {'A': 1, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 1, 'M': 0, 'L': 0, 'N': 0, 'Q': 1, 'P': 0, 'S': 1, 'R': 0, 'T': 1, 'W': 0, 'V': 1, 'Y': 0, 'X': 0}, 8: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 8, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 10, 'X': 0}} \ No newline at end of file +B_1501_9 = {0: {'A': 1, 'C': 0, 'D': -1, 'E': -1, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 1, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 1, 'S': 0, 'T': 0, 'V': 1, 'W': 0, 'X': 0, 'Y': 0}, 1: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 6, 'K': 0, 'L': 10, 'M': 0, 'N': 0, 'P': 0, 'Q': 10, 'R': 0, 'S': 0, 'T': 0, 'V': 8, 'W': 0, 'X': 0, 'Y': 0}, 2: {'A': 0, 'C': 0, 'D': -1, 'E': -1, 'F': 1, 'G': 0, 'H': 0, 'I': 1, 'K': 1, 'L': -1, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 1, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 3: {'A': 0, 'C': 0, 'D': 1, 'E': 1, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 1, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 4: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 1, 'H': 0, 'I': 1, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 1, 'W': 0, 'X': 0, 'Y': 0}, 5: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 1, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 1, 'V': 1, 'W': 0, 'X': 0, 'Y': 0}, 6: {'A': 0, 'C': 0, 'D': 0, 'E': 1, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 1, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 1, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 7: {'A': 1, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 1, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 1, 'R': 0, 'S': 1, 'T': 1, 'V': 1, 'W': 0, 'X': 0, 'Y': 0}, 8: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 8, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 10}} \ No newline at end of file diff --git a/epytope/Data/pssms/syfpeithi/mat/B_1510_9.py b/epytope/Data/pssms/syfpeithi/mat/B_1510_9.py index 299db883..65806484 100644 --- a/epytope/Data/pssms/syfpeithi/mat/B_1510_9.py +++ b/epytope/Data/pssms/syfpeithi/mat/B_1510_9.py @@ -1 +1 @@ -B_1510_9 = {0: {'A': 0, 'C': 0, 'E': 1, 'D': 0, 'G': 1, 'F': 0, 'I': 2, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 1, 'W': 0, 'V': 0, 'Y': 1, 'X': 0}, 1: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 10, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 2: {'A': 1, 'C': 0, 'E': 1, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 1, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 3: {'A': 0, 'C': 0, 'E': 1, 'D': 1, 'G': 1, 'F': 0, 'I': 0, 'H': 0, 'K': 1, 'M': 0, 'L': 0, 'N': 0, 'Q': 1, 'P': 2, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 1, 'Y': 0, 'X': 0}, 4: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 1, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 1, 'Q': 0, 'P': 1, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 5: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 1, 'H': 0, 'K': 1, 'M': 1, 'L': 0, 'N': 0, 'Q': 0, 'P': 1, 'S': 0, 'R': 1, 'T': 0, 'W': 0, 'V': 1, 'Y': 0, 'X': 0}, 6: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 1, 'S': 0, 'R': 2, 'T': 0, 'W': 0, 'V': 2, 'Y': 0, 'X': 0}, 7: {'A': 1, 'C': 0, 'E': 1, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 2, 'T': 1, 'W': 0, 'V': 2, 'Y': 0, 'X': 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b/epytope/Data/pssms/syfpeithi/mat/B_1516_9.py @@ -0,0 +1 @@ +B_1516_9 = {0: {'A': 2, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 1, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 2}, 1: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 6, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 10, 'T': 10, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 2: {'A': 0, 'C': 0, 'D': 2, 'E': 0, 'F': 0, 'G': 1, 'H': 0, 'I': 1, 'K': -1, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': -1, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 3: {'A': 0, 'C': 0, 'D': 0, 'E': 1, 'F': 0, 'G': 0, 'H': 0, 'I': 1, 'K': 1, 'L': 0, 'M': 0, 'N': 0, 'P': 6, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 4: {'A': 2, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 1, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 5: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 1, 'H': 0, 'I': 2, 'K': 0, 'L': 1, 'M': 0, 'N': 1, 'P': 0, 'Q': 1, 'R': 0, 'S': 0, 'T': 0, 'V': 1, 'W': 0, 'X': 0, 'Y': 0}, 6: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 1, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 1, 'S': 1, 'T': 0, 'V': 2, 'W': 0, 'X': 0, 'Y': 0}, 7: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 1, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 1, 'R': 1, 'S': 0, 'T': 2, 'V': 1, 'W': 0, 'X': 0, 'Y': 0}, 8: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 8, 'G': 0, 'H': 0, 'I': 10, 'K': 0, 'L': 0, 'M': 8, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 10, 'W': 0, 'X': 0, 'Y': 10}} \ No newline at end of file diff --git a/epytope/Data/pssms/syfpeithi/mat/B_1801_8.py b/epytope/Data/pssms/syfpeithi/mat/B_1801_8.py index c13213cd..8b3fc853 100644 --- a/epytope/Data/pssms/syfpeithi/mat/B_1801_8.py +++ b/epytope/Data/pssms/syfpeithi/mat/B_1801_8.py @@ -1 +1 @@ -B_1801_8 = {0: {'A': 0, 'C': 0, 'E': 2, 'D': 4, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 1, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 1: {'A': 0, 'C': 0, 'E': 10, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 2: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 1, 'I': 0, 'H': 1, 'K': 0, 'M': 1, 'L': 1, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 3, 'Y': 0, 'X': 0}, 3: {'A': 0, 'C': 0, 'E': 2, 'D': 0, 'G': 0, 'F': 0, 'I': 1, 'H': 0, 'K': 2, 'M': 0, 'L': 1, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 4: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 1, 'I': 1, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 1, 'R': 0, 'T': 1, 'W': 0, 'V': 2, 'Y': 0, 'X': 0}, 5: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 1, 'H': 0, 'K': 0, 'M': 0, 'L': 2, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 1, 'T': 1, 'W': 0, 'V': 1, 'Y': 0, 'X': 0}, 6: {'A': 0, 'C': 0, 'E': 1, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 1, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 1, 'T': 1, 'W': 0, 'V': 1, 'Y': 0, 'X': 0}, 7: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 10, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 8, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 10, 'X': 0}} \ No newline at end of file +B_1801_8 = {0: {'A': 0, 'C': 0, 'D': 4, 'E': 2, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 1, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 1: {'A': 0, 'C': 0, 'D': 0, 'E': 10, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 2: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 1, 'G': 0, 'H': 1, 'I': 0, 'K': 0, 'L': 1, 'M': 1, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 3, 'W': 0, 'X': 0, 'Y': 0}, 3: {'A': 0, 'C': 0, 'D': 0, 'E': 2, 'F': 0, 'G': 0, 'H': 0, 'I': 1, 'K': 2, 'L': 1, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 4: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 1, 'G': 0, 'H': 0, 'I': 1, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 1, 'T': 1, 'V': 2, 'W': 0, 'X': 0, 'Y': 0}, 5: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 1, 'K': 0, 'L': 2, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 1, 'S': 0, 'T': 1, 'V': 1, 'W': 0, 'X': 0, 'Y': 0}, 6: {'A': 0, 'C': 0, 'D': 0, 'E': 1, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 1, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 1, 'S': 0, 'T': 1, 'V': 1, 'W': 0, 'X': 0, 'Y': 0}, 7: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 10, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 8, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 10}} \ No newline at end of file diff --git a/epytope/Data/pssms/syfpeithi/mat/B_1801_9.py b/epytope/Data/pssms/syfpeithi/mat/B_1801_9.py index d8c4e4fd..f74f2e57 100644 --- a/epytope/Data/pssms/syfpeithi/mat/B_1801_9.py +++ b/epytope/Data/pssms/syfpeithi/mat/B_1801_9.py @@ -1 +1 @@ -B_1801_9 = {0: {'A': 0, 'C': 0, 'E': 1, 'D': 4, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': -1, 'M': 0, 'L': 0, 'N': 1, 'Q': 0, 'P': 0, 'S': 0, 'R': -1, 'T': 0, 'W': 0, 'V': -1, 'Y': 0, 'X': 0}, 1: {'A': 0, 'C': 0, 'E': 10, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 2: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 1, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 1, 'N': 0, 'Q': 0, 'P': -1, 'S': 0, 'R': 1, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 3: {'A': 0, 'C': 0, 'E': 2, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 1, 'N': -1, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 4: {'A': 0, 'C': 0, 'E': -1, 'D': 0, 'G': 0, 'F': 1, 'I': 1, 'H': 0, 'K': 0, 'M': 0, 'L': 2, 'N': 0, 'Q': 1, 'P': -1, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 5: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 1, 'M': 0, 'L': 1, 'N': 0, 'Q': 0, 'P': 1, 'S': 0, 'R': 1, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 6: {'A': 0, 'C': 0, 'E': 2, 'D': 0, 'G': 0, 'F': 0, 'I': 1, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 1, 'Y': 0, 'X': 0}, 7: {'A': 1, 'C': 0, 'E': 1, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 1, 'R': 0, 'T': 1, 'W': 0, 'V': 1, 'Y': 0, 'X': 0}, 8: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 10, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 8, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 6, 'V': 0, 'Y': 10, 'X': 0}} \ No newline at end of file +B_1801_9 = {0: {'A': 0, 'C': 0, 'D': 4, 'E': 1, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': -1, 'L': 0, 'M': 0, 'N': 1, 'P': 0, 'Q': 0, 'R': -1, 'S': 0, 'T': 0, 'V': -1, 'W': 0, 'X': 0, 'Y': 0}, 1: {'A': 0, 'C': 0, 'D': 0, 'E': 10, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 2: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 1, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 1, 'M': 0, 'N': 0, 'P': -1, 'Q': 0, 'R': 1, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 3: {'A': 0, 'C': 0, 'D': 0, 'E': 2, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 1, 'M': 0, 'N': -1, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 4: {'A': 0, 'C': 0, 'D': 0, 'E': -1, 'F': 1, 'G': 0, 'H': 0, 'I': 1, 'K': 0, 'L': 2, 'M': 0, 'N': 0, 'P': -1, 'Q': 1, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 5: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 1, 'L': 1, 'M': 0, 'N': 0, 'P': 1, 'Q': 0, 'R': 1, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 6: {'A': 0, 'C': 0, 'D': 0, 'E': 2, 'F': 0, 'G': 0, 'H': 0, 'I': 1, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 1, 'W': 0, 'X': 0, 'Y': 0}, 7: {'A': 1, 'C': 0, 'D': 0, 'E': 1, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 1, 'T': 1, 'V': 1, 'W': 0, 'X': 0, 'Y': 0}, 8: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 10, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 8, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 6, 'X': 0, 'Y': 10}} \ No newline at end of file diff --git a/epytope/Data/pssms/syfpeithi/mat/B_2705_10.py b/epytope/Data/pssms/syfpeithi/mat/B_2705_10.py new file mode 100644 index 00000000..d7fe031c --- /dev/null +++ b/epytope/Data/pssms/syfpeithi/mat/B_2705_10.py @@ -0,0 +1 @@ +B_2705_10 = {0: {'A': 1, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 3, 'H': 0, 'I': 1, 'K': 2, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 4, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 1: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 10, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 2: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 3, 'G': 0, 'H': 0, 'I': 2, 'K': 0, 'L': 2, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 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0}, 1: {'A': 0, 'C': 0, 'E': 10, 'D': 10, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 2: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 4, 'N': 1, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 3: {'A': 0, 'C': 0, 'E': 1, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 2, 'N': 0, 'Q': 1, 'P': 2, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 4: {'A': 0, 'C': 0, 'E': -1, 'D': -1, 'G': 0, 'F': 0, 'I': 0, 'H': 4, 'K': 4, 'M': 0, 'L': 1, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 6, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 5: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 1, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 1, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 1, 'Y': 0, 'X': 0}, 6: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 1, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 2, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 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'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 2, 'M': 0, 'N': 0, 'P': 2, 'Q': 1, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 4: {'A': 0, 'C': 0, 'D': -1, 'E': -1, 'F': 0, 'G': 0, 'H': 4, 'I': 0, 'K': 4, 'L': 1, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 6, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 5: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 1, 'K': 0, 'L': 0, 'M': 0, 'N': 1, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 1, 'W': 0, 'X': 0, 'Y': 0}, 6: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 1, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 2, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 7: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 1, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 2, 'T': 1, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 8: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 10, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 10, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}} \ No newline at end of file diff --git a/epytope/Data/pssms/syfpeithi/mat/B_3801_10.py b/epytope/Data/pssms/syfpeithi/mat/B_3801_10.py index 478245ed..366252f9 100644 --- a/epytope/Data/pssms/syfpeithi/mat/B_3801_10.py +++ b/epytope/Data/pssms/syfpeithi/mat/B_3801_10.py @@ -1 +1 @@ -B_3801_10 = {0: {'A': 0, 'C': 0, 'E': 1, 'D': 0, 'G': 0, 'F': 1, 'I': 1, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 1, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 1: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 10, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 6, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 2: {'A': 0, 'C': 0, 'E': 1, 'D': 4, 'G': 0, 'F': 0, 'I': 0, 'H': -1, 'K': -1, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': -1, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 3: {'A': 0, 'C': 0, 'E': 1, 'D': 1, 'G': 1, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 1, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 4: {'A': 0, 'C': 0, 'E': 0, 'D': 1, 'G': 0, 'F': 0, 'I': 1, 'H': 0, 'K': 0, 'M': 0, 'L': 1, 'N': 0, 'Q': 0, 'P': 1, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 1, 'Y': 0, 'X': 0}, 5: {'A': 0, 'C': 0, 'E': 1, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 6: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 1, 'H': 0, 'K': 1, 'M': 0, 'L': 1, 'N': 0, 'Q': 0, 'P': 1, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 1, 'Y': 0, 'X': 0}, 7: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 1, 'H': 0, 'K': 0, 'M': 0, 'L': 1, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 1, 'W': 0, 'V': 1, 'Y': 0, 'X': 0}, 8: {'A': 0, 'C': 0, 'E': 1, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 1, 'M': 1, 'L': 1, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 1, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 9: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 8, 'I': 6, 'H': 0, 'K': 0, 'M': 0, 'L': 10, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}} \ No newline at end of file +B_3801_10 = {0: {'A': 0, 'C': 0, 'D': 0, 'E': 1, 'F': 1, 'G': 0, 'H': 0, 'I': 1, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 1, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 1: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 10, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 6, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 2: {'A': 0, 'C': 0, 'D': 4, 'E': 1, 'F': 0, 'G': 0, 'H': -1, 'I': 0, 'K': -1, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': -1, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 3: {'A': 0, 'C': 0, 'D': 1, 'E': 1, 'F': 0, 'G': 1, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 1, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 4: {'A': 0, 'C': 0, 'D': 1, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 1, 'K': 0, 'L': 1, 'M': 0, 'N': 0, 'P': 1, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 1, 'W': 0, 'X': 0, 'Y': 0}, 5: {'A': 0, 'C': 0, 'D': 0, 'E': 1, 'F': 0, 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a/epytope/Data/pssms/syfpeithi/mat/B_3801_9.py +++ b/epytope/Data/pssms/syfpeithi/mat/B_3801_9.py @@ -1 +1 @@ -B_3801_9 = {0: {'A': 0, 'C': 0, 'E': 1, 'D': 0, 'G': 0, 'F': 1, 'I': 1, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 1, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 1: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 10, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 6, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 2: {'A': 0, 'C': 0, 'E': 1, 'D': 4, 'G': 0, 'F': 0, 'I': 0, 'H': -1, 'K': -1, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': -1, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 3: {'A': 0, 'C': 0, 'E': 0, 'D': 1, 'G': 1, 'F': -1, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 1, 'S': 0, 'R': 0, 'T': 0, 'W': -1, 'V': 0, 'Y': -1, 'X': 0}, 4: {'A': 0, 'C': 0, 'E': 0, 'D': 1, 'G': 0, 'F': 0, 'I': 1, 'H': 0, 'K': 0, 'M': 0, 'L': 1, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 1, 'Y': 0, 'X': 0}, 5: 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b/epytope/Data/pssms/syfpeithi/mat/B_3902_10.py @@ -0,0 +1 @@ +B_3902_10 = {0: {'A': 0, 'C': 0, 'D': -1, 'E': -1, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 4, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 4, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 1}, 1: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 10, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 8, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 2: {'A': 0, 'C': 0, 'D': 1, 'E': 0, 'F': 2, 'G': 0, 'H': -1, 'I': 1, 'K': -1, 'L': 1, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': -1, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 3: {'A': 0, 'C': 0, 'D': 2, 'E': 1, 'F': 0, 'G': 1, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 1, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 4: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 5: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 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No newline at end of file diff --git a/epytope/Data/pssms/syfpeithi/mat/B_4901_9.py b/epytope/Data/pssms/syfpeithi/mat/B_4901_9.py index 19730c19..c7b36a78 100644 --- a/epytope/Data/pssms/syfpeithi/mat/B_4901_9.py +++ b/epytope/Data/pssms/syfpeithi/mat/B_4901_9.py @@ -1 +1 @@ -B_4901_9 = {0: {'A': 1, 'C': 0, 'E': -1, 'D': -1, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': -1, 'Q': 0, 'P': -1, 'S': 0, 'R': 1, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 1: {'A': 0, 'C': 0, 'E': 10, 'D': 0, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 2: {'A': 0, 'C': 0, 'E': 0, 'D': 1, 'G': 0, 'F': 0, 'I': 1, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': -1, 'P': -1, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 3: {'A': 0, 'C': 0, 'E': 1, 'D': 1, 'G': 0, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 1, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 4: {'A': 0, 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a/epytope/Data/pssms/syfpeithi/mat/B_5101_8.py b/epytope/Data/pssms/syfpeithi/mat/B_5101_8.py index 48f5fd65..0e47b62b 100644 --- a/epytope/Data/pssms/syfpeithi/mat/B_5101_8.py +++ b/epytope/Data/pssms/syfpeithi/mat/B_5101_8.py @@ -1 +1 @@ -B_5101_8 = {0: {'A': 0, 'C': 0, 'E': 0, 'D': 4, 'G': 0, 'F': 1, 'I': 2, 'H': 0, 'K': 0, 'M': 1, 'L': 2, 'N': 1, 'Q': 0, 'P': 0, 'S': 0, 'R': 0, 'T': 1, 'W': 0, 'V': 1, 'Y': 2, 'X': 0}, 1: {'A': 10, 'C': 0, 'E': 0, 'D': 0, 'G': 6, 'F': 0, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 0, 'N': 0, 'Q': 0, 'P': 10, 'S': 0, 'R': 0, 'T': 0, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 2: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 3, 'I': 0, 'H': 0, 'K': 0, 'M': 0, 'L': 1, 'N': 0, 'Q': 0, 'P': 1, 'S': 0, 'R': 0, 'T': 0, 'W': 1, 'V': 1, 'Y': 1, 'X': 0}, 3: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 1, 'F': 0, 'I': 0, 'H': 0, 'K': 2, 'M': 0, 'L': 1, 'N': 0, 'Q': 0, 'P': 0, 'S': 0, 'R': 3, 'T': 1, 'W': 0, 'V': 0, 'Y': 0, 'X': 0}, 4: {'A': 0, 'C': 0, 'E': 0, 'D': 0, 'G': 0, 'F': 0, 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diff --git a/epytope/Data/pssms/syfpeithi/mat/B_5802_11.py b/epytope/Data/pssms/syfpeithi/mat/B_5802_11.py new file mode 100644 index 00000000..4693efbe --- /dev/null +++ b/epytope/Data/pssms/syfpeithi/mat/B_5802_11.py @@ -0,0 +1 @@ +B_5802_11 = {0: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 4, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 4, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 1: {'A': 6, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 10, 'T': 6, 'V': 8, 'W': 0, 'Y': 0, 'X': 0}, 2: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 1, 'G': 0, 'H': 0, 'I': 0, 'K': 1, 'L': 2, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 3: {'A': 1, 'C': 0, 'D': 0, 'E': 0, 'F': -1, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 3, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': -1, 'Y': -1, 'X': 0}, 4: {'A': 1, 'C': 0, 'D': 0, 'E': 1, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 1, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 5: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 1, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 6: {'A': 1, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 7: {'A': 0, 'C': 0, 'D': 0, 'E': 1, 'F': 0, 'G': 0, 'H': 0, 'I': 1, 'K': 0, 'L': 1, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 1, 'W': 0, 'Y': 0, 'X': 0}, 8: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 1, 'I': 0, 'K': 0, 'L': 1, 'M': 0, 'N': 0, 'P': 0, 'Q': 1, 'R': 2, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 9: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 2, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 10: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 10, 'G': 0, 'H': 0, 'I': 10, 'K': 0, 'L': 10, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}} \ No newline at end of file diff --git a/epytope/Data/pssms/syfpeithi/mat/B_5802_8.py b/epytope/Data/pssms/syfpeithi/mat/B_5802_8.py new file mode 100644 index 00000000..fc0b8d27 --- /dev/null +++ b/epytope/Data/pssms/syfpeithi/mat/B_5802_8.py @@ -0,0 +1 @@ +B_5802_8 = {0: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 1, 'K': 2, 'L': 1, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 1, 'S': 0, 'T': 0, 'V': 1, 'W': 0, 'Y': 0, 'X': 0}, 1: {'A': 10, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 10, 'T': 10, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 2: {'A': 1, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 1, 'M': 0, 'N': 1, 'P': 0, 'Q': 1, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 3: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 1, 'L': 1, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 1, 'W': 0, 'Y': 0, 'X': 0}, 4: {'A': 6, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 1, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 1, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 5: {'A': 0, 'C': 0, 'D': -1, 'E': -1, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 6, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 6: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 2, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 7: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 8, 'G': 0, 'H': 0, 'I': 10, 'K': 0, 'L': 10, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}} \ No newline at end of file diff --git a/epytope/Data/pssms/syfpeithi/mat/B_5802_9.py b/epytope/Data/pssms/syfpeithi/mat/B_5802_9.py new file mode 100644 index 00000000..67c2d3f4 --- /dev/null +++ b/epytope/Data/pssms/syfpeithi/mat/B_5802_9.py @@ -0,0 +1 @@ +B_5802_9 = {0: {'A': 0, 'C': 0, 'D': -1, 'E': -1, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 6, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 4, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 1: {'A': 8, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 10, 'T': 10, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 2: {'A': 0, 'C': 0, 'D': -1, 'E': -1, 'F': 1, 'G': 0, 'H': 0, 'I': 1, 'K': 1, 'L': 1, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 3: {'A': 0, 'C': 0, 'D': 0, 'E': 1, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 1, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 4: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 1, 'K': 0, 'L': 1, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 1, 'W': 0, 'Y': 0, 'X': 0}, 5: {'A': 1, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 1, 'K': 0, 'L': 1, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 1, 'W': 0, 'Y': 0, 'X': 0}, 6: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 3, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 7: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 1, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 1, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 8: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 10, 'G': 0, 'H': 0, 'I': 10, 'K': 0, 'L': 10, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}} \ No newline at end of file diff --git a/epytope/Data/pssms/syfpeithi/mat/C_0102_10.py b/epytope/Data/pssms/syfpeithi/mat/C_0102_10.py new file mode 100644 index 00000000..9b7c656c --- /dev/null +++ b/epytope/Data/pssms/syfpeithi/mat/C_0102_10.py @@ -0,0 +1 @@ +C_0102_10 = {0: {'A': 1, 'C': 0, 'D': 0, 'E': 0, 'F': 1, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 1, 'T': 0, 'V': 0, 'W': 0, 'Y': 1, 'X': 0}, 1: {'A': 2, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 2, 'K': 0, 'L': 6, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 2: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 6, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 10, 'Q': 0, 'R': 0, 'S': 6, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 3: {'A': 0, 'C': 0, 'D': 1, 'E': 2, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 4: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 1, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 1, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 5: {'A': 1, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 2, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 6: {'A': 0, 'C': 0, 'D': 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index 00000000..ddd58c87 --- /dev/null +++ b/epytope/Data/pssms/syfpeithi/mat/C_0501_9.py @@ -0,0 +1 @@ +C_0501_9 = {0: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 1, 'G': 0, 'H': 0, 'I': 1, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 1, 'T': 0, 'V': 1, 'W': 0, 'Y': 0, 'X': 0}, 1: {'A': 3, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 1, 'T': 0, 'V': 1, 'W': 0, 'Y': 0, 'X': 0}, 2: {'A': 0, 'C': 0, 'D': 10, 'E': 6, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 3: {'A': 0, 'C': 0, 'D': 1, 'E': 1, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 4: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 1, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 1, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 5: {'A': 0, 'C': 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'V': 0, 'W': 0, 'Y': 8, 'X': 0}} \ No newline at end of file diff --git a/epytope/Data/pssms/syfpeithi/mat/C_1402_8.py b/epytope/Data/pssms/syfpeithi/mat/C_1402_8.py new file mode 100644 index 00000000..659b75a1 --- /dev/null +++ b/epytope/Data/pssms/syfpeithi/mat/C_1402_8.py @@ -0,0 +1 @@ +C_1402_8 = {0: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 1, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 1, 'W': 0, 'Y': 1, 'X': 0}, 1: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 10, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 10, 'X': 0}, 2: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 1, 'M': 0, 'N': 0, 'P': 0, 'Q': 1, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 3: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 1, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 1, 'V': 1, 'W': 0, 'Y': 0, 'X': 0}, 4: 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'V': 0, 'W': 0, 'Y': 1, 'X': 0}, 7: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 6, 'G': 0, 'H': 0, 'I': 4, 'K': 0, 'L': 10, 'M': 4, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}} \ No newline at end of file diff --git a/epytope/Data/pssms/syfpeithi/mat/C_1701_9.py b/epytope/Data/pssms/syfpeithi/mat/C_1701_9.py new file mode 100644 index 00000000..28e2871e --- /dev/null +++ b/epytope/Data/pssms/syfpeithi/mat/C_1701_9.py @@ -0,0 +1 @@ +C_1701_9 = {0: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 3, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 1, 'T': 0, 'V': 0, 'W': 0, 'Y': 1, 'X': 0}, 1: {'A': 10, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 6, 'K': 0, 'L': 8, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 8, 'T': 0, 'V': 8, 'W': 0, 'Y': 0, 'X': 0}, 2: {'A': 1, 'C': 0, 'D': 1, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 1, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 1, 'W': 0, 'Y': 1, 'X': 0}, 3: 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0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}} \ No newline at end of file diff --git a/epytope/Data/pssms/syfpeithi/mat/G_0101_10.py b/epytope/Data/pssms/syfpeithi/mat/G_0101_10.py new file mode 100644 index 00000000..9a787013 --- /dev/null +++ b/epytope/Data/pssms/syfpeithi/mat/G_0101_10.py @@ -0,0 +1 @@ +G_0101_10 = {0: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 4, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 4, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 1: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 2, 'G': 0, 'H': 0, 'I': 1, 'K': 0, 'L': 2, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 2: {'A': 6, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 6, 'K': 0, 'L': 6, 'M': 0, 'N': 0, 'P': 10, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 8, 'W': 0, 'Y': 0, 'X': 0}, 3: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 1, 'H': 0, 'I': 0, 'K': 1, 'L': 0, 'M': 0, 'N': 0, 'P': 1, 'Q': 0, 'R': 0, 'S': 1, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 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0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}} \ No newline at end of file diff --git a/epytope/Data/pssms/syfpeithi/mat/G_0101_8.py b/epytope/Data/pssms/syfpeithi/mat/G_0101_8.py new file mode 100644 index 00000000..cfa9d41b --- /dev/null +++ b/epytope/Data/pssms/syfpeithi/mat/G_0101_8.py @@ -0,0 +1 @@ +G_0101_8 = {0: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 4, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 4, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 1: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 3, 'K': 0, 'L': 3, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 2: {'A': 6, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 6, 'K': 0, 'L': 6, 'M': 0, 'N': 0, 'P': 10, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 6, 'W': 0, 'Y': 0, 'X': 0}, 3: {'A': 0, 'C': 0, 'D': 0, 'E': 1, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 1, 'L': 0, 'M': 0, 'N': 0, 'P': 1, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 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'D': 0, 'E': 0, 'F': -1, 'G': 2, 'H': 0, 'I': -1, 'K': 0, 'L': 0, 'M': 2, 'N': 0, 'P': 0, 'Q': 1, 'R': 0, 'S': 2, 'T': 0, 'V': -1, 'W': 0, 'X': 0, 'Y': 0}, 2: {'A': 0, 'C': 0, 'D': 0, 'E': -1, 'F': 0, 'G': 1, 'H': 0, 'I': 2, 'K': -1, 'L': 2, 'M': 0, 'N': 0, 'P': 3, 'Q': 0, 'R': -1, 'S': 0, 'T': -1, 'V': 2, 'W': 0, 'X': 0, 'Y': 0}, 3: {'A': 0, 'C': 0, 'D': 1, 'E': 2, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 1, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 1, 'R': 1, 'S': 1, 'T': 1, 'V': 2, 'W': 0, 'X': 0, 'Y': 0}, 4: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 10, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 5: {'A': 1, 'C': 0, 'D': 0, 'E': 0, 'F': 1, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 2, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 6: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 7: {'A': 0, 'C': 0, 'D': 2, 'E': 2, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 1, 'R': 0, 'S': 1, 'T': 2, 'V': 1, 'W': 0, 'X': 0, 'Y': 0}, 8: {'A': 0, 'C': 0, 'D': 0, 'E': 2, 'F': 1, 'G': 0, 'H': 1, 'I': -1, 'K': 0, 'L': 1, 'M': -1, 'N': 0, 'P': 0, 'Q': 0, 'R': 1, 'S': 1, 'T': 2, 'V': 0, 'W': 0, 'X': 0, 'Y': 2}, 9: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 8, 'G': 0, 'H': 0, 'I': 10, 'K': 0, 'L': 10, 'M': 10, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 6, 'W': 0, 'X': 0, 'Y': 0}} \ No newline at end of file diff --git a/epytope/Data/pssms/syfpeithi/mat/H2_Db_9.py b/epytope/Data/pssms/syfpeithi/mat/H2_Db_9.py new file mode 100644 index 00000000..15ed9238 --- /dev/null +++ b/epytope/Data/pssms/syfpeithi/mat/H2_Db_9.py @@ -0,0 +1 @@ +H2_Db_9 = {0: {'A': 2, 'C': 0, 'D': 0, 'E': -1, 'F': 2, 'G': 0, 'H': 0, 'I': 0, 'K': 1, 'L': 0, 'M': 0, 'N': 0, 'P': -1, 'Q': 0, 'R': -1, 'S': 2, 'T': 1, 'V': 1, 'W': 0, 'X': 0, 'Y': 0}, 1: {'A': 3, 'C': 0, 'D': 0, 'E': 0, 'F': -1, 'G': 2, 'H': 0, 'I': -1, 'K': 0, 'L': 0, 'M': 2, 'N': 0, 'P': 0, 'Q': 1, 'R': 0, 'S': 2, 'T': 0, 'V': -1, 'W': 0, 'X': 0, 'Y': 0}, 2: {'A': 0, 'C': 0, 'D': 0, 'E': -1, 'F': 0, 'G': 1, 'H': 0, 'I': 2, 'K': -1, 'L': 2, 'M': 0, 'N': 0, 'P': 3, 'Q': 0, 'R': -1, 'S': 0, 'T': -1, 'V': 2, 'W': 0, 'X': 0, 'Y': 0}, 3: {'A': 0, 'C': 0, 'D': 1, 'E': 2, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 1, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 1, 'R': 1, 'S': 1, 'T': 1, 'V': 2, 'W': 0, 'X': 0, 'Y': 0}, 4: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 10, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 5: {'A': 1, 'C': 0, 'D': 0, 'E': 0, 'F': 1, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 2, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 6: {'A': 0, 'C': 0, 'D': 2, 'E': 2, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 1, 'R': 0, 'S': 1, 'T': 2, 'V': 1, 'W': 0, 'X': 0, 'Y': 0}, 7: {'A': 0, 'C': 0, 'D': 0, 'E': 2, 'F': 1, 'G': 0, 'H': 1, 'I': -1, 'K': 0, 'L': 1, 'M': -1, 'N': 0, 'P': 0, 'Q': 0, 'R': 1, 'S': 1, 'T': 2, 'V': 0, 'W': 0, 'X': 0, 'Y': 2}, 8: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 8, 'G': 0, 'H': 0, 'I': 10, 'K': 0, 'L': 10, 'M': 10, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 6, 'W': 0, 'X': 0, 'Y': 0}} \ No newline at end of file diff --git a/epytope/Data/pssms/syfpeithi/mat/H2_Kb_8.py b/epytope/Data/pssms/syfpeithi/mat/H2_Kb_8.py new file mode 100644 index 00000000..dfa6da8e --- /dev/null +++ b/epytope/Data/pssms/syfpeithi/mat/H2_Kb_8.py @@ -0,0 +1 @@ +H2_Kb_8 = {0: {'A': 1, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 1, 'K': 0, 'L': 1, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 1, 'S': 1, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 1: {'A': 1, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 1, 'H': 0, 'I': 1, 'K': 0, 'L': 0, 'M': 0, 'N': 1, 'P': 0, 'Q': 0, 'R': 0, 'S': 1, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 2: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 1, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 1, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 6}, 3: {'A': 0, 'C': 0, 'D': 1, 'E': 1, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 1, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 1, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 4: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 10, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 10}, 5: {'A': 0, 'C': 0, 'D': 0, 'E': 1, 'F': 0, 'G': 0, 'H': 0, 'I': 1, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 1, 'S': 1, 'T': 1, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 6: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 1, 'L': 0, 'M': 0, 'N': 1, 'P': 0, 'Q': 1, 'R': 0, 'S': 0, 'T': 1, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 7: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 6, 'K': 0, 'L': 10, 'M': 6, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 6, 'W': 0, 'X': 0, 'Y': 0}} \ No newline at end of file diff --git a/epytope/Data/pssms/syfpeithi/mat/H2_Kd_10.py b/epytope/Data/pssms/syfpeithi/mat/H2_Kd_10.py new file mode 100644 index 00000000..ae2a595d --- /dev/null +++ b/epytope/Data/pssms/syfpeithi/mat/H2_Kd_10.py @@ -0,0 +1 @@ +H2_Kd_10 = {0: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 1, 'K': 2, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 1, 'S': 3, 'T': 2, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 1: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 6, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 10}, 2: {'A': 1, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 1, 'K': 1, 'L': 3, 'M': 0, 'N': 0, 'P': 0, 'Q': 2, 'R': 0, 'S': 0, 'T': 0, 'V': 2, 'W': 0, 'X': 0, 'Y': 0}, 3: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 4: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 5: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 6: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 7: {'A': 0, 'C': 0, 'D': 0, 'E': 1, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 2, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 1, 'R': 0, 'S': 1, 'T': 4, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 8: {'A': 0, 'C': 0, 'D': 0, 'E': 1, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 1, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 2, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 1}, 9: {'A': 6, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 10, 'K': 0, 'L': 10, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 8, 'W': 0, 'X': 0, 'Y': 0}} \ No newline at end of file diff --git a/epytope/Data/pssms/syfpeithi/mat/H2_Kd_9.py b/epytope/Data/pssms/syfpeithi/mat/H2_Kd_9.py new file mode 100644 index 00000000..38659cc6 --- /dev/null +++ b/epytope/Data/pssms/syfpeithi/mat/H2_Kd_9.py @@ -0,0 +1 @@ +H2_Kd_9 = {0: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 1, 'K': 2, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 1, 'S': 3, 'T': 2, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 1: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 6, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 10}, 2: {'A': 1, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 1, 'K': 1, 'L': 3, 'M': 0, 'N': 0, 'P': 0, 'Q': 2, 'R': 0, 'S': 0, 'T': 0, 'V': 2, 'W': 0, 'X': 0, 'Y': 0}, 3: {'A': 0, 'C': 0, 'D': 1, 'E': 0, 'F': -1, 'G': 2, 'H': 0, 'I': -1, 'K': 0, 'L': -1, 'M': -1, 'N': 0, 'P': 3, 'Q': 0, 'R': 0, 'S': 2, 'T': 2, 'V': 1, 'W': 0, 'X': 0, 'Y': 0}, 4: {'A': 1, 'C': 0, 'D': 0, 'E': 0, 'F': -1, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 1, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 2, 'T': 1, 'V': 2, 'W': 0, 'X': 0, 'Y': 0}, 5: {'A': 2, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 2, 'H': 0, 'I': 1, 'K': 2, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': -1, 'T': 0, 'V': 1, 'W': 0, 'X': 0, 'Y': 0}, 6: {'A': 0, 'C': 0, 'D': 0, 'E': 1, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 2, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 1, 'R': 0, 'S': 1, 'T': 4, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 7: {'A': 0, 'C': 0, 'D': 0, 'E': 1, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 1, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 2, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 1}, 8: {'A': 6, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 10, 'K': 0, 'L': 10, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 8, 'W': 0, 'X': 0, 'Y': 0}} \ No newline at end of file diff --git a/epytope/Data/pssms/syfpeithi/mat/H2_Ld_9.py b/epytope/Data/pssms/syfpeithi/mat/H2_Ld_9.py new file mode 100644 index 00000000..db60313e --- /dev/null +++ b/epytope/Data/pssms/syfpeithi/mat/H2_Ld_9.py @@ -0,0 +1 @@ +H2_Ld_9 = {0: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 1, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 1}, 1: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 10, 'Q': 0, 'R': 0, 'S': 8, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 2: {'A': 1, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 1, 'H': 1, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 1, 'Q': 2, 'R': 0, 'S': 1, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 1}, 3: {'A': 1, 'C': 0, 'D': 0, 'E': 0, 'F': 1, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 1, 'M': 0, 'N': 0, 'P': 2, 'Q': 0, 'R': 1, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 4: {'A': 1, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 2, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 1, 'P': 0, 'Q': 0, 'R': 0, 'S': 1, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}, 5: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 1, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 1, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 1, 'S': 0, 'T': 0, 'V': 0, 'W': 1, 'X': 0, 'Y': 0}, 6: {'A': 0, 'C': 0, 'D': 0, 'E': 1, 'F': 1, 'G': 0, 'H': 1, 'I': 0, 'K': 0, 'L': 1, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 1, 'V': 1, 'W': 0, 'X': 0, 'Y': 0}, 7: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 2, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 1, 'W': 0, 'X': 0, 'Y': 1}, 8: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 10, 'G': 0, 'H': 0, 'I': 6, 'K': 0, 'L': 10, 'M': 6, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'X': 0, 'Y': 0}} \ No newline at end of file diff --git a/epytope/EpitopeAssembly/EpitopeAssembly.py b/epytope/EpitopeAssembly/EpitopeAssembly.py index 893927fa..8aa9be94 100644 --- a/epytope/EpitopeAssembly/EpitopeAssembly.py +++ b/epytope/EpitopeAssembly/EpitopeAssembly.py @@ -329,7 +329,7 @@ def __init__(self, peptides, cl_pred, ep_pred, alleles, threshold, comparator, l seq_to_pep = {} self.neo_cleavage = {} self.good_cleavage = {} - + if matrix is None: for start, stop in itr.combinations(pep_tmp, 2): if start == "Dummy" or stop == "Dummy": @@ -347,14 +347,16 @@ def __init__(self, peptides, cl_pred, ep_pred, alleles, threshold, comparator, l fragments[frag] = (start_str, stop_str) fragments[garf] = (stop_str, start_str) - + epi_pred = ep_pred.predict(generate_peptides_from_proteins(fragments.keys(), length), alleles=_alleles) + test = generate_peptides_from_proteins(fragments.keys(), length) + for index,row in epi_pred.iterrows(): - nof_epis = sum(comparator(row[a],threshold.get(a.name, 0)) for a in _alleles) \ - - for protein in index[0].proteins.values(): + nof_epis = int(sum(comparator(row[a],threshold.get(a.name, 0)) for a in _alleles)) + logging.warning(index.proteins.values()) + for protein in index.proteins.values(): start, stop = fragments[protein] - ep_edge_matrix[start,stop] += len(index[0].proteinPos[protein.transcript_id])*nof_epis + ep_edge_matrix[start,stop] += len(index.proteinPos[protein.transcript_id])*nof_epis cleave_pred = cl_pred.predict(list(fragments.keys())) #cleave_site_df = cleave_pred.xs((slice(None), (cleavage_pos-1))) @@ -393,7 +395,6 @@ def __init__(self, peptides, cl_pred, ep_pred, alleles, threshold, comparator, l model.E = Set(initialize=E) model.E_prime = Set(initialize=list(seq_to_pep.keys())) model.ExE = Set(initialize=itr.permutations(E,2), dimen=2) - model.w_ab = Param(model.E_prime, model.E_prime, initialize=cl_edge_matrix) model.e_ab = Param(model.E_prime, model.E_prime, initialize=ep_edge_matrix) model.card = Param(initialize=len(model.E_prime)) diff --git a/epytope/EpitopePrediction/ANN.py b/epytope/EpitopePrediction/ANN.py index 49837114..142620e6 100644 --- a/epytope/EpitopePrediction/ANN.py +++ b/epytope/EpitopePrediction/ANN.py @@ -15,8 +15,10 @@ import sys import tempfile import io +import math from abc import abstractmethod +from enum import IntEnum import pandas from collections import defaultdict @@ -71,7 +73,7 @@ def predict(self, peptides, alleles=None, binary=False, **kwargs): :param peptides: A single :class:`~epytope.Core.Peptide.Peptide` or a list of :class:`~epytope.Core.Peptide.Peptide` :type peptides: list(:class:`~epytope.Core.Peptide.Peptide`) or :class:`~epytope.Core.Peptide.Peptide` :param kwargs: optional parameter (not used yet) - :return: Returns a :class:`pandas.DataFrame` object with the prediction results + :return: Returns a nested dictionary {allele1: {scoreType1: {pep1: score1, pep2:..}, scoreType2: {..}, ..}, allele2:..} :rtype: :class:`pandas.DataFrame` """ @@ -181,7 +183,7 @@ def predict(self, peptides, alleles=None, binary=False, **kwargs): alleles = self.convert_alleles(alleles) # prepare results dictionary - result = defaultdict(defaultdict) + scores = defaultdict(defaultdict) # keep input peptide objects for later use peptide_objects = {} @@ -228,26 +230,32 @@ def predict(self, peptides, alleles=None, binary=False, **kwargs): for row in reader: content = row[0].split(',') # get original peptide object - peptide = peptide_objects[content[0]] - binding_affinity = content[1] + peptide = content[0] + binding_affinity = float(content[ScoreIndex.MHCNUGGETS_CLASS1_2_0]) if binary: if binding_affinity <= 500: - result[allele_repr][peptide] = 1.0 + scores[allele_repr][peptide] = 1.0 else: - result[allele_repr][peptide] = 0.0 + scores[allele_repr][peptide] = 0.0 else: - result[allele_repr][peptide] = binding_affinity + # convert ic50 to raw prediction score + scores[allele_repr][peptide] = 1- math.log(binding_affinity, 50000) - if not result: + if not scores: raise ValueError("No predictions could be made with " + self.name + " for given input. Check your epitope length and HLA allele combination.") + + # Convert str allele list to list with Allele objects + alleles = [self.revert_allele_repr(a) for a in alleles] + # Create dictionary with hierarchy: {'Allele1': {'Score': {'Pep1': AffScore1, 'Pep2': AffScore2,..}, 'Allele2':...} + result = {alleles: {"Score":(list(scores.values())[j])} for j, alleles in enumerate(alleles)} # create EpitopePredictionResult object. This is a multi-indexed DataFrame - # with Peptide and Method as multi-index and alleles as columns - df_result = EpitopePredictionResult.from_dict(result) - df_result.index = pandas.MultiIndex.from_tuples([tuple((i, self.name)) for i in df_result.index], - names=['Seq', 'Method']) + # with Allele, Method and Score type as multi-columns and peptides as rows + df_result = EpitopePredictionResult.from_dict(result, pep_groups, self.name) + return df_result + except BadSignatureException: logging.warning("Class MHCNuggetsPredictor_class1_2_0 cannot be constructed, because of a bad method signature (predict)") @@ -463,7 +471,7 @@ def predict(self, peptides, alleles=None, binary=False, **kwargs): alleles = self.convert_alleles(alleles) # prepare results dictionary - result = defaultdict(defaultdict) + scores = defaultdict(defaultdict) # keep input peptide objects for later use peptide_objects = {} @@ -510,25 +518,30 @@ def predict(self, peptides, alleles=None, binary=False, **kwargs): content = row[0].split(',') # get original peptide object peptide = peptide_objects[content[0]] - binding_affinity = content[1] + binding_affinity = float(content[ScoreIndex.MHCNUGGETS_CLASS2_2_0]) if binary: if binding_affinity <= 500: - result[allele_repr][peptide] = 1.0 + scores[allele_repr][peptide] = 1.0 else: - result[allele_repr][peptide] = 0.0 + scores[allele_repr][peptide] = 0.0 else: - result[allele_repr][peptide] = binding_affinity + # convert ic50 to raw prediction score + scores[allele_repr][peptide] = 1- math.log(binding_affinity, 50000) - if not result: + if not scores: raise ValueError("No predictions could be made with " + self.name + " for given input. Check your epitope length and HLA allele combination.") + # Convert str allele list to list with Allele type + alleles = [self.revert_allele_repr(a) for a in alleles] + # Create dictionary with hierarchy: {'Allele1': {'Score': {'Pep1': AffScore1, 'Pep2': AffScore2,..}, 'Allele2':...} + result = {allele: {"Score":(list(scores.values())[j])} for j, allele in enumerate(alleles)} + # create EpitopePredictionResult object. This is a multi-indexed DataFrame - # with Peptide and Method as multi-index and alleles as columns - df_result = EpitopePredictionResult.from_dict(result) - df_result.index = pandas.MultiIndex.from_tuples([tuple((i, self.name)) for i in df_result.index], - names=['Seq', 'Method']) + # with Allele, Method and Score type as multi-columns and peptides as rows + df_result = EpitopePredictionResult.from_dict(result, pep_groups, self.name) return df_result + except BadSignatureException: logging.warning("Class MHCNuggetsPredictor_class2_2_0 cannot be constructed, because of a bad method signature (predict)") @@ -742,7 +755,7 @@ def predict(self, peptides, alleles=None, binary=False, **kwargs): # test mhcflurry models are available => download if not p = subprocess.call(['mhcflurry-downloads', 'path', 'models_class1'], stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL) - if p is not 0: + if p != 0: logging.warn("mhcflurry models must be downloaded, as they were not found locally.") cp = subprocess.run(['mhcflurry-downloads', 'fetch', 'models_class1'], stdout=subprocess.PIPE, stderr=subprocess.STDOUT) if cp.returncode != 0: @@ -754,10 +767,17 @@ def predict(self, peptides, alleles=None, binary=False, **kwargs): predictor = Class1AffinityPredictor.load() # prepare results dictionary - result = defaultdict(defaultdict) + scores = defaultdict(defaultdict) + + # keep input peptide objects for later use + peptide_objects = {} + for peptide in peptides: + peptide_objects[str(peptide)] = peptide # group peptides by length - peptides.sort(key=len) + pep_groups = list(peptide_objects.keys()) + pep_groups.sort(key=len) + for length, peps in itertools.groupby(peptides, key=len): if length not in self.supportedLength: logging.warning("Peptide length must be at least %i or at most %i for %s but is %i" % (min(self.supportedLength), max(self.supportedLength), @@ -769,25 +789,30 @@ def predict(self, peptides, alleles=None, binary=False, **kwargs): for a in alleles: allele_repr = self.revert_allele_repr(a) for p in peps: - binding_affinity = predictor.predict(allele=a, peptides=[str(p)])[0] + binding_affinity = predictor.predict(allele=a, peptides=[str(p)])[ScoreIndex.MHCFLURRY] if binary: if binding_affinity <= 500: - result[allele_repr][p] = 1.0 + scores[allele_repr][p] = 1.0 else: - result[allele_repr][p] = 0.0 + scores[allele_repr][p] = 0.0 else: - result[allele_repr][p] = binding_affinity + # convert ic50 to raw prediction score + scores[allele_repr][p] = 1- math.log(binding_affinity, 50000) - if not result: + if not scores: raise ValueError("No predictions could be made with " + self.name + " for given input. Check your epitope length and HLA allele combination.") + + # Convert str allele list to list with Allele type + alleles = [self.revert_allele_repr(a) for a in alleles] + # Create dictionary with hierarchy: {'Allele1': {'Score': {'Pep1': AffScore1, 'Pep2': AffScore2,..}, 'Allele2':...} + result = {allele: {"Score":(list(scores.values())[j])} for j, allele in enumerate(alleles)} # create EpitopePredictionResult object. This is a multi-indexed DataFrame - # with Peptide and Method as multi-index and alleles as columns - df_result = EpitopePredictionResult.from_dict(result) - df_result.index = pandas.MultiIndex.from_tuples([tuple((i, self.name)) for i in df_result.index], - names=['Seq', 'Method']) + # with Allele, Method and Score type as multi-columns and peptides as rows + df_result = EpitopePredictionResult.from_dict(result, pep_groups, self.name) return df_result + except BadSignatureException: logging.warning("Class MHCFlurryPredictor_1_2_2 cannot be constructed, because of a bad method signature (predict)") @@ -868,3 +893,13 @@ def revert_allele_repr(self, name): return Allele(name) except BadSignatureException: logging.warning("Class MHCFlurryPredictor_1_4_3 cannot be constructed, because of a bad method signature (predict)") + + + +class ScoreIndex(IntEnum): + """ + Specifies the score column index in the respective output format + """ + MHCNUGGETS_CLASS1_2_0 = 1 + MHCNUGGETS_CLASS2_2_0 = 1 + MHCFLURRY = 0 diff --git a/epytope/EpitopePrediction/External.py b/epytope/EpitopePrediction/External.py index 3ed8e51c..e7ca18aa 100755 --- a/epytope/EpitopePrediction/External.py +++ b/epytope/EpitopePrediction/External.py @@ -17,8 +17,10 @@ import csv import os import math +import re from collections import defaultdict +from enum import IntEnum from epytope.Core.Allele import Allele, CombinedAllele, MouseAllele from epytope.Core.Peptide import Peptide @@ -85,15 +87,15 @@ def predict(self, peptides, alleles=None, command=None, options=None, **kwargs): if alleles is None: al = [Allele(a) for a in self.supportedAlleles] - allales_string = {conv_a: a for conv_a, a in zip(self.convert_alleles(al), al)} + alleles_string = {conv_a: a for conv_a, a in zip(self.convert_alleles(al), al)} else: if isinstance(alleles, Allele): alleles = [alleles] if any(not isinstance(p, Allele) for p in alleles): raise ValueError("Input is not of type Allele") - allales_string = {conv_a: a for conv_a, a in zip(self.convert_alleles(alleles), alleles)} + alleles_string = {conv_a: a for conv_a, a in zip(self.convert_alleles(alleles), alleles)} - result = defaultdict(defaultdict) + result = {} # group alleles in blocks of 80 alleles (NetMHC can't deal with more) _MAX_ALLELES = 50 @@ -108,18 +110,18 @@ def predict(self, peptides, alleles=None, command=None, options=None, **kwargs): allele_groups = [] c_a = 0 allele_group = [] - for a in allales_string.keys(): + for a in alleles_string.keys(): if c_a >= _MAX_ALLELES: c_a = 0 allele_groups.append(allele_group) - if str(allales_string[a]) not in self.supportedAlleles: - logging.warning("Allele %s is not supported by %s" % (str(allales_string[a]), self.name)) + if str(alleles_string[a]) not in self.supportedAlleles: + logging.warning("Allele %s is not supported by %s" % (str(alleles_string[a]), self.name)) allele_group = [] continue allele_group = [a] else: - if str(allales_string[a]) not in self.supportedAlleles: - logging.warning("Allele %s is not supported by %s" % (str(allales_string[a]), self.name)) + if str(alleles_string[a]) not in self.supportedAlleles: + logging.warning("Allele %s is not supported by %s" % (str(alleles_string[a]), self.name)) continue allele_group.append(a) c_a += 1 @@ -136,6 +138,7 @@ def predict(self, peptides, alleles=None, command=None, options=None, **kwargs): self.name, length)) continue peps = list(peps) + for i in range(0, len(peps), chunksize): # Create a temporary file for subprocess to write to. The # handle is not needed on the python end, as only the path will @@ -165,20 +168,24 @@ def predict(self, peptides, alleles=None, command=None, options=None, **kwargs): raise RuntimeError(e) res_tmp = self.parse_external_result(tmp_out_path) - for al, ep_dict in res_tmp.items(): - for p, v in ep_dict.items(): - result[allales_string[al]][pep_seqs[p]] = v + for allele, scores in res_tmp.items(): + if allele not in result.keys(): + result[allele] = {} + for scoretype, pep_scores in scores.items(): + if scoretype not in result[allele].keys(): + result[allele][scoretype] = {} + for pep, score in pep_scores.items(): + result[allele][scoretype][pep] = score + os.remove(tmp_file.name) os.remove(tmp_out_path) - + if not result: raise ValueError("No predictions could be made with " + self.name + " for given input. Check your epitope length and HLA allele combination.") + + df_result = EpitopePredictionResult.from_dict(result, list(pep_seqs.values()), self.name) - - df_result = EpitopePredictionResult.from_dict(result) - df_result.index = pandas.MultiIndex.from_tuples([tuple((i, self.name)) for i in df_result.index], - names=['Seq', 'Method']) return df_result @@ -286,8 +293,8 @@ def parse_external_result(self, file): for l in f: if not l: continue - pep_seq = l[2] - for ic_50, a in zip(l[3:], alleles): + pep_seq = l[PeptideIndex.NETMHC_3_4] + for ic_50, a in zip(l[ScoreIndex.NETMHC_3_0:], alleles): sc = 1.0 - math.log(float(ic_50), 50000) result[a][pep_seq] = sc if sc > 0.0 else 0.0 return dict(result) @@ -410,8 +417,8 @@ def parse_external_result(self, file): for l in csvr: if not l: continue - pep_seq = l[2] - for ic_50, a in zip(l[3:], alleles): + pep_seq = l[PeptideIndex.NETMHC_3_0] + for ic_50, a in zip(l[ScoreIndex.NETMHC_3_0:], alleles): sc = 1.0 - math.log(float(ic_50), 50000) result[a][pep_seq] = sc if sc > 0.0 else 0.0 if 'Average' in result: @@ -463,22 +470,24 @@ def parse_external_result(self, file): :return: A dictionary containing the prediction results :rtype: dict """ - result = defaultdict(defaultdict) + scores = defaultdict(defaultdict) + ranks = defaultdict(defaultdict) f = csv.reader(open(file, "r"), delimiter='\t') - pos_factor = 3 - # alleles = map(lambda x: x.split()[0], filter(lambda x: x.strip() != "", f.next())) - # f.next() - alleles = [x.split()[0] for x in [x for x in next(f) if x.strip() != ""]] + alleles = [Allele(x.split()[0][:5]+'*'+x.split()[0][5:7]+ ':' +x.split()[0][7:]) for x in [x for x in next(f) if x.strip() != ""]] next(f) for l in f: if not l: continue - pep_seq = l[1] + pep_seq = Peptide(l[PeptideIndex.NETMHC_4_0]) for i, a in enumerate(alleles): - ic_50 = l[(i+1)*pos_factor] + ic_50 = l[(i+1) * Offset.NETMHC_4_0] sc = 1.0 - math.log(float(ic_50), 50000) - result[a][pep_seq] = sc if sc > 0.0 else 0.0 - return dict(result) + rank = l[(i+1)* Offset.NETMHC_4_0 + 1] + scores[a][pep_seq] = sc if sc > 0.0 else 0.0 + ranks[a][pep_seq] = float(rank) + + result = {allele: {metric:(list(scores.values())[j] if metric == "Score" else list(ranks.values())[j]) for metric in ["Score", "Rank"]} for j, allele in enumerate(alleles)} + return result def get_external_version(self, path=None): """ @@ -912,15 +921,17 @@ def parse_external_result(self, file): :return: A dictionary containing the prediction results :rtype: dict """ - result = defaultdict(dict) - with open(file, "r") as f: - f = csv.reader(f, delimiter='\t') - alleles = f.next()[3:-1] - ic_pos = 3 - for row in f: - pep_seq = row[1] - for i, a in enumerate(alleles): - result[a][pep_seq] = float(row[ic_pos + i]) + f = csv.reader(open(file, "r"), delimiter = '\t') + scores = defaultdict(defaultdict) + alleles = [Allele(x[:5]+'*'+x[5:]) for x in next(f) if "HLA" in x] + # Rank is not supported in command line tool of NetMHCpan 2.4 + for row in f: + pep_seq = Peptide(row[PeptideIndex.NETMHCPAN_2_4]) + for i, a in enumerate(alleles): + scores[a][pep_seq] = float(row[ScoreIndex.NETMHCPAN_2_4 + i]) + # Create dictionary with hierarchy: {'Allele1': {'Score': {'Pep1': Score1, 'Pep2': Score2,..}, 'Allele2':...} + result = {allele: {"Score":(list(scores.values())[j])} for j, allele in enumerate(alleles)} + return result def get_external_version(self, path=None): @@ -1392,15 +1403,19 @@ def parse_external_result(self, file): :return: A dictionary containing the prediction results :rtype: dict """ - result = defaultdict(defaultdict) - f = csv.reader(open(file, "r"), delimiter='\t') - alleles = [x for x in next(f) if x != ""] + f = csv.reader(open(file, "r"), delimiter = '\t') + scores = defaultdict(defaultdict) + ranks = defaultdict(defaultdict) + alleles = [x[:5]+'*'+x[5:] for x in next(f) if x != ""] next(f) - ic_pos = 3 for row in f: - pep_seq = row[1] + pep_seq = row[PeptideIndex.NETMHCPAN_2_8] for i, a in enumerate(alleles): - result[a][pep_seq] = float(row[ic_pos + i * 3]) + if row[ScoreIndex.NETMHCPAN_2_8 + i * Offset.NETMHCPAN_2_8] != "1-log50k": # Avoid header column, only access raw and rank scores + scores[a][pep_seq] = float(row[ScoreIndex.NETMHCPAN_2_8 + i * Offset.NETMHCPAN_2_8]) + ranks[a][pep_seq] = float(row[RankIndex.NETMHCPAN_2_8 + i * Offset.NETMHCPAN_2_8]) + # Create dictionary with hierarchy: {'Allele1': {'Score': {'Pep1': Score1, 'Pep2': Score2,..}, 'Rank': {'Pep1': RankScore1, 'Pep2': RankScore2,..}}, 'Allele2':...} + result = {allele: {metric:(list(scores.values())[j] if metric == "Score" else list(ranks.values())[j]) for metric in ["Score", "Rank"]} for j, allele in enumerate(alleles)} return result @@ -1436,15 +1451,19 @@ def parse_external_result(self, file): :return: A dictionary containing the prediction results :rtype: dict """ - result = defaultdict(defaultdict) - f = csv.reader(open(file, "r"), delimiter='\t') - alleles = [x for x in next(f) if x != ""] - next(f) - ic_pos = 4 + f = csv.reader(open(file, "r"), delimiter = '\t') + scores = defaultdict(defaultdict) + ranks = defaultdict(defaultdict) + alleles = [Allele(x[:5]+'*'+x[5:]) for x in next(f) if x != ""] for row in f: - pep_seq = row[1] + pep_seq = Peptide(row[PeptideIndex.NETMHCPAN_3_0]) for i, a in enumerate(alleles): - result[a][pep_seq] = float(row[ic_pos + i * 4]) + if row[ScoreIndex.NETMHCPAN_3_0 + i * Offset.NETMHCPAN_3_0] != "1-log50k": # Avoid header column, only access raw and rank scores + scores[a][pep_seq] = float(row[ScoreIndex.NETMHCPAN_3_0 + i * Offset.NETMHCPAN_3_0]) + ranks[a][pep_seq] = float(row[RankIndex.NETMHCPAN_3_0 + i * Offset.NETMHCPAN_3_0]) + + # Create dictionary with hierarchy: {'Allele1': {'Score': {'Pep1': Score1, 'Pep2': Score2,..}, 'Rank': {'Pep1': RankScore1, 'Pep2': RankScore2,..}}, 'Allele2':...} + result = {allele: {metric:(list(scores.values())[j] if metric == "Score" else list(ranks.values())[j]) for metric in ["Score", "Rank"]} for j, allele in enumerate(alleles)} return result @@ -1472,15 +1491,18 @@ def parse_external_result(self, file): :return: A dictionary containing the prediction results :rtype: dict """ - result = defaultdict(defaultdict) - f = csv.reader(open(file, "r"), delimiter='\t') - alleles = [x for x in next(f) if x != ""] - next(f) - ic_pos = 5 + f = csv.reader(open(file, "r"), delimiter = '\t') + scores = defaultdict(defaultdict) + ranks = defaultdict(defaultdict) + alleles = [Allele(x[:5]+'*'+x[5:]) for x in next(f) if x != ""] for row in f: - pep_seq = row[1] + pep_seq = Peptide(row[PeptideIndex.NETMHCPAN_4_0]) for i, a in enumerate(alleles): - result[a][pep_seq] = float(row[ic_pos + i * 5]) + if row[ScoreIndex.NETMHCPAN_4_0 + i * Offset.NETMHCPAN_4_0] != "1-log50k": # Avoid header column, only access raw and rank scores + scores[a][pep_seq] = float(row[ScoreIndex.NETMHCPAN_4_0 + i * Offset.NETMHCPAN_4_0]) + ranks[a][pep_seq] = float(row[RankIndex.NETMHCPAN_4_0 + i * Offset.NETMHCPAN_4_0]) + # Create dictionary with hierarchy: {'Allele1': {'Score': {'Pep1': Score1, 'Pep2': Score2,..}, 'Rank': {'Pep1': RankScore1, 'Pep2': RankScore2,..}}, 'Allele2':...} + result = {allele: {metric:(list(scores.values())[j] if metric == "Score" else list(ranks.values())[j]) for metric in ["Score", "Rank"]} for j, allele in enumerate(alleles)} return result @@ -1916,20 +1938,29 @@ def parse_external_result(self, file): result = defaultdict(dict) with open(file, "r") as f: f = csv.reader(f, delimiter='\t') - alleles = [x for x in next(f) if x.strip() != ""] - logging.warning(alleles) - ic_pos = 4 + alleles = [x[:5]+'*'+x[5:] for x in next(f) if x != ""] + ranks = defaultdict(defaultdict) + rank_pos = 5 offset = 3 header = next(f) logging.warning("\t".join(header)) - if "Aff(nM)" in header: - ic_pos = 9 - offset = 8 - for row in f: - logging.warning("\t".join(row)) - pep_seq = row[1] - for i, a in enumerate(alleles): - result[a][pep_seq] = float(row[ic_pos +i*offset]) + if "Aff(nM)" in header: # With option command line option '-ia', which includes prediction score in output file + scores = defaultdict(defaultdict) + for row in f: + pep_seq = row[PeptideIndex.NETMHCSTABPAN_1_0] + for i, a in enumerate(alleles): + scores[a][pep_seq] = float(row[ScoreIndex.NETMHCSTABPAN_1_0 + i * Offset.NETMHCSTABPAN_1_0_W_SCORE]) + ranks[a][pep_seq] = float(row[RankIndex.NETMHCSTABPAN_1_0 + i * Offset.NETMHCSTABPAN_1_0_W_SCORE]) + # Create dictionary with hierarchy: {'Allele1': {'Score': {'Pep1': Score1, 'Pep2': Score2,..}, 'Rank': {'Pep1': RankScore1, 'Pep2': RankScore2,..}}, 'Allele2':...} + result = {allele: {metric:(list(scores.values())[j] if metric == "Score" else list(ranks.values())[j]) for metric in ["Score", "Rank"]} for j, allele in enumerate(alleles)} + else: + for row in f: + pep_seq = row[PeptideIndex.NETMHCSTABPAN_1_0] + for i, a in enumerate(alleles): + ranks[a][pep_seq] = float(row[RankIndex.NETMHCSTABPAN_1_0 + i * Offset.NETMHCSTABPAN_1_0_WO_SCORE]) + # Create dictionary with hierarchy: {'Allele1':{'Rank': {'Pep1': RankScore1, 'Pep2': RankScore2,..}}, 'Allele2':...} + result = {allele: {"Rank":list(ranks.values())[j]} for j, allele in enumerate(alleles)} + return result def get_external_version(self, path=None): @@ -2046,19 +2077,24 @@ def parse_external_result(self, file): :return: A dictionary containing the prediction results :rtype: dict """ - result = defaultdict(defaultdict) f = csv.reader(open(file, "r"), delimiter='\t') + scores = defaultdict(defaultdict) for r in f: if not r: continue - + row = r[0].split() if not len(row): continue - - if "HLA-" not in row[0]: + + if Allele.organism not in row[HLAIndex.NETMHCII_2_2]: continue - result[row[0]][row[2]] = float(row[4]) + allele = Allele(row[HLAIndex.NETMHCII_2_2][:8]+'*'+row[HLAIndex.NETMHCII_2_2][8:10]+':'+row[HLAIndex.NETMHCII_2_2][10:]) + pep = Peptide(row[PeptideIndex.NETMHCII_2_2]) + scores[allele][pep] = float(row[ScoreIndex.NETMHCII_2_2]) + + result = {allele: {"Score":list(scores.values())[j]} for j, allele in enumerate(scores.keys())} + return result def get_external_version(self, path=None): @@ -3937,15 +3973,20 @@ def parse_external_result(self, file): :return: A dictionary containing the prediction results :rtype: dict """ - result = defaultdict(defaultdict) f = csv.reader(open(file, "r"), delimiter='\t') - alleles = [x.replace("*", "_").replace(":", "") for x in set([x for x in next(f) if x != ""])] + scores = defaultdict(defaultdict) + ranks = defaultdict(defaultdict) + # NetMHCiipan 3.1 inherits from NetMHCiipan 3.0 thus has a slighty different allele nomenclature + alleles = [Allele('HLA-'+x) for x in set([x for x in next(f) if x != ""])] next(f) - ic_pos = 3 for row in f: - pep_seq = row[1] + pep_seq = Peptide(row[PeptideIndex.NETMHCIIPAN_3_0]) for i, a in enumerate(alleles): - result[a][pep_seq] = float(row[ic_pos + i * 3]) + scores[a][pep_seq] = float(row[ScoreIndex.NETMHCIIPAN_3_0 + i * Offset.NETMHCIIPAN_3_0]) + ranks[a][pep_seq] = float(row[RankIndex.NETMHCIIPAN_3_0 + i * Offset.NETMHCIIPAN_3_0]) + # Create dictionary with hierarchy: {'Allele1': {'Score': {'Pep1': Score1, 'Pep2': Score2,..}, 'Rank': {'Pep1': RankScore1, 'Pep2': RankScore2,..}}, 'Allele2':...} + result = {allele: {metric:(list(scores.values())[j] if metric == "Score" else list(ranks.values())[j]) for metric in ["Score", "Rank"]} for j, allele in enumerate(alleles)} + return result def get_external_version(self, path=None): @@ -5788,6 +5829,30 @@ def name(self): """The name of the predictor""" return self.__name + def parse_external_result(self, file): + """ + Parses external results and returns the result + + :param str file: The file path or the external prediction results + :return: A dictionary containing the prediction results + :rtype: dict + """ + f = csv.reader(open(file, "r"), delimiter='\t') + scores = defaultdict(defaultdict) + ranks = defaultdict(defaultdict) + # NetMHCiipan 3.1 inherits from NetMHCiipan 3.0 thus has a slighty different allele nomenclature + alleles = [Allele('HLA-'+x[:7].replace("_","*")+':'+x[7:]) for x in set([x for x in next(f) if x != ""])] + next(f) + for row in f: + pep_seq = Peptide(row[PeptideIndex.NETMHCIIPAN_3_1]) + for i, a in enumerate(alleles): + scores[a][pep_seq] = float(row[ScoreIndex.NETMHCIIPAN_3_1 + i * Offset.NETMHCIIPAN_3_1]) + ranks[a][pep_seq] = float(row[RankIndex.NETMHCIIPAN_3_1 + i * Offset.NETMHCIIPAN_3_1]) + # Create dictionary with hierarchy: {'Allele1': {'Score': {'Pep1': Score1, 'Pep2': Score2,..}, 'Rank': {'Pep1': RankScore1, 'Pep2': RankScore2,..}}, 'Allele2':...} + result = {allele: {metric:(list(scores.values())[j] if metric == "Score" else list(ranks.values())[j]) for metric in ["Score", "Rank"]} for j, allele in enumerate(alleles)} + + return result + class PickPocket_1_1(AExternalEpitopePrediction): """ @@ -6466,14 +6531,20 @@ def parse_external_result(self, file): :return: A dictionary containing the prediction results :rtype: dict """ - result = defaultdict(defaultdict) + scores = defaultdict(defaultdict) + alleles = [] with open(file, "r") as f: for row in f: if row[0] in ["#", "-"] or row.strip() == "" or "pos" in row: continue else: - s = row.split() - result[s[1].replace("*", "")][s[2]] = float(s[4]) + allele, pep, score = Allele(row.split()[HLAIndex.PICKPOCKET_1_1]), Peptide(row.split()[PeptideIndex.PICKPOCKET_1_1]), float(row.split()[ScoreIndex.PICKPOCKET_1_1]) + if allele not in alleles: + alleles.append(allele) + scores[allele][pep] = score + + result = {allele: {"Score": list(scores.values())[j]} for j, allele in enumerate(alleles)} + return result def get_external_version(self, path=None): @@ -6917,7 +6988,8 @@ def parse_external_result(self, file): :return: A dictionary containing the prediction results :rtype: dict """ - result = defaultdict(defaultdict) + scores = defaultdict(defaultdict) + alleles = [] with open(file, "r") as f: for l in f: if l.startswith("#") or l.startswith("-") or l.strip() == "": @@ -6925,9 +6997,15 @@ def parse_external_result(self, file): row = l.strip().split() if not row[0].isdigit(): continue + + epitope, allele, comb_score = Peptide(row[PeptideIndex.NETCTLPAN_1_1]), Allele(row[HLAIndex.NETCTLPAN_1_1]), float(row[ScoreIndex.NETCTLPAN_1_1]) + if allele not in alleles: + alleles.append(allele) + + scores[allele][epitope] = comb_score - epitope, allele, comb_score = row[3], row[2], row[7] - result[allele.replace("*", "")][epitope] = float(comb_score) + result = {allele: {"Score": list(scores.values())[j]} for j, allele in enumerate(alleles)} + return result def get_external_version(self, path=None): @@ -6956,3 +7034,71 @@ def prepare_input(self, input, file): :param File file: File-handler to input file for external tool """ file.write("\n".join(">pepe_%i\n%s" % (i, p) for i, p in enumerate(input))) + + +class PeptideIndex(IntEnum): + """ + Specifies the index of the peptide sequence from the parsed output format + """ + NETMHC_3_0 = 2 + NETMHC_3_4 = 2 + NETMHC_4_0 = 1 + NETMHCPAN_2_4 = 1 + NETMHCPAN_2_8 = 1 + NETMHCPAN_3_0 = 1 + NETMHCPAN_4_0 = 1 + NETMHCSTABPAN_1_0 = 1 + NETMHCII_2_2 = 2 + NETMHCIIPAN_3_0 = 1 + NETMHCIIPAN_3_1 = 1 + PICKPOCKET_1_1 = 2 + NETCTLPAN_1_1 = 3 + +class ScoreIndex(IntEnum): + """ + Specifies the score index from the parsed output format + """ + NETMHC_3_0 = 2 + NETMHC_3_4 = 3 + NETMHCPAN_2_4 = 3 + NETMHCPAN_2_8 = 3 + NETMHCPAN_3_0 = 4 + NETMHCPAN_4_0 = 5 + NETMHCSTABPAN_1_0 = 6 + NETMHCII_2_2 = 4 + NETMHCIIPAN_3_0 = 3 + NETMHCIIPAN_3_1 = 3 + PICKPOCKET_1_1 = 4 + NETCTLPAN_1_1 = 7 + +class RankIndex(IntEnum): + """ + Specifies the rank index from the parsed output format if there is a rank score provided by the predictor + """ + NETMHCPAN_2_8 = 5 + NETMHCPAN_3_0 = 6 + NETMHCPAN_4_0 = 7 + NETMHCSTABPAN_1_0 = 5 + NETMHCIIPAN_3_0 = 5 + NETMHCIIPAN_3_1 = 5 + +class Offset(IntEnum): + """ + Specifies the offset of columns for multiple predicted HLA-alleles in the given predictors in order to + correctly access score and rank per HLA-allele + """ + NETMHC_4_0 = 3 + NETMHCPAN_2_8 = 3 + NETMHCPAN_3_0 = 4 + NETMHCPAN_4_0 = 5 + NETMHCSTABPAN_1_0_W_SCORE = 8 + NETMHCSTABPAN_1_0_WO_SCORE = 3 + NETMHCIIPAN_3_0 = 3 + +class HLAIndex(IntEnum): + """ + Specifies the HLA-allele index in the parsed output of the predictor + """ + NETMHCII_2_2 = 0 + PICKPOCKET_1_1 = 1 + NETCTLPAN_1_1 = 2 diff --git a/epytope/EpitopePrediction/PSSM.py b/epytope/EpitopePrediction/PSSM.py index 004c701c..24a2df11 100644 --- a/epytope/EpitopePrediction/PSSM.py +++ b/epytope/EpitopePrediction/PSSM.py @@ -15,6 +15,7 @@ import csv import tempfile import pandas +import logging from epytope.Core.Allele import Allele from epytope.Core.Peptide import Peptide @@ -74,13 +75,12 @@ def __load_allele_model(allele, length): pep_groups = list(pep_seqs.keys()) pep_groups.sort(key=len) for length, peps in itertools.groupby(pep_groups, key=len): - peps = list(peps) # dynamicaly import prediction PSSMS for alleles and predict if self.supportedLength is not None and length not in self.supportedLength: warnings.warn("Peptide length of %i is not supported by %s" % (length, self.name)) continue - + for a in alleles_string.keys(): try: pssm = __load_allele_model(a, length) @@ -89,19 +89,18 @@ def __load_allele_model(allele, length): continue if alleles_string[a] not in result: - result[alleles_string[a]] = {} - ##here is the prediction and result object missing## + result[alleles_string[a]] = {'Score': {}} + for p in peps: score = sum(pssm[i].get(p[i], 0.0) for i in range(length)) + pssm.get(-1, {}).get("con", 0) - result[alleles_string[a]][pep_seqs[p]] = score + result[alleles_string[a]]['Score'][pep_seqs[p]] = score if not result: raise ValueError("No predictions could be made with " + self.name + " for given input. Check your epitope length and HLA allele combination.") - - df_result = EpitopePredictionResult.from_dict(result) - df_result.index = pandas.MultiIndex.from_tuples([tuple((i, self.name)) for i in df_result.index], - names=['Seq', 'Method']) + + df_result = EpitopePredictionResult.from_dict(result, pep_seqs.values(), self.name) + return df_result @@ -610,7 +609,7 @@ def __load_allele_model(allele, length): raise ValueError("Input is not of type Allele") alleles_string = {conv_a: a for conv_a, a in zip(self.convert_alleles(alleles), alleles)} - result = {} + scores = {} for length, peps in itertools.groupby(pep_seqs.keys(), key=lambda x: len(x)): peps = list(peps) # dynamicaly import prediction PSSMS for alleles and predict @@ -625,7 +624,7 @@ def __load_allele_model(allele, length): warnings.warn("No model found for %s with length %i" % (alleles_string[a], length)) continue - result[alleles_string[a]] = {} + scores[alleles_string[a]] = {} ##here is the prediction and result object missing## for p in peps: score = sum(pssm[i].get(p[i], 0.0) for i in range(length)) + pssm.get(-1, {}).get("con", 0) @@ -637,16 +636,15 @@ def __load_allele_model(allele, length): score = 0.0001 elif score > 1e6: score = 1e6 - result[alleles_string[a]][pep_seqs[p]] = score - # print a, score, result + scores[alleles_string[a]][pep_seqs[p]] = score - if not result: + if not scores: raise ValueError("No predictions could be made with " + self.name + " for given input. Check your" "epitope length and HLA allele combination.") + + result = {allele: {"Score":(list(scores.values())[j])} for j, allele in enumerate(alleles)} - df_result = EpitopePredictionResult.from_dict(result) - df_result.index = pandas.MultiIndex.from_tuples([tuple((i, self.name)) for i in df_result.index], - names=['Seq', 'Method']) + df_result = EpitopePredictionResult.from_dict(result, peps, self.name) return df_result @@ -989,7 +987,7 @@ def __load_allele_model(allele, length): raise ValueError("Input is not of type Allele") alleles_string = {conv_a: a for conv_a, a in zip(self.convert_alleles(alleles), alleles)} - result = {} + scores = {} pep_groups = list(pep_seqs.keys()) pep_groups.sort(key=len) for length, peps in itertools.groupby(pep_groups, key=len): @@ -1001,8 +999,8 @@ def __load_allele_model(allele, length): peps = list(peps) for a, allele in alleles_string.items(): - if alleles_string[a] not in result: - result[allele] = {} + if alleles_string[a] not in scores: + scores[allele] = {} # load matrix try: @@ -1016,15 +1014,15 @@ def __load_allele_model(allele, length): for p in peps: score = sum(self.__log_enrichment.get(p[i], 0.0) * importance[i] for i in range(length) if i not in pssm) - result[allele][pep_seqs[p]] = score + scores[allele][pep_seqs[p]] = score - if not result: + if not scores: raise ValueError("No predictions could be made with " + self.name + " for given input. Check your" "epitope length and HLA allele combination.") - df_result = EpitopePredictionResult.from_dict(result) - df_result.index = pandas.MultiIndex.from_tuples([tuple((i, self.name)) for i in df_result.index], - names=['Seq', 'Method']) + result = {allele: {"Score":(list(scores.values())[j])} for j, allele in enumerate(alleles)} + + df_result = EpitopePredictionResult.from_dict(result, peps, self.name) return df_result def convert_alleles(self, alleles): diff --git a/epytope/EpitopeSelection/OptiTope.py b/epytope/EpitopeSelection/OptiTope.py index ebbb964e..830b2bd8 100644 --- a/epytope/EpitopeSelection/OptiTope.py +++ b/epytope/EpitopeSelection/OptiTope.py @@ -39,6 +39,7 @@ from pyomo.opt import SolverFactory, TerminationCondition from epytope.Core.Result import EpitopePredictionResult +from epytope.Core.Peptide import Peptide from epytope.IO.Utils import capture_stdout class OptiTope(object): @@ -61,7 +62,7 @@ class OptiTope(object): Jean-Paul Watson and David L. Woodruff. Springer, 2012. """ - def __init__(self, results, threshold=None, k=10, solver="glpk", verbosity=0): + def __init__(self, results, threshold=None, k=10, solver="glpk", verbosity=0, rank=False): """ :param result: Epitope prediction result object from which the epitope selection should be performed :type result: :class:`~epytope.Core.Result.EpitopePredictionResult` @@ -70,14 +71,18 @@ def __init__(self, results, threshold=None, k=10, solver="glpk", verbosity=0): :param int k: The number of epitopes to select :param str solver: The solver to be used (default glpk) :param int verbosity: Integer defining whether additional debugg prints are made >0 => debug mode + :param bool rank: Boolean specifying whether optimization should be done based on a `rank` metric (default False) """ #check input data if not isinstance(results, EpitopePredictionResult): raise ValueError("first input parameter is not of type EpitopePredictionResult") + + # Check if input data supports rank metric + if not 'Rank' in results.columns.get_level_values(2) and rank: + raise ValueError("Rank metric cannot be found in the provided input") - _alleles = copy.deepcopy(results.columns.values.tolist()) - + _alleles = copy.deepcopy(list(set([cols[0] for cols in results.columns.values]))) #test if allele prob is set, if not set allele prob uniform #if only partly set infer missing values (assuming uniformity of missing value) prob = [] @@ -128,11 +133,22 @@ def __init__(self, results, threshold=None, k=10, solver="glpk", verbosity=0): peps = {} cons = {} - #unstack multiindex df to get normal df based on first prediction method - #and filter for binding epitopes - method = results.index.values[0][1] - res_df = results.xs(results.index.values[0][1], level="Method") - res_df = res_df[res_df.apply(lambda x: any(x[a] > self.__thresh.get(a.name, -float("inf")) + # unstack multiindex df to get normal df based on first prediction method and score metric + method = results.columns[1][1] + metric = 1 if rank else 0 + res_df = copy.deepcopy(results) + res_df.columns = res_df.columns.droplevel(1) + # Keep only the neceessary information: Allele, and Score/Rank of Peptides + # Multiindex structure is broken up here + res_df = res_df.xs(res_df.columns.values[metric][1], level="ScoreType", axis=1) + + # and filter for binding epitopes depending on a (high) score or a (low) rank + # with respect to the given threshold + if rank: + res_df = res_df[res_df.apply(lambda x: any(x[a] < self.__thresh.get(a, float("inf")) + for a in res_df.columns), axis=1)] + else: + res_df = res_df[res_df.apply(lambda x: any(x[a] > self.__thresh.get(a, -float("inf")) for a in res_df.columns), axis=1)] for tup in res_df.itertuples(): @@ -146,15 +162,22 @@ def __init__(self, results, threshold=None, k=10, solver="glpk", verbosity=0): 50000))) if a.name in self.__thresh else -float("inf") except: thr = 0 - + if s >= thr: alleles_I.setdefault(a.name, set()).add(seq) imm[seq, a.name] = min(1., max(0.0, 1.0 - math.log(s, 50000))) else: - if s > self.__thresh.get(a.name, -float("inf")): - alleles_I.setdefault(a.name, set()).add(seq) - imm[seq, a.name] = s - + # Determine the high scoring / low ranked peptides. If an allele is present in the result df but + # not in the specified threshold, the scores with respect to the allel will be kept + if rank: + if s < self.__thresh.get(a, float("inf")): + alleles_I.setdefault(a.name, set()).add(seq) + imm[seq, a.name] = s + else: + if s > self.__thresh.get(a, -float("inf")): + alleles_I.setdefault(a.name, set()).add(seq) + imm[seq, a.name] = s + prots = set(pr for pr in p.get_all_proteins()) cons[seq] = len(prots) for prot in prots: @@ -176,7 +199,7 @@ def __init__(self, results, threshold=None, k=10, solver="glpk", verbosity=0): model.Q = Set(initialize=variations) model.E = Set(initialize=set(peps.keys())) - + model.A = Set(initialize=list(alleles_I.keys())) model.E_var = Set(model.Q, initialize=lambda mode, v: epi_var[v]) model.A_I = Set(model.A, initialize=lambda model, a: alleles_I[a]) @@ -201,8 +224,8 @@ def __init__(self, results, threshold=None, k=10, solver="glpk", verbosity=0): # Objective definition model.Obj = Objective( - rule=lambda model: sum(model.x[e] * sum(model.p[a] * model.i[e, a] for a in model.A) for e in model.E), - sense=maximize) + rule=lambda model: sum(model.x[e] * sum(model.p[a] * model.i[e, a] for a in model.A) for e in model.E), + sense=maximize) #Obligatory Constraint (number of selected epitopes) diff --git a/epytope/test/TestEpitopeAssembly.py b/epytope/test/TestEpitopeAssembly.py index 58d26171..e3ec9833 100644 --- a/epytope/test/TestEpitopeAssembly.py +++ b/epytope/test/TestEpitopeAssembly.py @@ -20,7 +20,7 @@ def test_simple_assembly(self): :return: """ pred = CleavageSitePredictorFactory("PCM") - assembler = EpitopeAssembly(self.peptides, pred, solver="cbc", verbosity=0) + assembler = EpitopeAssembly(self.peptides, pred, solver="glpk", verbosity=0) r = assembler.solve() self.assertEqual(r, [Peptide("KLLPRLPGV"), Peptide("ALYDVVSTL"), Peptide("YLYDHLAPM")]) @@ -36,7 +36,7 @@ def test_pareto_assembly(self): print(ep_pred.predict(self.peptides,alleles=allele)) #cl_pred, ep_pred, alleles, threshold, comparator, length=9 - assembler = ParetoEpitopeAssembly(self.peptides,cl_pred, ep_pred, allele, thresh, comp, solver="cbc", verbosity=1) + assembler = ParetoEpitopeAssembly(self.peptides,cl_pred, ep_pred, allele, thresh, comp, solver="glpk", verbosity=1) r = assembler.solve(eps=1e10, order=(1,0)) print(r) @@ -49,7 +49,7 @@ def test_pareto_front_assembly(self): thresh = {a.name:10000 for a in allele} comp = lambda a,b: a <= b - assembler = ParetoEpitopeAssembly(self.peptides,cl_pred, ep_pred, allele, thresh, comp, solver="cbc", verbosity=0) + assembler = ParetoEpitopeAssembly(self.peptides,cl_pred, ep_pred, allele, thresh, comp, solver="glpk", verbosity=0) r = assembler.paretosolve() print(r) diff --git a/epytope/test/TestOptiTope.py b/epytope/test/TestOptiTope.py index f6bd7418..8cbe4613 100644 --- a/epytope/test/TestOptiTope.py +++ b/epytope/test/TestOptiTope.py @@ -53,7 +53,7 @@ def test_selection_without_constraints(self): :return: """ - opt = OptiTope(self.result, self.thresh, k=3, solver="cbc", verbosity=0) + opt = OptiTope(self.result, self.thresh, k=3, solver="glpk", verbosity=0) r =opt.solve() self.assertTrue(len(set(str(p) for p in r) - set(["GPTPLLYRL", "QYLAGLSTL", "ALYDVVSTL"])) == 0) @@ -67,7 +67,7 @@ def test_allele_cov_constraint(self): #self.alleles.extend([Allele("HLA-A*02:01"),Allele("HLA-B*15:01")]) #self.thresh.update({"A*02:01":0,"B*15:01":0}) self.result= EpitopePredictorFactory("BIMAS").predict(self.peptides, self.alleles) - opt = OptiTope(self.result, self.thresh, k=3, solver="cbc", verbosity=0) + opt = OptiTope(self.result, self.thresh, k=3, solver="glpk", verbosity=0) opt.activate_allele_coverage_const(0.99) r = opt.solve() @@ -77,9 +77,9 @@ def test_epitope_conservation_constraint(self): import random self.result = EpitopePredictorFactory("BIMAS").predict(self.peptides, self.alleles) conservation = {} - for e in self.result.index.levels[0]: + for e in self.result.index: conservation[str(e)] = random.random() - pt = OptiTope(self.result, self.thresh, k=3, solver="cbc", verbosity=0) + pt = OptiTope(self.result, self.thresh, k=3, solver="glpk", verbosity=0) pt.activate_epitope_conservation_const(0.5, conservation=conservation) for e in pt.solve(): print(e, conservation[e]) diff --git a/epytope/test/TestSpacerDesign.py b/epytope/test/TestSpacerDesign.py index 16aaf016..6755537e 100644 --- a/epytope/test/TestSpacerDesign.py +++ b/epytope/test/TestSpacerDesign.py @@ -15,8 +15,8 @@ class SpacerDesignTestCase(unittest.TestCase): """ def setUp(self): - epis = """GHRMAWDMM - VYEADDVIL""".split("\n") + epis = """GHRMAWDM + VYEADDVI""".split("\n") self.epis = [Peptide(x.strip()) for x in epis] self.alleles = [Allele("HLA-A*02:01", prob=0.5)] @@ -30,10 +30,10 @@ def test_standart_functions(self): epi_pred = EpitopePredictorFactory("Syfpeithi") cl_pred = CleavageSitePredictorFactory("PCM") - sbws = EpitopeAssemblyWithSpacer(self.epis, cl_pred, epi_pred, self.alleles, solver="cbc") + sbws = EpitopeAssemblyWithSpacer(self.epis, cl_pred, epi_pred, self.alleles, solver="glpk") sol = sbws.solve() print(sol) - assert all(i == str(j) for i, j in zip(["GHRMAWDMM", "WWQW", "VYEADDVIL"], sol)) + assert all(i == str(j) for i, j in zip(["GHRMAWDM", "WWQW", "VYEADDVI"], sol)) def test_unsupported_allele_length_combination(self): """ @@ -44,10 +44,10 @@ def test_unsupported_allele_length_combination(self): epi_pred = EpitopePredictorFactory("Syfpeithi") cl_pred = CleavageSitePredictorFactory("PCM") alleles = [Allele("HLA-A*02:01", prob=0.5), Allele("HLA-A*26:01", prob=0.5)] - sbws = EpitopeAssemblyWithSpacer(self.epis, cl_pred, epi_pred, alleles, solver="cbc") + sbws = EpitopeAssemblyWithSpacer(self.epis, cl_pred, epi_pred, alleles, solver="glpk") sol = sbws.solve() print(sol) - assert all(i == str(j) for i, j in zip(["GHRMAWDMM", "WWQW", "VYEADDVIL"], sol)) + assert all(i == str(j) for i, j in zip(["GHRMAWDM", "WWRW", "VYEADDVI"], sol)) def test_unsupported_allele_length_combination_exception(self): """ @@ -58,7 +58,7 @@ def test_unsupported_allele_length_combination_exception(self): epi_pred = EpitopePredictorFactory("Syfpeithi") cl_pred = CleavageSitePredictorFactory("PCM") alleles = [Allele("HLA-A*26:01", prob=0.5)] - sbws = EpitopeAssemblyWithSpacer(self.epis, cl_pred, epi_pred, alleles, solver="cbc") + sbws = EpitopeAssemblyWithSpacer(self.epis, cl_pred, epi_pred, alleles, solver="glpk", en=8) self.assertRaises(ValueError, sbws.solve) diff --git a/epytope/tutorials/CleavageAndTAPPrediction.ipynb b/epytope/tutorials/CleavageAndTAPPrediction.ipynb index a4a9a3e5..b92070b2 100644 --- a/epytope/tutorials/CleavageAndTAPPrediction.ipynb +++ b/epytope/tutorials/CleavageAndTAPPrediction.ipynb @@ -53,9 +53,12 @@ { "data": { "text/plain": [ - "PROTEIN: AAAAAAAAAAA (aa-seq)\n", - "\t\t Dummy (orig transcript)\n", - "\t\t VARIANTS:" + "[PROTEIN: IPVIIERYKGEKQLPVLDKTKFLVPDHVNMSELVKI (aa-seq)\n", + " \t\t NP_852610_part2 (orig transcript)\n", + " \t\t VARIANTS:,\n", + " PROTEIN: MKMRFFSSPCGKAAVDPADRCKEVQQIRDQHPSK (aa-seq)\n", + " \t\t NP_852610.1 (orig transcript)\n", + " \t\t VARIANTS:]" ] }, "execution_count": 2, @@ -66,7 +69,7 @@ "source": [ "protein = Protein(\"AAAAAAAAAAA\", gene_id=\"Dummy\", transcript_id=\"Dummy\")\n", "proteins = read_fasta(\"./data/proteins.fasta\", id_position=3, in_type=Protein)\n", - "protein" + "proteins" ] }, { @@ -106,7 +109,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 5, "metadata": {}, "outputs": [ { @@ -143,46 +146,87 @@ " \n", " \n", " \n", - " NP_852610.1\n", + " NP_852610_part2\n", " 0\n", - " M\n", + " I\n", " 0.00\n", " \n", " \n", " 1\n", - " K\n", + " P\n", " 0.00\n", " \n", " \n", " 2\n", - " M\n", + " V\n", " 0.00\n", " \n", " \n", " 3\n", - " R\n", - " 0.60\n", + " I\n", + " -1.93\n", " \n", " \n", " 4\n", - " F\n", - " -0.66\n", + " I\n", + " -0.89\n", + " \n", + " \n", + " ...\n", + " ...\n", + " ...\n", + " ...\n", + " \n", + " \n", + " NP_852610.1\n", + " 29\n", + " Q\n", + " -1.50\n", + " \n", + " \n", + " 30\n", + " H\n", + " -0.34\n", + " \n", + " \n", + " 31\n", + " P\n", + " -2.93\n", + " \n", + " \n", + " 32\n", + " S\n", + " 0.00\n", + " \n", + " \n", + " 33\n", + " K\n", + " 0.00\n", " \n", " \n", "\n", + "

70 rows × 2 columns

\n", "" ], "text/plain": [ - " Seq pcm\n", - "ID Pos \n", - "NP_852610.1 0 M 0.00\n", - " 1 K 0.00\n", - " 2 M 0.00\n", - " 3 R 0.60\n", - " 4 F -0.66" + " Seq pcm\n", + "ID Pos \n", + "NP_852610_part2 0 I 0.00\n", + " 1 P 0.00\n", + " 2 V 0.00\n", + " 3 I -1.93\n", + " 4 I -0.89\n", + "... .. ...\n", + "NP_852610.1 29 Q -1.50\n", + " 30 H -0.34\n", + " 31 P -2.93\n", + " 32 S 0.00\n", + " 33 K 0.00\n", + "\n", + "[70 rows x 2 columns]" ] }, - "execution_count": 4, + "execution_count": 5, "metadata": {}, "output_type": "execute_result" } @@ -190,7 +234,7 @@ "source": [ "pcm = CleavageSitePredictorFactory(\"PCM\")\n", "site_result = pcm.predict(proteins)\n", - "site_result.head()" + "site_result" ] }, { @@ -202,7 +246,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 6, "metadata": {}, "outputs": [ { @@ -239,46 +283,46 @@ " \n", " \n", " \n", - " NP_852610.1\n", + " NP_852610_part2\n", " 0\n", - " M\n", + " I\n", " 0.00\n", " \n", " \n", " 1\n", - " K\n", + " P\n", " 0.00\n", " \n", " \n", " 2\n", - " M\n", + " V\n", " 0.00\n", " \n", " \n", " 3\n", - " R\n", - " 0.60\n", + " I\n", + " -1.93\n", " \n", " \n", " 4\n", - " F\n", - " -0.66\n", + " I\n", + " -0.89\n", " \n", " \n", "\n", "" ], "text/plain": [ - " Seq pcm\n", - "ID Pos \n", - "NP_852610.1 0 M 0.00\n", - " 1 K 0.00\n", - " 2 M 0.00\n", - " 3 R 0.60\n", - " 4 F -0.66" + " Seq pcm\n", + "ID Pos \n", + "NP_852610_part2 0 I 0.00\n", + " 1 P 0.00\n", + " 2 V 0.00\n", + " 3 I -1.93\n", + " 4 I -0.89" ] }, - "execution_count": 5, + "execution_count": 6, "metadata": {}, "output_type": "execute_result" } @@ -305,7 +349,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 7, "metadata": {}, "outputs": [ { @@ -366,7 +410,7 @@ "(C, K, E, V, Q, Q, I, R, D) -17.682320" ] }, - "execution_count": 6, + "execution_count": 7, "metadata": {}, "output_type": "execute_result" } @@ -385,12 +429,12 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 8, "metadata": {}, "outputs": [ { "data": { - "image/png": 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lj54Y4aduBT4fEZXeVgMQEa8B5wMflVTt1S/X9tJt/hK4GrhO0uQ6Yq6bpHdIml+yaAGH3zG0rnI5fRsYkPTfS7Z/asbbyW8Dg5L+omRZxStXavTFxcCaiHhrRAxFxFzgZ8DvN1iOSEZH3yHp25qje0mzgFtITtCqUz9V5I6vnnpzHHN5+6yec6KmHG38GDBV0sfSmCYCXyDZ130NlGskxlzna41+GLf4qqnnvG6oX+t9xWn3g4xXRWqMyNO/x068C1uxvfT5A8Dljb5y5ylH8nbuB8BTwHbgG8DMJsrlje14kitNngN2AA8B8zPKzSaZtvgZyXzuvwFL6+0LkqSxuOz/XA18qWxZrnIl6y4ieSte6YPiQyRXZe0AtgHXAROa6K+8+5Gr3rzHXN4+y3NOlMU39rixyj7XauO5JPPnPwV+AXy5mXJ5+yNP29XZ/zXjy6hzGU2M8GngvK7Wr+UP31rBzMaNpN8jeSfw4Yio+CFz3nKd0u3x5eWEb2ZWEL00h29mZk1wwjczK4hJnQ6gmpkzZ8bQ0FCnwzAz6xlbtmx5KSr8pm1XJ/yhoSE2b97c6TDMzHqGpIqXZ3tKx8ysIJzwzcwKoqundOw3hq5/6IhlIzd+sAORmFmv6rmE//rrrzM6Osr+/fs7Hcq4GBwcZM6cOUyePK53cDCzAuq5hD86Osq0adMYGhpCaubGet0nIti7dy+jo6OccMIJHY2l3e8oyuvzuxez1uu5Ofz9+/czY8aMvkv2AJKYMWNG3757MbPO6rmED/Rlsh/Tz/tmZp3Vc1M6ZmZ5eJrwSD2f8LPmmpvhg8LM+lVPTumYmVn9en6E324jIyMsXryYRYsWsXXrVk488UTWrFnDjh07uOaaa3j11VcZGBjgscce4+677+bee+/l0KFDDA8Pc+2113LgwAFuv/12BgYGWLduHccee2ynd8nMCsIj/AY888wzLF++nO3btzN9+nRWrVrF0qVLuemmm9i2bRvr169nypQpAAwPD3PHHXfwxBNPsHLlSqZOncrWrVs544wzWLNmTYf3xMyKxAm/AXPnzuXMM88E4LLLLuPhhx9m9uzZnHrqqQBMnz6dSZOSN09nn30206ZNY9asWRx99NFccMEFAJx88smMjIx0JH4zKyYn/AaUXzo5ffr0ipdTDgwMvPH3hAkT3ng+YcIEDh48OH5BmpmVccJvwPPPP8+GDRsAWLt2Laeffjq7d+9m06ZNALz88stO5mbWdXr+Q9tOXEZ50kkncdttt3HFFVcwf/58VqxYwTnnnMOKFSvYt28fU6ZMYf369W2Py8ysmp5P+J0wYcIEbrnllsOWnXrqqWzcuPGwZcuWLWPZsmVvPC+dsy9fZ2Y23jylY2ZWEE74dRoaGmJ4eLjTYZiZ1a0np3Qiom9vMhYRnQ7BUv7RGes3PTfCHxwcZO/evX2ZGMfuhz84ONjpUMysD/XcCH/OnDmMjo6yZ8+eTocyLsZ+8crMrNV6LuFPnjy5478GZWbWi3puSsfMzBrjhG9mVhBO+GZmBdHWhC9psaRnJD0r6fp21m1mVnRtS/iSJgI3Ax8Afge4VNLvtKt+M7Oia+cI/zTg2YjYGREHgDuBC9tYv5lZoaldX2CSdDGwOCL+PH1+ObAoIq4qK7ccWA4wb968U3bt2tWW+Erl+bX7PN/CzPtNzTz15eH6ujOmvPW1av9a+Q3hdrd50fZvPL65LWlLRCzMWtfOEX7WvRCOeLWJiNURsTAiFs6aNasNYZmZFUM7E/4oMLfk+RxgdxvrNzMrtHZ+03YTMF/SCcALwCXAR9pYv5lZ3frphnltS/gRcVDSVcDDwETg1ojY0a76zcyKrq330omIdcC6dtZpnddPIySzZnT6XPA3bc3MCqLn7pZpZv2r0yPgfucRvplZQXiEP448WrFO8HFnlXiEb2ZWEB7hm7WBR93WDZzwu4CTgeXlY8Wa4YRvZj3FL3qN8xy+mVlBOOGbmRWEE76ZWUE44ZuZFYQ/tDWzivr9A9J+379yHuGbmRWER/gNKtrIwMx6n0f4ZmYF4RF+H2n3uw6/yzHrLR7hm5kVhBO+mVlBeErH+oqnmcwq8wjfzKwgPMI36xK9+u6kV+MuIo/wzcwKwgnfzKwgPKVjZm3hqZ/O8wjfzKwgPMK3QvJo04rII3wzs4JwwjczKwgnfDOzgnDCNzMrCCd8M7OCcMI3MysIJ3wzs4JoS8KX9HeSnpa0XdI9ko5pR71mZvYb7fri1aPApyPioKS/AT4NfKpNdZuZjbte+DJfWxJ+RDxS8nQjcHE76m1UL3ScmVm9OjGH/6fANyutlLRc0mZJm/fs2dPGsMzM+lvLRviS1gNvyVi1MiLuS8usBA4CX6+0nYhYDawGWLhwYbQqPjOzomtZwo+I86qtl/Rx4Hzg3IhwIjcza7O2zOFLWkzyIe37IuK1dtRpZmaHa9dVOquAAeBRSQAbI+LKNtVtZfyhtFkxtesqnbe3ox4zM6vM37Q1MysIJ3wzs4JwwjczKwgnfDOzgnDCNzMrCCd8M7OCcMI3MysIJ3wzs4JwwjczKwgnfDOzgnDCNzMriHbdPM2sab7pm1lzPMI3MysIJ3wzs4LwlI5ZEzzNZL3EI3wzs4JwwjczKwgnfDOzgnDCNzMrCEVEp2OoSNIeYFfJopnASzn+a55y7Szj+vo/pn6vrxtj6vf6Go3prRExK7NkRPTMA9jcqnLtLOP6+j+mfq+vG2Pq9/paGdPYw1M6ZmYF4YRvZlYQvZbwV7ewXDvLuL72l3F97S/j+tpfpp5y3f2hrZmZtU6vjfDNzKxBTvhmZgXRUwlf0is11h+S9KSkYUn/ImlqybrvSPqjsvJ/JemLjdZXZ0xjj+trxP2ApGPK1kvS9yV9oGTZn0j6VqVYJC2R9FNJ8zLqe7OkOyTtlLRF0gZJFzUQd836JM2RdF+6bqekVZIGqm2rkmr9m67P3cd19NsOSdskfVLSEedLzjaYUdKO/0fSCyXP/0s92yqLbewx1MD+5WqrWm1eVqZiW5XHI2mZpFUNxhSSvlDy/DpJN2SUub3k+SRJeyQ9mBH/yjT27el+LKqwfxXPhax9zFifd/9yHQd56jxC3us3u+EBvJJ3PfB14JMlz68AvlZWfiNwVqP11RtTzrhvA1ZmlHk38GNgEHgT8FPgbVnbAc4Fnitfn64TsAG4smTZW4EVjcZdqb60rieAT6TPJwJfBW5qQTsd1r/19nGdx9JxwHrgc/W2QUb5G4DrGmnPFh+XudqqVpvnbavyeIBlwKoGY9oP/AyYmT6/DrihvD5gKzAlff4B4EngwbJyZ6Tnw0D6fCZwfL3tPR5tnueYyhvb2KOnRvh1+h7w9pLn/wqcPza6TEdFxwPfb39oVW0Afqt8YUQMAw8AnwL+B7AmIp4rLyfpLOCfgA9mrQfOAQ5ExC0l294VEf/YSLA16jsH2B8RX0vrOQT8NfAxSUc1Ul+J8v6FcerjiHgRWA5cJUnl63O0eW6t3FYNjbRVVpsfplZbtSimgyRXpvx1je19Exi7f/WlwNqMMrOBlyLi12n8L0XE7jrjzit3m4/XcdCXCV/SJJJX9B+NLYuIvSSjzcXpokuAuyJ9mRxHU8reDi6tVFDSRJJX9fsrFPkc8BGSffvbjPUDwH3AhyLi6QrbeBfwwxbFXau+dwFbShdExK+AEWokjmqy+jfd9rj1cUTsJDlfjitblafN88q7rdK+uaeRiuptq0ptXmHbWW112PEEfL7JmG4GPirp6Cqh3AlcImkQeA/w7xllHgHmSvqJpC9Kel9GmdzncDV17F8rj6nD9FvCn5IeTJuB50mmD0qtJWlk0n+zXvFbbV9ELCh53JVRZizuvcCxwKNZG4qIV4G7gNvHRiRlXgd+APxZ3uAk3ZzOu25qIO5a9QnIOlnrHfmNqdW/ML59nBV33W1eRd5tlfbNRTXKVpOnrfK0eZbytjrseAI+20RMYwOHNcDVlQKIiO3AEMnofl2FMq8Ap5C8K9kD3CVpWbXYK5wLeeXZv1YeU4erZ/6n0w+anC8HjgJeBN4LPNNsfa2IqbQMcDTJ2+arq5S9gSpzwMDU9GD5TIUy5wLfLVs2ExhpJO5q9QHnAY+XLZsO/Jx0brWVbV1PH9fbb8Bvk7wgq942b2X/tbutGqkrq60yyiyjbA6/3phIBkcjJFOcN1Qo89k0lpOB91M2h5+x7YuBB+ptg1a3ed5jKm9sY49+G+FXFcmr+XeAW2nP6L4uEfFLkhHLdZImN7iN14DzSd7uZo0Qvg0MSvqLkmVHXHnRovoeA6ZK+hi8MWX1BZITfV+jddaIp+V9LGkWcAtJ3Ee8Y8nR5rm1cls56mp7W7Uypoj4T+CfqT4SvhX4fERkTkVJeoek+SWLFnD4HXpbKu/+jdtxUM+rQ6cftGY0fRHJNMM7W/SKXSumQyRXB4w9bqy1DZIPZy+vsL0bqHGVR/r3XJIrGS7MKDebZH7zZyRziv8GLG0m7kr1pcvvJ7mq6BfAlyvE/v+A0ZJH1atBmu3jWvWV7P8OYBvJlSATGm3zFvdfnuOyZnvmaaucddVsq4xjfBkZI/x6YwLeDLxGhRF+2bL3c+RVOqeQjKSfArYD3yC9+qeec2G82rzWMZX3nBh7+NYK1jaSfo9kVPPhiNhSq7yZtZYTvplZQRRqDt/MrMic8M3MCsIJ38ysIJzwzcwKYlKnAzDrVpIOkdxKYBLJjes+Hsn10WY9ySN8s8rGvlL/buAAcGWnAzJrhhO+WT7fA94u6VhJ96b3Tt8o6T0Akt5XcnOtrZKmdThesyM44ZvVUHanyM8BWyPiPcBnSG7gBcm3S/8ykhuDnQWMy60jzJrhhG9WWdadIn8fuB0gIr4NzEhv0fu/gX+QdDVwTEQc7EzIZpX5Q1uzyvalI/Y3VPhRj4iIGyU9BCwBNko6L1p8L3OzZnmEb1afx4GPAkh6P8mvJf1K0tsi4kcR8Tck7wje2bkQzbL5XjpmFUh6JSKOKlt2LPA14ASSuzQuj4jtkv4ROJvkzopPAcsi+0dqzDrGCd/MrCA8pWNmVhBO+GZmBeGEb2ZWEE74ZmYF4YRvZlYQTvhmZgXhhG9mVhD/H3XyLgVpSr4zAAAAAElFTkSuQmCC\n", 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\n", 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" ] @@ -419,7 +463,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": 9, "metadata": {}, "outputs": [ { @@ -458,65 +502,65 @@ " \n", " \n", " \n", - " NP_852610.1\n", + " NP_852610_part2\n", " 0\n", - " M\n", + " I\n", " 0.00\n", " 0.000000\n", " \n", " \n", " 1\n", - " K\n", + " P\n", " 0.00\n", " 0.000000\n", " \n", " \n", " 2\n", - " M\n", + " V\n", " 0.00\n", " 0.000000\n", " \n", " \n", " 3\n", - " R\n", - " 0.60\n", + " I\n", + " -1.93\n", " 0.000000\n", " \n", " \n", " 4\n", - " F\n", - " -0.66\n", + " I\n", + " -0.89\n", " 0.000000\n", " \n", " \n", " 5\n", - " F\n", - " 0.41\n", - " 0.967189\n", + " E\n", + " -0.39\n", + " 0.994765\n", " \n", " \n", " 6\n", - " S\n", - " -0.78\n", - " 0.848493\n", + " R\n", + " -0.53\n", + " 0.857179\n", " \n", " \n", "\n", "" ], "text/plain": [ - " Seq pcm proteasmm_c\n", - "ID Pos \n", - "NP_852610.1 0 M 0.00 0.000000\n", - " 1 K 0.00 0.000000\n", - " 2 M 0.00 0.000000\n", - " 3 R 0.60 0.000000\n", - " 4 F -0.66 0.000000\n", - " 5 F 0.41 0.967189\n", - " 6 S -0.78 0.848493" + " Seq pcm proteasmm_c\n", + "ID Pos \n", + "NP_852610_part2 0 I 0.00 0.000000\n", + " 1 P 0.00 0.000000\n", + " 2 V 0.00 0.000000\n", + " 3 I -1.93 0.000000\n", + " 4 I -0.89 0.000000\n", + " 5 E -0.39 0.994765\n", + " 6 R -0.53 0.857179" ] }, - "execution_count": 8, + "execution_count": 9, "metadata": {}, "output_type": "execute_result" } @@ -541,7 +585,7 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": 10, "metadata": {}, "outputs": [ { @@ -580,6 +624,37 @@ " \n", " \n", " \n", + " NP_852610_part2\n", + " 7\n", + " Y\n", + " 1.26\n", + " 1.093200\n", + " \n", + " \n", + " 10\n", + " E\n", + " 1.19\n", + " 1.029347\n", + " \n", + " \n", + " 13\n", + " L\n", + " 1.18\n", + " 1.123535\n", + " \n", + " \n", + " 17\n", + " D\n", + " 0.51\n", + " 1.173126\n", + " \n", + " \n", + " 29\n", + " M\n", + " 1.07\n", + " 1.064119\n", + " \n", + " \n", " NP_852610.1\n", " 3\n", " R\n", @@ -628,37 +703,6 @@ " 0.94\n", " 1.130923\n", " \n", - " \n", - " NP_852610_part2\n", - " 7\n", - " Y\n", - " 1.26\n", - " 1.093200\n", - " \n", - " \n", - " 10\n", - " E\n", - " 1.19\n", - " 1.029347\n", - " \n", - " \n", - " 13\n", - " L\n", - " 1.18\n", - " 1.123535\n", - " \n", - " \n", - " 17\n", - " D\n", - " 0.51\n", - " 1.173126\n", - " \n", - " \n", - " 29\n", - " M\n", - " 1.07\n", - " 1.064119\n", - " \n", " \n", "\n", "" @@ -666,6 +710,11 @@ "text/plain": [ " Seq pcm proteasmm_c\n", "ID Pos \n", + "NP_852610_part2 7 Y 1.26 1.093200\n", + " 10 E 1.19 1.029347\n", + " 13 L 1.18 1.123535\n", + " 17 D 0.51 1.173126\n", + " 29 M 1.07 1.064119\n", "NP_852610.1 3 R 0.60 0.000000\n", " 5 F 0.41 0.967189\n", " 12 A 0.43 1.071828\n", @@ -673,15 +722,10 @@ " 15 D 0.29 1.160524\n", " 23 V 0.86 0.988586\n", " 26 I 0.42 1.094651\n", - " 28 D 0.94 1.130923\n", - "NP_852610_part2 7 Y 1.26 1.093200\n", - " 10 E 1.19 1.029347\n", - " 13 L 1.18 1.123535\n", - " 17 D 0.51 1.173126\n", - " 29 M 1.07 1.064119" + " 28 D 0.94 1.130923" ] }, - "execution_count": 9, + "execution_count": 10, "metadata": {}, "output_type": "execute_result" } @@ -709,7 +753,7 @@ }, { "cell_type": "code", - 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"(F, S, S, P, C, G, K, A, A) 1.96" + "(E, K, Q, L, P, V, L, D, K) 0.14\n", + "(E, R, Y, K, G, E, K, Q, L) -1.56\n", + "(G, E, K, Q, L, P, V, L, D) 1.62\n", + "(I, E, R, Y, K, G, E, K, Q) 0.23\n", + "(I, I, E, R, Y, K, G, E, K) 1.65" ] }, - "execution_count": 11, + "execution_count": 12, "metadata": {}, "output_type": "execute_result" } @@ -817,7 +861,7 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": 13, "metadata": {}, "outputs": [ { @@ -847,29 +891,79 @@ " \n", " \n", " \n", - " (A, A, V, D, P, A, D, R, C)\n", - " -2.65\n", - " 1.186\n", + " (E, K, Q, L, P, V, L, D, K)\n", + " 0.14\n", + " -0.331\n", " \n", " \n", - " (A, V, D, P, A, D, R, C, K)\n", - " -0.72\n", - " 0.179\n", + " (E, R, Y, K, G, E, K, Q, L)\n", + " -1.56\n", + " -0.347\n", " \n", " \n", - " (C, G, K, A, A, V, D, P, A)\n", - " 3.05\n", - " -2.070\n", + " (G, E, K, Q, L, P, V, L, D)\n", + " 1.62\n", + " -0.456\n", " \n", " \n", - " (F, F, S, S, P, C, G, K, A)\n", - " 2.37\n", - " -1.544\n", + " (I, E, R, Y, K, G, E, K, Q)\n", + " 0.23\n", + " 0.204\n", " \n", " \n", - 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"execution_count": 13, + "execution_count": 14, "metadata": {}, "output_type": "execute_result" } @@ -1015,7 +1114,7 @@ "source": [ "from operator import ge\n", "\n", - "tap_result.filter_result([(\"smmtap\",ge, -30)])" + "tap_result.filter_result([(\"smmtap\",ge, -1)])" ] }, { @@ -1040,7 +1139,7 @@ }, { "cell_type": "code", - "execution_count": 14, + "execution_count": 17, "metadata": { "scrolled": false }, @@ -1051,8 +1150,129 @@ "text": [ "Number of peptides: 50\n", "Number of peptides after proteasomal cleavage: 31\n", - "Number of peptides after TAP transport: 31\n" + "Number of peptides after TAP transport: 13\n" ] + }, + { + "data": { + "text/html": [ + "
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AlleleHLA-A*02:01
Methodsmm
ScoreTypeScore
Peptides
(D, K, T, K, F, L, V, P, D)2.455331e+06
(D, P, A, D, R, C, K, E, V)8.338924e+04
(F, F, S, S, P, C, G, K, A)1.690869e+04
(F, S, S, P, C, G, K, A, A)1.429256e+04
(G, K, A, A, V, D, P, A, D)5.522173e+05
(I, I, E, R, Y, K, G, E, K)6.096913e+05
(L, V, P, D, H, V, N, M, S)1.247699e+04
(P, A, D, R, C, K, E, V, Q)1.660007e+07
(P, C, G, K, A, A, V, D, P)3.381505e+07
(P, D, H, V, N, M, S, E, L)4.028190e+05
(S, P, C, G, K, A, A, V, D)2.649171e+06
(V, D, P, A, D, R, C, K, E)1.455828e+07
(V, P, D, H, V, N, M, S, E)1.156405e+06
\n", + "
" + ], + "text/plain": [ + "Allele HLA-A*02:01\n", + "Method smm\n", + "ScoreType Score\n", + "Peptides \n", + "(D, K, T, K, F, L, V, P, D) 2.455331e+06\n", + "(D, P, A, D, R, C, K, E, V) 8.338924e+04\n", + "(F, F, S, S, P, C, G, K, A) 1.690869e+04\n", + "(F, S, S, P, C, G, K, A, A) 1.429256e+04\n", + "(G, K, A, A, V, D, P, A, D) 5.522173e+05\n", + "(I, I, E, R, Y, K, G, E, K) 6.096913e+05\n", + "(L, V, P, D, H, V, N, M, S) 1.247699e+04\n", + "(P, A, D, R, C, K, E, V, Q) 1.660007e+07\n", + "(P, C, G, K, A, A, V, D, P) 3.381505e+07\n", + "(P, D, H, V, N, M, S, E, L) 4.028190e+05\n", + "(S, P, C, G, K, A, A, V, D) 2.649171e+06\n", + "(V, D, P, A, D, R, C, K, E) 1.455828e+07\n", + "(V, P, D, H, V, N, M, S, E) 1.156405e+06" + ] + }, + "execution_count": 17, + "metadata": {}, + "output_type": "execute_result" } ], "source": [ @@ -1070,12 +1290,12 @@ "print(\"Number of peptides after proteasomal cleavage: \", len(df_cl))\n", "\n", "#tap prediction and filtering\n", - "df_tap = TAPPredictorFactory(\"smmtap\").predict(df_cl.index).filter_result((\"smmtap\",ge,-30))\n", + "df_tap = TAPPredictorFactory(\"smmtap\").predict(df_cl.index).filter_result((\"smmtap\",ge,1))\n", "print(\"Number of peptides after TAP transport: \", len(df_tap))\n", "\n", "#epitope prediction and filtering\n", - "#df_epi = EpitopePredictorFactory(\"UniTope\").predict(df_tap.index,alleles=allele)\n", - "#df_epi" + "df_epi = EpitopePredictorFactory(\"smm\").predict(df_tap.index,alleles=allele)\n", + "df_epi" ] }, { @@ -1096,7 +1316,7 @@ }, { "cell_type": "code", - "execution_count": 15, + "execution_count": 27, "metadata": { "scrolled": true }, @@ -1106,7 +1326,7 @@ "output_type": "stream", "text": [ "Number of peptides after proteasomal cleavage: 62\n", - "Number of peptides after TAP transport: 47\n" + "Number of peptides after TAP transport: 17\n" ] }, { @@ -1122,316 +1342,111 @@ " vertical-align: top;\n", " }\n", "\n", - " .dataframe thead th {\n", + " .dataframe thead tr th {\n", + " text-align: left;\n", + " }\n", + "\n", + " .dataframe thead tr:last-of-type th {\n", " text-align: right;\n", " }\n", "\n", "\n", " \n", - " \n", - " \n", - " \n", + " \n", + " \n", " \n", " \n", " \n", - " \n", " \n", - " \n", + " \n", " \n", - " \n", - " \n", " \n", - " \n", - " \n", - " \n", + " \n", + " \n", " \n", " \n", - " \n", - " \n", - " \n", + " \n", + " \n", " \n", + " \n", + " \n", " \n", " \n", - " \n", " \n", " \n", " \n", " \n", - " \n", " \n", " \n", " \n", " \n", - " \n", " \n", " \n", " \n", " \n", - " \n", " \n", " \n", " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", " \n", - " \n", " \n", " \n", " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", " \n", - " \n", " \n", " \n", " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", " \n", - " \n", " \n", " \n", " \n", " \n", - " \n", " \n", " \n", " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", " \n", - " \n", " \n", " \n", " \n", " \n", - " \n", " \n", " \n", " \n", " \n", - " \n", " \n", " \n", " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", " \n", - " \n", " \n", " \n", " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", " \n", - " \n", " \n", " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", " \n", "
AlleleHLA-A*02:01
SeqMethodsmm
(A, D, R, C, K, E, V, Q, Q)smm1.718344e+07ScoreTypeScore
(A, V, D, P, A, D, R, C, K)smm3.444372e+05Peptides
(C, G, K, A, A, V, D, P, A)smm1.644788e+05
(C, K, E, V, Q, Q, I, R, D)smm1.306502e+07
(D, H, V, N, M, S, E, L, V)smm1.625961e+05
(D, K, T, K, F, L, V, P, D)smm2.455331e+06
(D, P, A, D, R, C, K, E, V)smm8.338924e+04
(D, R, C, K, E, V, Q, Q, I)smm1.799327e+06
(E, K, Q, L, P, V, L, D, K)smm5.421382e+07
(E, R, Y, K, G, E, K, Q, L)smm2.085019e+06
(E, V, Q, Q, I, R, D, Q, H)smm1.025912e+07
(F, F, S, S, P, C, G, K, A)smm1.690869e+04
(F, L, V, P, D, H, V, N, M)smm2.133585e+02
(F, S, S, P, C, G, K, A, A)smm1.429256e+04
(G, E, K, Q, L, P, V, L, D)smm5.822507e+06
(H, V, N, M, S, E, L, V, K)smm4.427005e+05
(I, E, R, Y, K, G, E, K, Q)smm5.769126e+07
(I, I, E, R, Y, K, G, E, K)smm6.096913e+05
(I, P, V, I, I, E, R, Y, K)smm2.307332e+06
(K, E, V, Q, Q, I, R, D, Q)smm9.956576e+06
(K, F, L, V, P, D, H, V, N)smm4.657040e+05
(K, G, E, K, Q, L, P, V, L)smm4.257062e+04
(K, Q, L, P, V, L, D, K, T)smm2.588869e+03
(K, T, K, F, L, V, P, D, H)smm6.181730e+05
(L, D, K, T, K, F, L, V, P)smm2.483762e+06
(L, P, V, L, D, K, T, K, F)smm1.762422e+06
(L, V, P, D, H, V, N, M, S)smm1.247699e+04
(M, R, F, F, S, S, P, C, G)smm1.734243e+05
(P, A, D, R, C, K, E, V, Q)smm1.660007e+07
(P, C, G, K, A, A, V, D, P)smm3.381505e+07
(P, D, H, V, N, M, S, E, L)smm4.028190e+05
(P, V, I, I, E, R, Y, K, G)smm7.518133e+05
(P, V, L, D, K, T, K, F, L)smm7.535464e+03
(Q, I, R, D, Q, H, P, S, K)smm2.911454e+05
(Q, L, P, V, L, D, K, T, K)smm2.559234e+05
(Q, Q, I, R, D, Q, H, P, S)smm2.094643e+04
(R, C, K, E, V, Q, Q, I, R)smm3.767992e+06
(R, Y, K, G, E, K, Q, L, P)smm7.246195e+06
(S, P, C, G, K, A, A, V, D)smm2.649171e+06
(S, S, P, C, G, K, A, A, V)smm7.818258e+03
(T, K, F, L, V, P, D, H, V)smm8.592311e+03
(V, I, I, E, R, Y, K, G, E)smm2.399441e+05
(V, L, D, K, T, K, F, L, V)smm3.785385e+01
(V, N, M, S, E, L, V, K, I)smm7.675559e+03
(V, P, D, H, V, N, M, S, E)smm1.156405e+06
(V, Q, Q, I, R, D, Q, H, P)smm3.214475e+05
(Y, K, G, E, K, Q, L, P, V)smm9.662956e+02
\n", "" ], "text/plain": [ - " HLA-A*02:01\n", - "Seq Method \n", - "(A, D, R, C, K, E, V, Q, Q) smm 1.718344e+07\n", - "(A, V, D, P, A, D, R, C, K) smm 3.444372e+05\n", - "(C, G, K, A, A, V, D, P, A) smm 1.644788e+05\n", - "(C, K, E, V, Q, Q, I, R, D) smm 1.306502e+07\n", - "(D, H, V, N, M, S, E, L, V) smm 1.625961e+05\n", - "(D, K, T, K, F, L, V, P, D) smm 2.455331e+06\n", - "(D, P, A, D, R, C, K, E, V) smm 8.338924e+04\n", - "(D, R, C, K, E, V, Q, Q, I) smm 1.799327e+06\n", - "(E, K, Q, L, P, V, L, D, K) smm 5.421382e+07\n", - "(E, R, Y, K, G, E, K, Q, L) smm 2.085019e+06\n", - "(E, V, Q, Q, I, R, D, Q, H) smm 1.025912e+07\n", - "(F, F, S, S, P, C, G, K, A) smm 1.690869e+04\n", - "(F, L, V, P, D, H, V, N, M) smm 2.133585e+02\n", - "(F, S, S, P, C, G, K, A, A) smm 1.429256e+04\n", - "(G, E, K, Q, L, P, V, L, D) smm 5.822507e+06\n", - "(H, V, N, M, S, E, L, V, K) smm 4.427005e+05\n", - "(I, E, R, Y, K, G, E, K, Q) smm 5.769126e+07\n", - "(I, I, E, R, Y, K, G, E, K) smm 6.096913e+05\n", - "(I, P, V, I, I, E, R, Y, K) smm 2.307332e+06\n", - "(K, E, V, Q, Q, I, R, D, Q) smm 9.956576e+06\n", - "(K, F, L, V, P, D, H, V, N) smm 4.657040e+05\n", - "(K, G, E, K, Q, L, P, V, L) smm 4.257062e+04\n", - "(K, Q, L, P, V, L, D, K, T) smm 2.588869e+03\n", - "(K, T, K, F, L, V, P, D, H) smm 6.181730e+05\n", - "(L, D, K, T, K, F, L, V, P) smm 2.483762e+06\n", - "(L, P, V, L, D, K, T, K, F) smm 1.762422e+06\n", - "(L, V, P, D, H, V, N, M, S) smm 1.247699e+04\n", - "(M, R, F, F, S, S, P, C, G) smm 1.734243e+05\n", - "(P, A, D, R, C, K, E, V, Q) smm 1.660007e+07\n", - "(P, C, G, K, A, A, V, D, P) smm 3.381505e+07\n", - "(P, D, H, V, N, M, S, E, L) smm 4.028190e+05\n", - "(P, V, I, I, E, R, Y, K, G) smm 7.518133e+05\n", - "(P, V, L, D, K, T, K, F, L) smm 7.535464e+03\n", - "(Q, I, R, D, Q, H, P, S, K) smm 2.911454e+05\n", - "(Q, L, P, V, L, D, K, T, K) smm 2.559234e+05\n", - "(Q, Q, I, R, D, Q, H, P, S) smm 2.094643e+04\n", - "(R, C, K, E, V, Q, Q, I, R) smm 3.767992e+06\n", - "(R, Y, K, G, E, K, Q, L, P) smm 7.246195e+06\n", - "(S, P, C, G, K, A, A, V, D) smm 2.649171e+06\n", - "(S, S, P, C, G, K, A, A, V) smm 7.818258e+03\n", - "(T, K, F, L, V, P, D, H, V) smm 8.592311e+03\n", - "(V, I, I, E, R, Y, K, G, E) smm 2.399441e+05\n", - "(V, L, D, K, T, K, F, L, V) smm 3.785385e+01\n", - "(V, N, M, S, E, L, V, K, I) smm 7.675559e+03\n", - "(V, P, D, H, V, N, M, S, E) smm 1.156405e+06\n", - "(V, Q, Q, I, R, D, Q, H, P) smm 3.214475e+05\n", - "(Y, K, G, E, K, Q, L, P, V) smm 9.662956e+02" + "Allele HLA-A*02:01\n", + "Method smm\n", + "ScoreType Score\n", + "Peptides \n", + "(C, G, K, A, A, V, D, P, A) 1.644788e+05\n", + "(C, K, E, V, Q, Q, I, R, D) 1.306502e+07\n", + "(D, H, V, N, M, S, E, L, V) 1.625961e+05\n", + "(D, K, T, K, F, L, V, P, D) 2.455331e+06\n", + "(E, V, Q, Q, I, R, D, Q, H) 1.025912e+07\n", + "(G, E, K, Q, L, P, V, L, D) 5.822507e+06\n", + "(I, I, E, R, Y, K, G, E, K) 6.096913e+05\n", + "(I, P, V, I, I, E, R, Y, K) 2.307332e+06\n", + "(P, A, D, R, C, K, E, V, Q) 1.660007e+07\n", + "(P, C, G, K, A, A, V, D, P) 3.381505e+07\n", + "(P, D, H, V, N, M, S, E, L) 4.028190e+05\n", + "(S, P, C, G, K, A, A, V, D) 2.649171e+06\n", + "(V, P, D, H, V, N, M, S, E) 1.156405e+06" ] }, - "execution_count": 15, + "execution_count": 27, "metadata": {}, "output_type": "execute_result" } @@ -1462,12 +1477,12 @@ "\n", "\n", "#tap prediction and filtering\n", - "df_tap = TAPPredictorFactory(\"smmtap\").predict(peps).filter_result((\"smmtap\",ge,-27))\n", + "df_tap = TAPPredictorFactory(\"smmtap\").predict(peps).filter_result((\"smmtap\",ge,1))\n", "print(\"Number of peptides after TAP transport: \", len(df_tap))\n", "\n", "\n", "#epitope prediction and filtering\n", - "df_epi = EpitopePredictorFactory(\"smm\").predict(df_tap.index,alleles=allele).filter_result((\"smm\",ge,-1.0))\n", + "df_epi = EpitopePredictorFactory(\"smm\").predict(df_tap.index,alleles=allele).filter_result((\"smm\",ge,100000.0))\n", "df_epi" ] }, @@ -1495,9 +1510,9 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.0" + "version": "3.6.13" } }, "nbformat": 4, "nbformat_minor": 1 -} \ No newline at end of file +} diff --git a/epytope/tutorials/EpitopePrediction.ipynb b/epytope/tutorials/EpitopePrediction.ipynb index 31bfa85e..7c302b28 100644 --- a/epytope/tutorials/EpitopePrediction.ipynb +++ b/epytope/tutorials/EpitopePrediction.ipynb @@ -30,7 +30,15 @@ "cell_type": "code", "execution_count": 1, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Using TensorFlow backend.\n" + ] + } + ], "source": [ "%matplotlib inline\n", "%reload_ext autoreload\n", @@ -69,10 +77,59 @@ "cell_type": "code", "execution_count": 3, "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/plain": [ + "[PEPTIDE:\n", + " YNTVATLIS,\n", + " PEPTIDE:\n", + " ATLISINTH,\n", + " PEPTIDE:\n", + " ISLANGHDA,\n", + " PEPTIDE:\n", + " ANGHDAKAK,\n", + " PEPTIDE:\n", + " NTHISLANG,\n", + " PEPTIDE:\n", + " TVATLISIN,\n", + " PEPTIDE:\n", + " INTHISLAN,\n", + " PEPTIDE:\n", + " NTVATLISI,\n", + " PEPTIDE:\n", + " TLISINTHI,\n", + " PEPTIDE:\n", + " THISLANGH,\n", + " PEPTIDE:\n", + " SLYNTVATL,\n", + " PEPTIDE:\n", + " SINTHISLA,\n", + " PEPTIDE:\n", + " LYNTVATLI,\n", + " PEPTIDE:\n", + " SLANGHDAK,\n", + " PEPTIDE:\n", + " HISLANGHD,\n", + " PEPTIDE:\n", + " VATLISINT,\n", + " PEPTIDE:\n", + " ISINTHISL,\n", + " PEPTIDE:\n", + " LANGHDAKA,\n", + " PEPTIDE:\n", + " LISINTHIS]" + ] + }, + "execution_count": 3, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "peptides2 = read_lines(\"./data/peptides.txt\", in_type=Peptide)\n", - "alleles = read_lines(\"./data/alleles.txt\", in_type=Allele)" + "alleles = read_lines(\"./data/alleles.txt\", in_type=Allele)\n", + "peptides2" ] }, { @@ -197,68 +254,77 @@ " vertical-align: top;\n", " }\n", "\n", - " .dataframe thead th {\n", + " .dataframe thead tr th {\n", + " text-align: left;\n", + " }\n", + "\n", + " .dataframe thead tr:last-of-type th {\n", " text-align: right;\n", " }\n", "\n", "\n", " \n", - " \n", - " \n", - " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", " \n", " \n", - " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", " \n", " \n", - " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", " \n", " \n", - " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", " \n", " \n", - " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", " \n", " \n", "
AlleleHLA-B*15:01HLA-A*02:01
SeqMethodsyfpeithisyfpeithi
ScoreTypeScoreScore
Peptides
(T, V, A, T, L, I, S, I, N)syfpeithi911(Y, N, T, V, A, T, L, I, S)2.04.0
(S, L, A, N, G, H, D, A, K)syfpeithi1217(A, T, L, I, S, I, N, T, H)2.015.0
(S, I, N, T, H, I, S, L, A)syfpeithi719(I, S, L, A, N, G, H, D, A)-1.09.0
(S, L, Y, N, T, V, A, T, L)syfpeithi1231(A, N, G, H, D, A, K, A, K)2.02.0
(Y, N, T, V, A, T, L, I, S)syfpeithi24(N, T, H, I, S, L, A, N, G)0.010.0
\n", "" ], "text/plain": [ - " HLA-B*15:01 HLA-A*02:01\n", - "Seq Method \n", - "(T, V, A, T, L, I, S, I, N) syfpeithi 9 11\n", - "(S, L, A, N, G, H, D, A, K) syfpeithi 12 17\n", - "(S, I, N, T, H, I, S, L, A) syfpeithi 7 19\n", - "(S, L, Y, N, T, V, A, T, L) syfpeithi 12 31\n", - "(Y, N, T, V, A, T, L, I, S) syfpeithi 2 4" + "Allele HLA-B*15:01 HLA-A*02:01\n", + "Method syfpeithi syfpeithi\n", + "ScoreType Score Score\n", + "Peptides \n", + "(Y, N, T, V, A, T, L, I, S) 2.0 4.0\n", + "(A, T, L, I, S, I, N, T, H) 2.0 15.0\n", + "(I, S, L, A, N, G, H, D, A) -1.0 9.0\n", + "(A, N, G, H, D, A, K, A, K) 2.0 2.0\n", + "(N, T, H, I, S, L, A, N, G) 0.0 10.0" ] }, "execution_count": 7, @@ -297,68 +363,77 @@ " vertical-align: top;\n", " }\n", "\n", - " .dataframe thead th {\n", + " .dataframe thead tr th {\n", + " text-align: left;\n", + " }\n", + "\n", + " .dataframe thead tr:last-of-type th {\n", " text-align: right;\n", " }\n", "\n", "\n", " \n", - " \n", - " \n", - " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", " \n", " \n", - " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", " \n", " \n", - " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", " \n", " \n", - " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", " \n", " \n", - " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", " \n", " \n", "
AlleleHLA-B*15:01HLA-A*02:01
SeqMethodsyfpeithisyfpeithi
ScoreTypeScoreScore
Peptides
(T, V, A, T, L, I, S, I, N)syfpeithi911(Y, N, T, V, A, T, L, I, S)2.04.0
(S, L, A, N, G, H, D, A, K)syfpeithi1217(A, T, L, I, S, I, N, T, H)2.015.0
(S, I, N, T, H, I, S, L, A)syfpeithi719(I, S, L, A, N, G, H, D, A)-1.09.0
(S, L, Y, N, T, V, A, T, L)syfpeithi1231(A, N, G, H, D, A, K, A, K)2.02.0
(Y, N, T, V, A, T, L, I, S)syfpeithi24(N, T, H, I, S, L, A, N, G)0.010.0
\n", "" ], "text/plain": [ - " HLA-B*15:01 HLA-A*02:01\n", - "Seq Method \n", - "(T, V, A, T, L, I, S, I, N) syfpeithi 9 11\n", - "(S, L, A, N, G, H, D, A, K) syfpeithi 12 17\n", - "(S, I, N, T, H, I, S, L, A) syfpeithi 7 19\n", - "(S, L, Y, N, T, V, A, T, L) syfpeithi 12 31\n", - "(Y, N, T, V, A, T, L, I, S) syfpeithi 2 4" + "Allele HLA-B*15:01 HLA-A*02:01\n", + "Method syfpeithi syfpeithi\n", + "ScoreType Score Score\n", + "Peptides \n", + "(Y, N, T, V, A, T, L, I, S) 2.0 4.0\n", + "(A, T, L, I, S, I, N, T, H) 2.0 15.0\n", + "(I, S, L, A, N, G, H, D, A) -1.0 9.0\n", + "(A, N, G, H, D, A, K, A, K) 2.0 2.0\n", + "(N, T, H, I, S, L, A, N, G) 0.0 10.0" ] }, "execution_count": 8, @@ -397,68 +472,77 @@ " vertical-align: top;\n", " }\n", "\n", - " .dataframe thead th {\n", + " .dataframe thead tr th {\n", + " text-align: left;\n", + " }\n", + "\n", + " .dataframe thead tr:last-of-type th {\n", " text-align: right;\n", " }\n", "\n", "\n", " \n", - " \n", - " \n", - " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", - " \n", " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", " \n", - " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", " \n", " \n", - " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", " \n", " \n", - " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", " \n", " \n", - " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", " \n", " \n", - " \n", - " \n", - " \n", - " \n", + " \n", + " \n", + " \n", " \n", " \n", "
AlleleHLA-B*15:01HLA-A*02:01
SeqMethodsyfpeithisyfpeithi
ScoreTypeScoreScore
Peptides
(T, V, A, T, L, I, S, I, N)syfpeithi911(Y, N, T, V, A, T, L, I, S)2.04.0
(S, L, A, N, G, H, D, A, K)syfpeithi1217(A, T, L, I, S, I, N, T, H)2.015.0
(S, I, N, T, H, I, S, L, A)syfpeithi719(I, S, L, A, N, G, H, D, A)-1.09.0
(S, L, Y, N, T, V, A, T, L)syfpeithi1231(A, N, G, H, D, A, K, A, K)2.02.0
(Y, N, T, V, A, T, L, I, S)syfpeithi24(N, T, H, I, S, L, A, N, G)0.010.0
\n", "" ], "text/plain": [ - " HLA-B*15:01 HLA-A*02:01\n", - "Seq Method \n", - "(T, V, A, T, L, I, S, I, N) syfpeithi 9 11\n", - "(S, L, A, N, G, H, D, A, K) syfpeithi 12 17\n", - "(S, I, N, T, H, I, S, L, A) syfpeithi 7 19\n", - "(S, L, Y, N, T, V, A, T, L) syfpeithi 12 31\n", - "(Y, N, T, V, A, T, L, I, S) syfpeithi 2 4" + "Allele HLA-B*15:01 HLA-A*02:01\n", + "Method syfpeithi syfpeithi\n", + "ScoreType Score Score\n", + "Peptides \n", + "(Y, N, T, V, A, T, L, I, S) 2.0 4.0\n", + "(A, T, L, I, S, I, N, T, H) 2.0 15.0\n", + "(I, S, L, A, N, G, H, D, A) -1.0 9.0\n", + "(A, N, G, H, D, A, K, A, K) 2.0 2.0\n", + "(N, T, H, I, S, L, A, N, G) 0.0 10.0" ] }, "execution_count": 9, @@ -507,8 +591,9 @@ { "data": { "text/plain": [ - "array([[,\n", - " ]], dtype=object)" + "array([[,\n", + " ]],\n", + " dtype=object)" ] }, "execution_count": 11, @@ -517,7 +602,7 @@ }, { "data": { - "image/png": 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tjrrUiyMQtStmN31Y35E0lSxJr4yI+2vXR8S+iBjOH68GpkqaWXGYZu9wora+omwEjDuA7RHxrXHKHJWXQ9KpZJ+Tl6uL0mx/bvqwfnMGcCGwRdKmfNm1wDEAEbEcOB+4XNII8CawJCKiC7GaAU7U1mciYi2gBmVuBm6uJiKzxtz0YWaWOCdqM7PElU7UkqZI+ntJD3cyIDMz299kzqivIruKy8zMKlQqUUuaDXwauL2z4ZiZWa2yvT6+DXwJOGK8AmUupy2rHZddtnq5arN68TLXUb0cu9mBrGGilnQOsCciNkhaOF65MpfTltWOyy5bvVy1Wb14meuoXo7d7EBWpunjDOAzknYC9wJnSvrbjkZlZmbvaJioI+LLETE7IuYCS4C/i4g/6XhkZmYGuB+1mVnyJnUJeUQMAoMdicTMzOryGbWZWeKcqM3MEudEbWaWOCdqM7PEOVGbmSXOidrMLHFO1NZXJM2R9DNJ2yVtk3RVnTKSdJOkHZKeknRKN2I1G+WhuKzfjADLImKjpCOADZLWRMTThTJnA/Py6TTg1vyvWVf4jNr6SkTsjoiN+ePXyO6xPqum2LnAisisA2ZIOrriUM3e4TNq61uS5gInA0/UrJoFPFeYH8qX7a7ZvuGtfZu53S40d8vdsscamN58XADfWflQU9stmz/5bYqvQy/ehrddMTtRW1+SdDjwQ+DqiNhXu7rOJjFmQYlb+zZzu11o7pa7ZY+1bP4IN2zpjY9+8XXoxdvwtitmN31Y35E0lSxJr4yI++sUGQLmFOZnA7uqiM2sHidq6yuSBNwBbI+Ib41TbBVwUd7743Rgb0TsHqesWcf1xvcfs/Y5A7gQ2CJpU77sWuAYgIhYDqwGFgM7gDeAS6sP0+xdTtTWVyJiLfXboItlAriimojMGnPTh5lZ4pyozcwS50RtZpY4J2ozs8Q5UZuZJc6J2swscQ0TtaRpkp6UtDm/LeT1VQRmZmaZMv2o3wLOjIjh/NLbtZIeye8qZmZmHdYwUeed/4fz2an5NOYGNWZm1hmlrkyUNAXYAPwmcEtE1N4WstQtH8sq3hpwy/N7m9pHq7dUbFaZ2xo2+5zmz3pfU9uV1cotGVN9TmYHglKJOiLeBk6SNAN4QNIJEbG1pkzDWz6WVbw1YLO3iWxGM7eWrFXmtoZV3vpyMlq5JWOqz8nsQDCpXh8R8SowCCzqRDBmZjZWmV4fR+Zn0kiaDpwFPNPhuMzMLFem6eNo4O68nfog4L6IeLizYZmZ2agyvT6eIhtXzszMusBXJpqZJc6J2swscU7U1lck3Slpj6St46xfKGmvpE359JWqYzSr5aG4rN/cBdwMrJigzOMRcU414Zg15jNq6ysR8RjwSrfjMJsMn1GbjfURSZuBXcAXI2JbvUJlbpuwbP5IUwE0cyl/2WMNTG8+rqoVX4dWbnHQLe2K2YnabH8bgWPzu0UuBh4E5tUrWOa2CVVeWl/2WMvmj3DDlt746Bdfh1ZucdAt7YrZTR9mBRGxLyKG88ergamSZnY5LOtzTtRmBZKOkqT88alkn5GXuxuV9bve+P5j1iaS7gEWAjMlDQFfJbvHOhGxHDgfuFzSCPAmsCS/J7tZ1zhRW1+JiAsarL+ZrPueWTLc9GFmljgnajOzxDlRm5klzonazCxxTtRmZolzojYzS5wTtZlZ4pyozcwS50RtZpa4hola0hxJP5O0XdI2SVdVEZiZmWXKXEI+AiyLiI2SjgA2SFoTEU93ODYzM6PEGXVE7I6Ijfnj14DtwKxOB2ZmZplJtVFLmgucDDzRkWjMzGyM0nfPk3Q48EPg6ojYV2d9w2GJtjy/t9SxBqbDd1Y+BMCy+WUjbF07hswpM/ROlcMzTUYrwwal+pzMDgSlErWkqWRJemVE3F+vTDuHJerWUEHNDH9Uq8zQO1UOzzQZrQwblOpzMjsQlOn1IeAOYHtEfKvzIZmZWVGZNuozgAuBMyVtyqfFHY7LzMxyDdsXImItoApiMes4SXcC5wB7IuKEOusF3AgsBt4ALhnt9WTWLb4y0frNXcCiCdafDczLp6XArRXEZDYhJ2rrKxHxGPDKBEXOBVZEZh0wQ9LR1URnVp8HtzXb3yzgucL8UL5sd23BMl1Sm+22ONo9dTLKdmUdmN58XFUrvg7FbrsTmT/rfZ0MaT+NuhzXi7mZ+JyozfZX7/eYqFewnV1Sq9St7q+tKht3lV0+G72/9WJuJj43fZjtbwiYU5ifDezqUixmgBO1Wa1VwEXKnA7sjYgxzR5mVeq97z9mLZB0D7AQmClpCPgqMBUgIpYDq8m65u0g6553aXciNXuXE7X1lYi4oMH6AK6oKByzUtz0YWaWOCdqM7PEOVGbmSXOidrMLHFO1GZmiXOiNjNLnBO1mVninKjNzBLnRG1mljgnajOzxDlRm5klzonazCxxTtRmZolrmKgl3Slpj6StVQRkZmb7K3NGfRcTj9psZmYd1DBRlxi12czMOqhtAwe0c0Tmbo2SXC/myRoeHm64n2afWzPxNRoluWh0xORmRkmu8jmZ9Zu2Jep2jsjcrVGS2zF68eDgIPWee1GzI1M3E99kjjX6unf6OEVVjhgNIGkRcCMwBbg9Iv66Zv1C4CHgH/NF90fEX1YZo1ktD8VlfUPSFOAW4PfJRhv/uaRVEfF0TdHHI+KcygM0G4e751k/ORXYERHPRsSvgHuBc7sck1lDDc+o643aHBF3dDowsw6YBTxXmB8CTqtT7iOSNgO7gC9GxLZ6O2vn7zJV6tZvQK0qG3eVv3s0iqdezM3E1zBRNxq12ayHqM6yqJnfCBwbEcOSFgMPAvPq7aydv8tUqVu/AbWqbNxV/u7R6P2tF3Mz8bnpw/rJEDCnMD+b7Kz5HRGxLyKG88ergamSZlYXotlYTtTWT34OzJP065IOAZYAq4oFJB0lSfnjU8k+Iy9XHqlZQe99/zFrUkSMSLoS+AlZ97w7I2KbpMvy9cuB84HLJY0AbwJLIqK2ecSsUk7U1lfy5ozVNcuWFx7fDNxcdVxmE3HTh5lZ4pyozcwS50RtZpY4J2ozs8Q5UZuZJc6J2swscU7UZmaJc6I2M0ucE7WZWeKcqM3MEudEbWaWOCdqM7PEOVGbmSXOidrMLHFO1GZmiXOiNjNLnBO1mVniSiVqSYsk/ULSDknXdDoos05pVJeVuSlf/5SkU7oRp1lRw0QtaQpwC3A2cDxwgaTjOx2YWbuVrMtnA/PyaSlwa6VBmtVR5oz6VGBHRDwbEb8C7gXO7WxYZh1Rpi6fC6yIzDpghqSjqw7UrEiNBliWdD6wKCL+Uz5/IXBaRFxZU24p2RkIwHHAL1qIaybwUgvbd5Njb49jI+LIdu6wTF2W9DDw1xGxNp//KfDfImJ9nf21s85XKaX3eTJ6Me7JxDxunS8zCrnqLBuT3SPiNuC2kgFNfEBpfUQsaMe+qubYk1amLpeq79DeOl+lXn2fezHudsVcpuljCJhTmJ8N7Gr1wGZdUKYuu75bcsok6p8D8yT9uqRDgCXAqs6GZdYRZeryKuCivPfH6cDeiNhddaBmRQ2bPiJiRNKVwE+AKcCdEbGtw3H13NfJAseeqPHqsqTL8vXLgdXAYmAH8AZwabfi7aBefZ97Me72NAc3+jHRzMy6y1cmmpklzonazCxxSSXqXr9UXdJOSVskbZI0pt9tSiTdKWmPpK2FZf9G0hpJ/zf/+/5uxmit68X3WdIcST+TtF3SNklX5ctTj3uapCclbc7jvj5f3nLcySTqA+hS9Y9HxEk90N/zLmBRzbJrgJ9GxDzgp/m89ba76L33eQRYFhG/DZwOXJHngtTjfgs4MyJOBE4CFuU9h1qOO5lEjS9Vr1REPAa8UrP4XODu/PHdwHlVxmTt14vvc0TsjoiN+ePXgO3ALNKPOyJiOJ+dmk9BG+JOKVHPAp4rzA/ly3pJAI9K2pBfXtxrBkb7DOd/P9jleKwzeuZ9ljQXOBl4gh6IW9IUSZuAPcCaiGhL3GUuIa9K6Ut3E3ZGROyS9EFgjaRn8jMaM5skSYcDPwSujoh9Ur0UkZaIeBs4SdIM4AFJJ7RjvymdUff8pbsRsSv/uwd4gKw5p5e8OHqnuPzvni7HY52R/PssaSpZkl4ZEffni5OPe1REvAoMkv0+0HLcKSXqnr5UXdJhko4YfQx8Etg68VbJWQVcnD++GHioi7FY5yT9Pis7db4D2B4R3yqsSj3uI/MzaSRNB84CnqENcSd1ZaKkxcC3effy3r/qbkTlSfoQ2Vk0ZE1KP0g5fkn3AAvJbsP4IvBV4EHgPuAY4P8B/yEian+Ish7Si++zpI8CjwNbgH/NF19L1k6dctwfJvuxcArZSfB9EfGXkj5Ai3EnlajNzGyslJo+zMysDidqM7PEOVGbmSXOidrMLHFO1GZmiXOiNjNLnBO1mVni/j+qRo2pbqnDOgAAAABJRU5ErkJggg==\n", 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HLA-B*15:01HLA-A*02:01
SeqMethodAlleleHLA-B*15:01HLA-A*02:01
(F, I, A, S, N, G, V, K, L)MethodbimasNaNNaN
smmNaNNaN
syfpeithiNaNNaN
(L, L, G, A, T, C, M, F, V)bimasNaNNaNsmmsyfpeithi
smmNaNNaNScoreTypeScoreScoreScoreScoreScoreScore
syfpeithiNaNNaNPeptides
(S, Y, F, P, E, I, T, H, I)bimasNaNNaN(S, Y, F, P, E, I, T, H, I)0.01447014.5529844.00.0123312931.63568917.0
smmNaNNaN(F, I, A, S, N, G, V, K, L)0.60004315.1907687.013.511718438.64178525.0
syfpeithiNaNNaN(L, L, G, A, T, C, M, F, V)4.00003689.77598610.0650.31120027.10878222.0
\n", "" ], "text/plain": [ - " HLA-B*15:01 HLA-A*02:01\n", - "Seq Method \n", - "(F, I, A, S, N, G, V, K, L) bimas NaN NaN\n", - " smm NaN NaN\n", - " syfpeithi NaN NaN\n", - "(L, L, G, A, T, C, M, F, V) bimas NaN NaN\n", - " smm NaN NaN\n", - " syfpeithi NaN NaN\n", - "(S, Y, F, P, E, I, T, H, I) bimas NaN NaN\n", - " smm NaN NaN\n", - " syfpeithi NaN NaN" + "Allele HLA-B*15:01 HLA-A*02:01 \\\n", + "Method bimas smm syfpeithi bimas \n", + "ScoreType Score Score Score Score \n", + "Peptides \n", + "(S, Y, F, P, E, I, T, H, I) 0.0144 7014.552984 4.0 0.012331 \n", + "(F, I, A, S, N, G, V, K, L) 0.6000 4315.190768 7.0 13.511718 \n", + "(L, L, G, A, T, C, M, F, V) 4.0000 3689.775986 10.0 650.311200 \n", + "\n", + "Allele \n", + "Method smm syfpeithi \n", + "ScoreType Score Score \n", + "Peptides \n", + "(S, Y, F, P, E, I, T, H, I) 2931.635689 17.0 \n", + "(F, I, A, S, N, G, V, K, L) 438.641785 25.0 \n", + "(L, L, G, A, T, C, M, F, V) 27.108782 22.0 " ] }, "execution_count": 12, @@ -670,14 +762,114 @@ "metadata": { "scrolled": true }, - "outputs": [], + "outputs": [ + { + "data": { + "text/html": [ + "
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AlleleHLA-B*15:01HLA-A*02:01
Methodbimassmmsyfpeithibimassmmsyfpeithi
ScoreTypeScoreScoreScoreScoreScoreScore
Peptides
(F, I, A, S, N, G, V, K, L)0.64315.1907687.013.511718438.64178525.0
(L, L, G, A, T, C, M, F, V)4.03689.77598610.0650.31120027.10878222.0
\n", + "
" + ], + "text/plain": [ + "Allele HLA-B*15:01 HLA-A*02:01 \\\n", + "Method bimas smm syfpeithi bimas \n", + "ScoreType Score Score Score Score \n", + "Peptides \n", + "(F, I, A, S, N, G, V, K, L) 0.6 4315.190768 7.0 13.511718 \n", + "(L, L, G, A, T, C, M, F, V) 4.0 3689.775986 10.0 650.311200 \n", + "\n", + "Allele \n", + "Method smm syfpeithi \n", + "ScoreType Score Score \n", + "Peptides \n", + "(F, I, A, S, N, G, V, K, L) 438.641785 25.0 \n", + "(L, L, G, A, T, C, M, F, V) 27.108782 22.0 " + ] + }, + "execution_count": 13, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "#you can either use pre-defined operators from `operator`\n", "from operator import ge\n", "#or define you own comparator function like this\n", "comparator = lambda a,b: a > b\n", "\n", - "#df.filter_result([(\"svmhc\",comparator,0.0)])\n" + "df.filter_result(['HLA-A*02:01', 'syfpeithi', 'Score'], comparator, 20.0)" ] }, { @@ -694,7 +886,7 @@ }, { "cell_type": "code", - "execution_count": 14, + "execution_count": 16, "metadata": {}, "outputs": [], "source": [ @@ -707,6 +899,7 @@ " __alleles = [\"A*02:01\"]\n", " __supported_length = [9]\n", " __name = \"random\"\n", + " __scoretype = \"Score\"\n", " __version= \"1.0\"\n", " \n", " #the interface defines three class properties\n", @@ -756,21 +949,23 @@ " #filter for supported alleles\n", " alleles = filter(lambda a: a.name in self.supportedAlleles, alleles) \n", " \n", - " result = {}\n", + " scores = {}\n", " #now predict binding/non-binding for each peptide at random\n", " for a in alleles:\n", - " result[a] = {}\n", + " scores[a] = {}\n", " for p in peptides:\n", " if random.random() >= 0.5:\n", - " result[a][p] = 1.0\n", + " scores[a][p] = 1.0\n", " else:\n", - " result[a][p] = 0.0\n", + " scores[a][p] = 0.0\n", + " \n", + " #create EpitopePredictionResult object from nested dictionary. This is a multi-column DataFrame \n", + " #with allele, method and scoretype as columns and peptides as indices\n", + " result = {allele: {self.__scoretype: list(scores.values())[i]} for i, allele in enumerate(alleles)}\n", + " \n", + " # converts the nested dictionary to a EpitopePredictionResult\n", + " df_result = EpitopePredictionResult.from_dict(result, peptides, self.__name)\n", " \n", - " #create EpitopePredictionResult object. This is a multi-indexed DataFrame \n", - " #with Peptide and Method as multi-index and alleles as columns\n", - " df_result = EpitopePredictionResult.from_dict(result)\n", - " df_result.index = pandas.MultiIndex.from_tuples([tuple((i,self.name)) for i in df_result.index],\n", - " names=['Seq','Method'])\n", " return df_result\n", " \n", " \n", @@ -787,7 +982,7 @@ }, { "cell_type": "code", - "execution_count": 15, + "execution_count": 17, "metadata": {}, "outputs": [ { @@ -803,37 +998,44 @@ " vertical-align: top;\n", " }\n", "\n", - " .dataframe thead th {\n", + " .dataframe thead tr th {\n", + " text-align: left;\n", + " }\n", + "\n", + " .dataframe thead tr:last-of-type th {\n", " text-align: right;\n", " }\n", "\n", "\n", " \n", - " \n", - " \n", - " \n", + " \n", + " \n", " \n", " \n", " \n", - " \n", " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", " \n", " \n", - " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", - " \n", + " \n", " \n", " \n", " \n", - " \n", - " \n", + " \n", " \n", " \n", " \n", @@ -841,14 +1043,16 @@ "" ], "text/plain": [ - " A*02:01\n", - "Seq Method \n", - "(F, I, A, S, N, G, V, K, L) random 1.0\n", - "(L, L, G, A, T, C, M, F, V) random 1.0\n", - "(S, Y, F, P, E, I, T, H, I) random 0.0" + "Allele A*02:01\n", + "Method random\n", + "ScoreType Score\n", + "Peptides \n", + "(S, Y, F, P, E, I, T, H, I) 1.0\n", + "(F, I, A, S, N, G, V, K, L) 1.0\n", + "(L, L, G, A, T, C, M, F, V) 0.0" ] }, - "execution_count": 15, + "execution_count": 17, "metadata": {}, "output_type": "execute_result" } @@ -881,9 +1085,9 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.0" + "version": "3.6.13" } }, "nbformat": 4, "nbformat_minor": 1 -} \ No newline at end of file +} diff --git a/epytope/tutorials/HLATyping.ipynb b/epytope/tutorials/HLATyping.ipynb index ac61fc18..8f03c6ba 100644 --- a/epytope/tutorials/HLATyping.ipynb +++ b/epytope/tutorials/HLATyping.ipynb @@ -8,13 +8,13 @@ "source": [ "

HLA Typing

\n", "\n", - "This short tutorial illustrates the use of epytope to predict the HLA type from NGS data.\n", + "This short tutorial illustrates the use of Epytope to predict the HLA type from NGS data.\n", "\n", "**Note1**:\n", "The HLA Typing tools have to be globally executable!\n", "\n", "**Note2**:\n", - "epytope only provides shallow wrapper classes. That means epytope directly forwards the input to the command line tools without any sanity checking and also only returns the most probable HLA genotype without any additional information, as the algorithms are very different." + "Epytope only provides shallow wrapper classes. That means Epytope directly forwards the input to the command line tools without any sanity checking and also only returns the most probable HLA genotype without any additional information, as the algorithms are very different." ] }, { @@ -28,7 +28,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": 1, "metadata": {}, "outputs": [], "source": [ @@ -76,25 +76,23 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 2, "metadata": {}, "outputs": [ { - "ename": "RuntimeError", - "evalue": "OptiType 1.0 could not be found in PATH", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mRuntimeError\u001b[0m Traceback (most recent call last)", - "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[0mopti\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mHLATypingFactory\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"OptiType\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 2\u001b[0;31m \u001b[0mopti\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpredict\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"./Data/CRC_81_N_1_fished.fastq\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m\"/tmp/\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0moptions\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m\"./Data/CRC_81_N_2_fished.fastq -r\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m", - "\u001b[0;32m~/PycharmProjects/Kfred/epytope/HLAtyping/External.py\u001b[0m in \u001b[0;36mpredict\u001b[0;34m(self, ngsFile, output, command, options, delete, **kwargs)\u001b[0m\n\u001b[1;32m 40\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mis_in_path\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0;34m\"path\"\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mkwargs\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 41\u001b[0m raise RuntimeError(\"{name} {version} could not be found in PATH\".format(name=self.name,\n\u001b[0;32m---> 42\u001b[0;31m version=self.version))\n\u001b[0m\u001b[1;32m 43\u001b[0m \u001b[0mexternal_version\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget_external_version\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mcommand\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 44\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mversion\u001b[0m \u001b[0;34m!=\u001b[0m \u001b[0mexternal_version\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mexternal_version\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;31mRuntimeError\u001b[0m: OptiType 1.0 could not be found in PATH" - ] + "data": { + "text/plain": [ + "[HLA-A*31:01, HLA-A*68:01, HLA-B*40:01, HLA-B*51:01, HLA-C*15:02, HLA-C*03:04]" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" } ], "source": [ "opti = HLATypingFactory(\"OptiType\")\n", - "opti.predict(\"./Data/CRC_81_N_1_fished.fastq\", \"/tmp/\", options=\"./Data/CRC_81_N_2_fished.fastq -r\")" + "opti.predict(\"./data/CRC_81_N_1_fished.fastq\", \"/tmp/\", options=\"./data/CRC_81_N_2_fished.fastq -r\")" ] } ], @@ -114,7 +112,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.0" + "version": "3.6.13" } }, "nbformat": 4, diff --git a/epytope/tutorials/PolymorphicEpitopePrediction.ipynb b/epytope/tutorials/PolymorphicEpitopePrediction.ipynb index ee9d9b97..ef89260a 100644 --- a/epytope/tutorials/PolymorphicEpitopePrediction.ipynb +++ b/epytope/tutorials/PolymorphicEpitopePrediction.ipynb @@ -18,7 +18,15 @@ "cell_type": "code", "execution_count": 1, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Using TensorFlow backend.\n" + ] + } + ], "source": [ "%matplotlib inline\n", "%reload_ext autoreload\n", @@ -88,12 +96,12 @@ "name": "stderr", "output_type": "stream", "text": [ - "/Users/antonia/PycharmProjects/Kfred/epytope/Core/Generator.py:57: UserWarning: For NM_001190266 bp does not match ref of assigned variant Variant(g.234183368A>G). Pos 645, var ref A, seq ref C \n", + "/Users/jonas/Desktop/epytope/epytope/Core/Generator.py:57: UserWarning: For NM_001190266 bp does not match ref of assigned variant Variant(g.234183368A>G). Pos 645, var ref A, seq ref C \n", " seq[pos]))\n", "WARNING:root:No Information on transcript NM_001293557\n", - "/Users/antonia/PycharmProjects/Kfred/epytope/Core/Generator.py:352: UserWarning: Transcript with ID NM_001293557 not found in DB\n", + "/Users/jonas/Desktop/epytope/epytope/Core/Generator.py:352: UserWarning: Transcript with ID NM_001293557 not found in DB\n", " warnings.warn(\"Transcript with ID %s not found in DB\"%tId)\n", - "/Users/antonia/opt/miniconda3/envs/epy/lib/python3.7/site-packages/Bio/Seq.py:2338: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future.\n", + "/Users/jonas/opt/anaconda3/envs/epytope/lib/python3.6/site-packages/Bio/Seq.py:2983: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future.\n", " BiopythonWarning,\n" ] } @@ -121,7 +129,7 @@ "output_type": "stream", "text": [ "WARNING:root:No Information on transcript NM_001293557\n", - "/Users/antonia/PycharmProjects/Kfred/epytope/Core/Generator.py:246: UserWarning: Transcript with ID NM_001293557 not found in DB\n", + "/Users/jonas/Desktop/epytope/epytope/Core/Generator.py:246: UserWarning: Transcript with ID NM_001293557 not found in DB\n", " warnings.warn(\"Transcript with ID %s not found in DB\"%tId)\n" ] } @@ -166,21 +174,33 @@ " vertical-align: top;\n", " }\n", "\n", - " .dataframe thead th {\n", + " .dataframe thead tr th {\n", + " text-align: left;\n", + " }\n", + "\n", + " .dataframe thead tr:last-of-type th {\n", " text-align: right;\n", " }\n", "\n", "
AlleleA*02:01
SeqMethodrandom
ScoreTypeScore
Peptides
(F, I, A, S, N, G, V, K, L)random(S, Y, F, P, E, I, T, H, I)1.0
(L, L, G, A, T, C, M, F, V)random(F, I, A, S, N, G, V, K, L)1.0
(S, Y, F, P, E, I, T, H, I)random(L, L, G, A, T, C, M, F, V)0.0
\n", " \n", - " \n", - " \n", - " \n", - " \n", + " \n", + " \n", " \n", + " \n", " \n", " \n", - " \n", " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", " \n", " \n", " \n", @@ -188,46 +208,43 @@ " \n", " \n", " \n", - " \n", - " \n", " \n", + " \n", " \n", " \n", " \n", - " \n", - " \n", " \n", + " \n", " \n", " \n", " \n", - " \n", - " \n", " \n", + " \n", " \n", " \n", " \n", - " \n", - " \n", " \n", + " \n", " \n", " \n", " \n", - " \n", - " \n", " \n", + " \n", " \n", " \n", "
HLA-A*02:01
AlleleHLA-B*15:01HLA-A*02:01
SeqMethodsmmsmm
ScoreTypeScoreScore
Peptides
(M, N, Q, V, T, I, Q, W, D)smm905962.037856269153.480393905962.037856
(N, Q, V, T, I, Q, W, D, A)smm3540.87014439719.1549473540.870144
(Q, V, T, I, Q, W, D, A, V)smm6793.75686170631.7554266793.756861
(V, T, I, Q, W, D, A, V, I)smm1766.4851871409.2887981766.485187
(T, I, Q, W, D, A, V, I, A)smm4276.71194923713.7370574276.711949
\n", "" ], "text/plain": [ - " HLA-A*02:01 HLA-B*15:01\n", - "Seq Method \n", - "(M, N, Q, V, T, I, Q, W, D) smm 905962.037856 269153.480393\n", - "(N, Q, V, T, I, Q, W, D, A) smm 3540.870144 39719.154947\n", - "(Q, V, T, I, Q, W, D, A, V) smm 6793.756861 70631.755426\n", - "(V, T, I, Q, W, D, A, V, I) smm 1766.485187 1409.288798\n", - "(T, I, Q, W, D, A, V, I, A) smm 4276.711949 23713.737057" + "Allele HLA-B*15:01 HLA-A*02:01\n", + "Method smm smm\n", + "ScoreType Score Score\n", + "Peptides \n", + "(M, N, Q, V, T, I, Q, W, D) 269153.480393 905962.037856\n", + "(N, Q, V, T, I, Q, W, D, A) 39719.154947 3540.870144\n", + "(Q, V, T, I, Q, W, D, A, V) 70631.755426 6793.756861\n", + "(V, T, I, Q, W, D, A, V, I) 1409.288798 1766.485187\n", + "(T, I, Q, W, D, A, V, I, A) 23713.737057 4276.711949" ] }, "execution_count": 6, @@ -304,7 +321,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.0" + "version": "3.6.13" } }, "nbformat": 4, diff --git a/epytope/tutorials/VaccineDesign.ipynb b/epytope/tutorials/VaccineDesign.ipynb index badaa1c8..1b40d1ec 100644 --- a/epytope/tutorials/VaccineDesign.ipynb +++ b/epytope/tutorials/VaccineDesign.ipynb @@ -22,7 +22,15 @@ "cell_type": "code", "execution_count": 1, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Using TensorFlow backend.\n" + ] + } + ], "source": [ "%matplotlib inline\n", "%reload_ext autoreload\n", @@ -77,25 +85,326 @@ "metadata": {}, "outputs": [ { - "ename": "ValueError", - "evalue": "No predictions could be made with bimas for given input. Check your epitope length and HLA allele combination.", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mValueError\u001b[0m Traceback (most recent call last)", - "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[0mbimas\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mEpitopePredictorFactory\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"BIMAS\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 2\u001b[0m \u001b[0msupported_alleles\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mfilter\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;32mlambda\u001b[0m \u001b[0ma\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0ma\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mname\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mbimas\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msupportedAlleles\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0malleles\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 3\u001b[0;31m \u001b[0mepi_df\u001b[0m \u001b[0;34m=\u001b[0m\u001b[0mbimas\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpredict\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mpeptides\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0malleles\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0msupported_alleles\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 4\u001b[0m \u001b[0mepi_df\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mhead\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 5\u001b[0m \u001b[0mthreshold\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m{\u001b[0m\u001b[0ma\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mname\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;36m1\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0ma\u001b[0m \u001b[0;32min\u001b[0m \u001b[0msupported_alleles\u001b[0m\u001b[0;34m}\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m~/PycharmProjects/Kfred/epytope/EpitopePrediction/PSSM.py\u001b[0m in \u001b[0;36mpredict\u001b[0;34m(self, peptides, alleles, **kwargs)\u001b[0m\n\u001b[1;32m 234\u001b[0m return EpitopePredictionResult(\n\u001b[1;32m 235\u001b[0m super(BIMAS, self).predict(peptides, alleles=alleles,\n\u001b[0;32m--> 236\u001b[0;31m **kwargs).applymap(lambda x: math.pow(math.e, x)))\n\u001b[0m\u001b[1;32m 237\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 238\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m~/PycharmProjects/Kfred/epytope/EpitopePrediction/PSSM.py\u001b[0m in \u001b[0;36mpredict\u001b[0;34m(self, peptides, alleles, **kwargs)\u001b[0m\n\u001b[1;32m 98\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mresult\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 99\u001b[0m raise ValueError(\"No predictions could be made with \"\n\u001b[0;32m--> 100\u001b[0;31m + self.name + \" for given input. Check your epitope length and HLA allele combination.\")\n\u001b[0m\u001b[1;32m 101\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 102\u001b[0m \u001b[0mdf_result\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mEpitopePredictionResult\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfrom_dict\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mresult\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;31mValueError\u001b[0m: No predictions could be made with bimas for given input. Check your epitope length and HLA allele combination." - ] + "data": { + "text/html": [ + "
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AlleleHLA-B*15:01HLA-B*44:03HLA-A*03:01HLA-A*11:01HLA-A*01:01HLA-B*08:01HLA-C*04:01HLA-C*07:02HLA-B*27:05HLA-A*68:01...HLA-B*51:01HLA-B*51:02HLA-A*24:02HLA-B*35:01HLA-B*52:01HLA-B*40:06HLA-B*40:01HLA-B*39:02HLA-B*39:01HLA-B*07:02
Methodbimasbimasbimasbimasbimasbimasbimasbimasbimasbimas...bimasbimasbimasbimasbimasbimasbimasbimasbimasbimas
ScoreTypeScoreScoreScoreScoreScoreScoreScoreScoreScoreScore...ScoreScoreScoreScoreScoreScoreScoreScoreScoreScore
Peptides
(M, K, M, R, F, F, S, S, P)0.0020.0020.000270.000040.0000050.000200.00110.040.010.002...0.002600.00220.00180.0010.00450.00200.0020.1200.020.003
(K, M, R, F, F, S, S, P, C)0.6000.0101.800000.001200.0005000.100000.10000.4015.000.010...0.050000.05000.20000.6000.04950.01000.0100.0360.031.000
(M, R, F, F, S, S, P, C, G)0.0010.0010.000100.000040.0010000.000100.00100.04100.000.002...0.005720.01000.00100.0010.01650.00300.0010.0100.100.001
(R, F, F, S, S, P, C, G, K)0.0010.0010.100001.200000.0100000.000050.50000.0215.000.600...0.011000.05000.10000.0020.05000.00330.0010.0100.020.001
(F, F, S, S, P, C, G, K, A)0.0100.0150.000090.002000.0005000.001005.50000.240.100.010...0.130000.40000.55000.0100.10000.05000.0220.1000.100.015
\n", + "

5 rows × 21 columns

\n", + "
" + ], + "text/plain": [ + "Allele HLA-B*15:01 HLA-B*44:03 HLA-A*03:01 HLA-A*11:01 \\\n", + "Method bimas bimas bimas bimas \n", + "ScoreType Score Score Score Score \n", + "Peptides \n", + "(M, K, M, R, F, F, S, S, P) 0.002 0.002 0.00027 0.00004 \n", + "(K, M, R, F, F, S, S, P, C) 0.600 0.010 1.80000 0.00120 \n", + "(M, R, F, F, S, S, P, C, G) 0.001 0.001 0.00010 0.00004 \n", + "(R, F, F, S, S, P, C, G, K) 0.001 0.001 0.10000 1.20000 \n", + "(F, F, S, S, P, C, G, K, A) 0.010 0.015 0.00009 0.00200 \n", + "\n", + "Allele HLA-A*01:01 HLA-B*08:01 HLA-C*04:01 HLA-C*07:02 \\\n", + "Method bimas bimas bimas bimas \n", + "ScoreType Score Score Score Score \n", + "Peptides \n", + "(M, K, M, R, F, F, S, S, P) 0.000005 0.00020 0.0011 0.04 \n", + "(K, M, R, F, F, S, S, P, C) 0.000500 0.10000 0.1000 0.40 \n", + "(M, R, F, F, S, S, P, C, G) 0.001000 0.00010 0.0010 0.04 \n", + "(R, F, F, S, S, P, C, G, K) 0.010000 0.00005 0.5000 0.02 \n", + "(F, F, S, S, P, C, G, K, A) 0.000500 0.00100 5.5000 0.24 \n", + "\n", + "Allele HLA-B*27:05 HLA-A*68:01 ... HLA-B*51:01 \\\n", + "Method bimas bimas ... bimas \n", + "ScoreType Score Score ... Score \n", + "Peptides ... \n", + "(M, K, M, R, F, F, S, S, P) 0.01 0.002 ... 0.00260 \n", + "(K, M, R, F, F, S, S, P, C) 15.00 0.010 ... 0.05000 \n", + "(M, R, F, F, S, S, P, C, G) 100.00 0.002 ... 0.00572 \n", + "(R, F, F, S, S, P, C, G, K) 15.00 0.600 ... 0.01100 \n", + "(F, F, S, S, P, C, G, K, A) 0.10 0.010 ... 0.13000 \n", + "\n", + "Allele HLA-B*51:02 HLA-A*24:02 HLA-B*35:01 HLA-B*52:01 \\\n", + "Method bimas bimas bimas bimas \n", + "ScoreType Score Score Score Score \n", + "Peptides \n", + "(M, K, M, R, F, F, S, S, P) 0.0022 0.0018 0.001 0.0045 \n", + "(K, M, R, F, F, S, S, P, C) 0.0500 0.2000 0.600 0.0495 \n", + "(M, R, F, F, S, S, P, C, G) 0.0100 0.0010 0.001 0.0165 \n", + "(R, F, F, S, S, P, C, G, K) 0.0500 0.1000 0.002 0.0500 \n", + "(F, F, S, S, P, C, G, K, A) 0.4000 0.5500 0.010 0.1000 \n", + "\n", + "Allele HLA-B*40:06 HLA-B*40:01 HLA-B*39:02 HLA-B*39:01 \\\n", + "Method bimas bimas bimas bimas \n", + "ScoreType Score Score Score Score \n", + "Peptides \n", + "(M, K, M, R, F, F, S, S, P) 0.0020 0.002 0.120 0.02 \n", + "(K, M, R, F, F, S, S, P, C) 0.0100 0.010 0.036 0.03 \n", + "(M, R, F, F, S, S, P, C, G) 0.0030 0.001 0.010 0.10 \n", + "(R, F, F, S, S, P, C, G, K) 0.0033 0.001 0.010 0.02 \n", + "(F, F, S, S, P, C, G, K, A) 0.0500 0.022 0.100 0.10 \n", + "\n", + "Allele HLA-B*07:02 \n", + "Method bimas \n", + "ScoreType Score \n", + "Peptides \n", + "(M, K, M, R, F, F, S, S, P) 0.003 \n", + "(K, M, R, F, F, S, S, P, C) 1.000 \n", + "(M, R, F, F, S, S, P, C, G) 0.001 \n", + "(R, F, F, S, S, P, C, G, K) 0.001 \n", + "(F, F, S, S, P, C, G, K, A) 0.015 \n", + "\n", + "[5 rows x 21 columns]" + ] + }, + "execution_count": 3, + "metadata": {}, + "output_type": "execute_result" } ], "source": [ - "bimas = EpitopePredictorFactory(\"BIMAS\")\n", - "supported_alleles = filter(lambda a: a.name in bimas.supportedAlleles, alleles)\n", + "bimas = EpitopePredictorFactory(\"bimas\")\n", + "supported_alleles = [allele for allele in filter(lambda a: a in bimas.supportedAlleles, alleles)]\n", "epi_df =bimas.predict(peptides, alleles=supported_alleles)\n", - "epi_df.head()\n", - "threshold = {a.name:1 for a in supported_alleles}\n" + "threshold = {a.name:1 for a in supported_alleles}\n", + "epi_df.head()" ] }, { @@ -277,7 +586,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.0" + "version": "3.6.13" } }, "nbformat": 4, diff --git a/epytope/tutorials/data/allele_probabilities_europe.csv b/epytope/tutorials/data/allele_probabilities_europe.csv index 6bc12107..b47c747a 100644 --- a/epytope/tutorials/data/allele_probabilities_europe.csv +++ b/epytope/tutorials/data/allele_probabilities_europe.csv @@ -102,4 +102,4 @@ HLA-A*24:05 0.000273523 HLA-B*27:09 0.000274424 HLA-C*15:07 0.000934871 HLA-B*15:17 0.003018661 -HLA-B*13:03 0.000274424 \ No newline at end of file +HLA-B*13:03 0.000274424 diff --git a/epytope/tutorials/data/test.csv b/epytope/tutorials/data/test.csv index 5f43388a..45bea66f 100644 --- a/epytope/tutorials/data/test.csv +++ b/epytope/tutorials/data/test.csv @@ -1,20 +1,23 @@ -Seq Method HLA-B*15:01 HLA-A*02:01 -TVATLISIN syfpeithi 9 11 -SLANGHDAK syfpeithi 12 17 -SINTHISLA syfpeithi 7 19 -SLYNTVATL syfpeithi 12 31 -YNTVATLIS syfpeithi 2 4 -VATLISINT syfpeithi 2 8 -ISINTHISL syfpeithi 2 16 -TLISINTHI syfpeithi 13 20 -LISINTHIS syfpeithi 7 13 -INTHISLAN syfpeithi 3 3 -LANGHDAKA syfpeithi 1 17 -HISLANGHD syfpeithi 6 8 -NTHISLANG syfpeithi 0 10 -NTVATLISI syfpeithi 1 18 -ATLISINTH syfpeithi 2 15 -THISLANGH syfpeithi 1 5 -ANGHDAKAK syfpeithi 2 2 -ISLANGHDA syfpeithi -1 9 -LYNTVATLI syfpeithi 2 11 +Allele HLA-B*15:01 HLA-A*02:01 +Method syfpeithi syfpeithi +ScoreType Score Score +Peptides +YNTVATLIS 2.0 4.0 +ATLISINTH 2.0 15.0 +ISLANGHDA -1.0 9.0 +ANGHDAKAK 2.0 2.0 +NTHISLANG 0.0 10.0 +TVATLISIN 9.0 11.0 +INTHISLAN 3.0 3.0 +NTVATLISI 1.0 18.0 +TLISINTHI 13.0 20.0 +THISLANGH 1.0 5.0 +SLYNTVATL 12.0 31.0 +SINTHISLA 7.0 19.0 +LYNTVATLI 2.0 11.0 +SLANGHDAK 12.0 17.0 +HISLANGHD 6.0 8.0 +VATLISINT 2.0 8.0 +ISINTHISL 2.0 16.0 +LANGHDAKA 1.0 17.0 +LISINTHIS 7.0 13.0 diff --git a/setup.py b/setup.py index f7800e0d..ec07b34f 100644 --- a/setup.py +++ b/setup.py @@ -126,7 +126,7 @@ # Run-time dependencies. (will be installed by pip when epytope is installed) # TODO: find alternative for SMVlight scikitlearn install_requires=[ - 'setuptools>=18.2', + 'setuptools<=57', 'pandas', 'pyomo>=4.0', 'PyMySQL', From 492d6e7c2f288eb70696329ce343699a4df29d06 Mon Sep 17 00:00:00 2001 From: Jonas Scheid <43858870+jonasscheid@users.noreply.github.com> Date: Wed, 22 Dec 2021 12:17:24 +0100 Subject: [PATCH 11/25] Fixed issues #38, #44 and #45 (#46) * Fixed issues #44 and #45 * Fix #48, include review suggestions --- epytope/EpitopePrediction/ANN.py | 46 +- epytope/EpitopePrediction/External.py | 8064 +++++++++++++++---------- 2 files changed, 4730 insertions(+), 3380 deletions(-) diff --git a/epytope/EpitopePrediction/ANN.py b/epytope/EpitopePrediction/ANN.py index 142620e6..b3b7ba1e 100644 --- a/epytope/EpitopePrediction/ANN.py +++ b/epytope/EpitopePrediction/ANN.py @@ -180,7 +180,8 @@ def predict(self, peptides, alleles=None, binary=False, **kwargs): else: # filter for supported alleles alleles = [a for a in alleles if a in self.supportedAlleles] - alleles = self.convert_alleles(alleles) + # Create a dictionary with Allele Obj as key and the respective allele predictor representation as value + alleles_repr = {allele: self._represent(allele) for allele in alleles} # prepare results dictionary scores = defaultdict(defaultdict) @@ -208,14 +209,12 @@ def predict(self, peptides, alleles=None, binary=False, **kwargs): # predict binding affinities for a in alleles: - allele_repr = self.revert_allele_repr(a) - # workaround for mhcnuggets file i/o buffer bug mhcnuggets_output = io.StringIO() with capture_stdout(mhcnuggets_output): mhcnuggets_predict(class_='I', peptides_path=tmp_input_file, - mhc=a) + mhc=alleles_repr[a]) # read predicted binding affinities back mhcnuggets_output.seek(0) @@ -234,19 +233,17 @@ def predict(self, peptides, alleles=None, binary=False, **kwargs): binding_affinity = float(content[ScoreIndex.MHCNUGGETS_CLASS1_2_0]) if binary: if binding_affinity <= 500: - scores[allele_repr][peptide] = 1.0 + scores[a][peptide] = 1.0 else: - scores[allele_repr][peptide] = 0.0 + scores[a][peptide] = 0.0 else: # convert ic50 to raw prediction score - scores[allele_repr][peptide] = 1- math.log(binding_affinity, 50000) + scores[a][peptide] = 1- math.log(binding_affinity, 50000) if not scores: raise ValueError("No predictions could be made with " + self.name + " for given input. Check your epitope length and HLA allele combination.") - # Convert str allele list to list with Allele objects - alleles = [self.revert_allele_repr(a) for a in alleles] # Create dictionary with hierarchy: {'Allele1': {'Score': {'Pep1': AffScore1, 'Pep2': AffScore2,..}, 'Allele2':...} result = {alleles: {"Score":(list(scores.values())[j])} for j, alleles in enumerate(alleles)} @@ -468,7 +465,9 @@ def predict(self, peptides, alleles=None, binary=False, **kwargs): else: # filter for supported alleles alleles = [a for a in alleles if a in self.supportedAlleles] - alleles = self.convert_alleles(alleles) + + # Create a dictionary with Allele Obj as key and the respective allele predictor representation as value + alleles_repr = {allele: self._represent(allele) for allele in alleles} # prepare results dictionary scores = defaultdict(defaultdict) @@ -496,14 +495,12 @@ def predict(self, peptides, alleles=None, binary=False, **kwargs): # predict bindings for a in alleles: - allele_repr = self.revert_allele_repr(a) - # workaround for mhcnuggets file i/o buffer bug mhcnuggets_output = io.StringIO() with capture_stdout(mhcnuggets_output): mhcnuggets_predict(class_='II', peptides_path=tmp_input_file, - mhc=a) + mhc=alleles_repr[a]) # read predicted binding affinities back mhcnuggets_output.seek(0) @@ -521,19 +518,17 @@ def predict(self, peptides, alleles=None, binary=False, **kwargs): binding_affinity = float(content[ScoreIndex.MHCNUGGETS_CLASS2_2_0]) if binary: if binding_affinity <= 500: - scores[allele_repr][peptide] = 1.0 + scores[a][peptide] = 1.0 else: - scores[allele_repr][peptide] = 0.0 + scores[a][peptide] = 0.0 else: # convert ic50 to raw prediction score - scores[allele_repr][peptide] = 1- math.log(binding_affinity, 50000) + scores[a][peptide] = 1- math.log(binding_affinity, 50000) if not scores: raise ValueError("No predictions could be made with " + self.name + " for given input. Check your epitope length and HLA allele combination.") - # Convert str allele list to list with Allele type - alleles = [self.revert_allele_repr(a) for a in alleles] # Create dictionary with hierarchy: {'Allele1': {'Score': {'Pep1': AffScore1, 'Pep2': AffScore2,..}, 'Allele2':...} result = {allele: {"Score":(list(scores.values())[j])} for j, allele in enumerate(alleles)} @@ -750,7 +745,9 @@ def predict(self, peptides, alleles=None, binary=False, **kwargs): else: # filter for supported alleles alleles = [a for a in alleles if a in self.supportedAlleles] - alleles = self.convert_alleles(alleles) + + # Create a dictionary with Allele Obj as key and the respective allele predictor representation as value + alleles_repr = {allele: self._represent(allele) for allele in alleles} # test mhcflurry models are available => download if not p = subprocess.call(['mhcflurry-downloads', 'path', 'models_class1'], @@ -787,24 +784,21 @@ def predict(self, peptides, alleles=None, binary=False, **kwargs): # predict and assign binding affinities for a in alleles: - allele_repr = self.revert_allele_repr(a) for p in peps: - binding_affinity = predictor.predict(allele=a, peptides=[str(p)])[ScoreIndex.MHCFLURRY] + binding_affinity = predictor.predict(allele=alleles_repr[a], peptides=[str(p)])[ScoreIndex.MHCFLURRY] if binary: if binding_affinity <= 500: - scores[allele_repr][p] = 1.0 + scores[a][p] = 1.0 else: - scores[allele_repr][p] = 0.0 + scores[a][p] = 0.0 else: # convert ic50 to raw prediction score - scores[allele_repr][p] = 1- math.log(binding_affinity, 50000) + scores[a][p] = 1- math.log(binding_affinity, 50000) if not scores: raise ValueError("No predictions could be made with " + self.name + " for given input. Check your epitope length and HLA allele combination.") - # Convert str allele list to list with Allele type - alleles = [self.revert_allele_repr(a) for a in alleles] # Create dictionary with hierarchy: {'Allele1': {'Score': {'Pep1': AffScore1, 'Pep2': AffScore2,..}, 'Allele2':...} result = {allele: {"Score":(list(scores.values())[j])} for j, allele in enumerate(alleles)} diff --git a/epytope/EpitopePrediction/External.py b/epytope/EpitopePrediction/External.py index e7ca18aa..8d93edcc 100755 --- a/epytope/EpitopePrediction/External.py +++ b/epytope/EpitopePrediction/External.py @@ -86,15 +86,17 @@ def predict(self, peptides, alleles=None, command=None, options=None, **kwargs): chunksize = kwargs['chunks'] if alleles is None: - al = [Allele(a) for a in self.supportedAlleles] - alleles_string = {conv_a: a for conv_a, a in zip(self.convert_alleles(al), al)} + alleles = [Allele(a) for a in self.supportedAlleles] else: if isinstance(alleles, Allele): alleles = [alleles] if any(not isinstance(p, Allele) for p in alleles): raise ValueError("Input is not of type Allele") - alleles_string = {conv_a: a for conv_a, a in zip(self.convert_alleles(alleles), alleles)} + # Create dictionary containing the predictors string representation and the Allele Obj representation of the allele + alleles_string = {conv_a: a for conv_a, a in zip(self.convert_alleles(alleles), alleles)} + + # Create empty result dictionary to fill downstream result = {} # group alleles in blocks of 80 alleles (NetMHC can't deal with more) @@ -167,15 +169,17 @@ def predict(self, peptides, alleles=None, command=None, options=None, **kwargs): except Exception as e: raise RuntimeError(e) + # Obtain parsed output dataframe containing the peptide scores and/or ranks res_tmp = self.parse_external_result(tmp_out_path) - for allele, scores in res_tmp.items(): + for allele_string, scores in res_tmp.items(): + allele = alleles_string[allele_string] if allele not in result.keys(): result[allele] = {} for scoretype, pep_scores in scores.items(): if scoretype not in result[allele].keys(): result[allele][scoretype] = {} for pep, score in pep_scores.items(): - result[allele][scoretype][pep] = score + result[allele][scoretype][pep_seqs[pep]] = score os.remove(tmp_file.name) os.remove(tmp_out_path) @@ -214,7 +218,7 @@ class NetMHC_3_4(AExternalEpitopePrediction): 'HLA-B*44:03', 'HLA-B*45:01', 'HLA-B*46:01', 'HLA-B*48:01', 'HLA-B*51:01', 'HLA-B*53:01', 'HLA-B*54:01', 'HLA-B*57:01', 'HLA-B*58:01', 'HLA-B*73:01', 'HLA-B*83:01', 'HLA-C*03:03', 'HLA-C*04:01', 'HLA-C*05:01', 'HLA-C*06:02', 'HLA-C*07:01', 'HLA-C*07:02', 'HLA-C*08:02', 'HLA-C*12:03', 'HLA-C*14:02', 'HLA-C*15:02', 'HLA-E*01:01', - 'H2-Db', 'H2-Dd', 'H2-Kb', 'H2-Kd', 'H2-Kk', 'H2-Ld']) + 'H-2-Db', 'H-2-Dd', 'H-2-Kb', 'H-2-Kd', 'H-2-Kk', 'H-2-Ld']) __supported_length = frozenset([8, 9, 10, 11]) __name = "netmhc" __command = "netMHC -p {peptides} -a {alleles} -x {out} {options}" @@ -279,10 +283,11 @@ def supportedLength(self): def parse_external_result(self, file): """ - Parses external results and returns the result + Parses external results and returns the result containing the predictors string representation + of alleles and peptides. :param str file: The file path or the external prediction results - :return: A dictionary containing the prediction results + :return: A dictionary containing the prediction results :rtype: dict """ result = defaultdict(defaultdict) @@ -349,7 +354,7 @@ class NetMHC_3_0(NetMHC_3_4): 'HLA-A*69:01', 'HLA-B*07:02', 'HLA-B*08:01', 'HLA-B*08:02', 'HLA-B*15:01', 'HLA-B*18:01', 'HLA-B*27:05', 'HLA-B*35:01', 'HLA-B*39:01', 'HLA-B*40:01', 'HLA-B*40:02', 'HLA-B*44:02', 'HLA-B*44:03', 'HLA-B*45:01', 'HLA-B*51:01', 'HLA-B*53:01', 'HLA-B*54:01', 'HLA-B*57:01', 'HLA-B*58:01', - 'H2-Db', 'H2-Dd', 'H2-Kb', 'H2-Kd', 'H2-Kk', 'H2-Ld']) # no PSSM predictors + 'H-2-Db', 'H-2-Dd', 'H-2-Kb', 'H-2-Kd', 'H-2-Kk', 'H-2-Ld']) # no PSSM predictors __supported_length = frozenset([8, 9, 10, 11]) __name = "netmhc" @@ -402,7 +407,8 @@ def _represent(self, allele): def parse_external_result(self, file): """ - Parses external results and returns the result + Parses external results and returns the result containing the predictors string representation + of alleles and peptides. :param str file: The file path or the external prediction results :return: A dictionary containing the prediction results @@ -464,7 +470,8 @@ def _represent(self, allele): def parse_external_result(self, file): """ - Parses external results and returns the result + Parses external results and returns the result containing the predictors string representation + of alleles and peptides. :param str file: The file path or the external prediction results :return: A dictionary containing the prediction results @@ -473,12 +480,12 @@ def parse_external_result(self, file): scores = defaultdict(defaultdict) ranks = defaultdict(defaultdict) f = csv.reader(open(file, "r"), delimiter='\t') - alleles = [Allele(x.split()[0][:5]+'*'+x.split()[0][5:7]+ ':' +x.split()[0][7:]) for x in [x for x in next(f) if x.strip() != ""]] + alleles = [x.split()[0] for x in [x for x in next(f) if x.strip() != ""]] next(f) for l in f: if not l: continue - pep_seq = Peptide(l[PeptideIndex.NETMHC_4_0]) + pep_seq = l[PeptideIndex.NETMHC_4_0] for i, a in enumerate(alleles): ic_50 = l[(i+1) * Offset.NETMHC_4_0] sc = 1.0 - math.log(float(ic_50), 50000) @@ -853,7 +860,7 @@ class NetMHCpan_2_4(AExternalEpitopePrediction): 'HLA-C*16:24', 'HLA-C*16:25', 'HLA-C*16:26', 'HLA-C*17:01', 'HLA-C*17:02', 'HLA-C*17:03', 'HLA-C*17:04', 'HLA-C*17:05', 'HLA-C*17:06', 'HLA-C*17:07', 'HLA-C*18:01', 'HLA-C*18:02', 'HLA-C*18:03', 'HLA-E*01:01', 'HLA-G*01:01', 'HLA-G*01:02', 'HLA-G*01:03', 'HLA-G*01:04', 'HLA-G*01:06', 'HLA-G*01:07', 'HLA-G*01:08', 'HLA-G*01:09', - 'H2-Db', 'H2-Dd', 'H2-Kb', 'H2-Kd', 'H2-Kk', 'H2-Ld']) + 'H-2-Db', 'H-2-Dd', 'H-2-Kb', 'H-2-Kd', 'H-2-Kk', 'H-2-Ld']) __version = "2.4" @property @@ -915,7 +922,8 @@ def convert_alleles(self, alleles): def parse_external_result(self, file): """ - Parses external results and returns the result + Parses external results and returns the result containing the predictors string representation + of alleles and peptides. :param str file: The file path or the external prediction results :return: A dictionary containing the prediction results @@ -923,10 +931,10 @@ def parse_external_result(self, file): """ f = csv.reader(open(file, "r"), delimiter = '\t') scores = defaultdict(defaultdict) - alleles = [Allele(x[:5]+'*'+x[5:]) for x in next(f) if "HLA" in x] + alleles = [x for x in next(f) if "HLA" in x] # Rank is not supported in command line tool of NetMHCpan 2.4 for row in f: - pep_seq = Peptide(row[PeptideIndex.NETMHCPAN_2_4]) + pep_seq = row[PeptideIndex.NETMHCPAN_2_4] for i, a in enumerate(alleles): scores[a][pep_seq] = float(row[ScoreIndex.NETMHCPAN_2_4 + i]) # Create dictionary with hierarchy: {'Allele1': {'Score': {'Pep1': Score1, 'Pep2': Score2,..}, 'Allele2':...} @@ -1310,7 +1318,7 @@ class NetMHCpan_2_8(AExternalEpitopePrediction): 'HLA-C*16:24', 'HLA-C*16:25', 'HLA-C*16:26', 'HLA-C*17:01', 'HLA-C*17:02', 'HLA-C*17:03', 'HLA-C*17:04', 'HLA-C*17:05', 'HLA-C*17:06', 'HLA-C*17:07', 'HLA-C*18:01', 'HLA-C*18:02', 'HLA-C*18:03', 'HLA-E*01:01', 'HLA-G*01:01', 'HLA-G*01:02', 'HLA-G*01:03', 'HLA-G*01:04', 'HLA-G*01:06', 'HLA-G*01:07', 'HLA-G*01:08', 'HLA-G*01:09', - 'H2-Db', 'H2-Dd', 'H2-Kb', 'H2-Kd', 'H2-Kk', 'H2-Ld', "H2-Qa1", "H2-Qa2"]) + 'H-2-Db', 'H-2-Dd', 'H-2-Kb', 'H-2-Kd', 'H-2-Kk', 'H-2-Ld', "H-2-Qa1", "H-2-Qa2"]) @property def version(self): @@ -1397,7 +1405,8 @@ def prepare_input(self, input, file): def parse_external_result(self, file): """ - Parses external results and returns the result + Parses external results and returns the result containing the predictors string representation + of alleles and peptides. :param str file: The file path or the external prediction results :return: A dictionary containing the prediction results @@ -1406,7 +1415,7 @@ def parse_external_result(self, file): f = csv.reader(open(file, "r"), delimiter = '\t') scores = defaultdict(defaultdict) ranks = defaultdict(defaultdict) - alleles = [x[:5]+'*'+x[5:] for x in next(f) if x != ""] + alleles = [x for x in next(f) if x != ""] next(f) for row in f: pep_seq = row[PeptideIndex.NETMHCPAN_2_8] @@ -1454,9 +1463,9 @@ def parse_external_result(self, file): f = csv.reader(open(file, "r"), delimiter = '\t') scores = defaultdict(defaultdict) ranks = defaultdict(defaultdict) - alleles = [Allele(x[:5]+'*'+x[5:]) for x in next(f) if x != ""] + alleles = [x for x in next(f) if x != ""] for row in f: - pep_seq = Peptide(row[PeptideIndex.NETMHCPAN_3_0]) + pep_seq = row[PeptideIndex.NETMHCPAN_3_0] for i, a in enumerate(alleles): if row[ScoreIndex.NETMHCPAN_3_0 + i * Offset.NETMHCPAN_3_0] != "1-log50k": # Avoid header column, only access raw and rank scores scores[a][pep_seq] = float(row[ScoreIndex.NETMHCPAN_3_0 + i * Offset.NETMHCPAN_3_0]) @@ -1485,7 +1494,8 @@ def command(self): def parse_external_result(self, file): """ - Parses external results and returns the result + Parses external results and returns the result containing the predictors string representation + of alleles and peptides. :param str file: The file path or the external prediction results :return: A dictionary containing the prediction results @@ -1494,9 +1504,9 @@ def parse_external_result(self, file): f = csv.reader(open(file, "r"), delimiter = '\t') scores = defaultdict(defaultdict) ranks = defaultdict(defaultdict) - alleles = [Allele(x[:5]+'*'+x[5:]) for x in next(f) if x != ""] + alleles = [x for x in next(f) if x != ""] for row in f: - pep_seq = Peptide(row[PeptideIndex.NETMHCPAN_4_0]) + pep_seq = row[PeptideIndex.NETMHCPAN_4_0] for i, a in enumerate(alleles): if row[ScoreIndex.NETMHCPAN_4_0 + i * Offset.NETMHCPAN_4_0] != "1-log50k": # Avoid header column, only access raw and rank scores scores[a][pep_seq] = float(row[ScoreIndex.NETMHCPAN_4_0 + i * Offset.NETMHCPAN_4_0]) @@ -1929,7 +1939,8 @@ def convert_alleles(self, alleles): def parse_external_result(self, file): """ - Parses external results and returns the result + Parses external results and returns the result containing the predictors string representation + of alleles and peptides. :param str file: The file path or the external prediction results :return: A dictionary containing the prediction results @@ -1938,12 +1949,11 @@ def parse_external_result(self, file): result = defaultdict(dict) with open(file, "r") as f: f = csv.reader(f, delimiter='\t') - alleles = [x[:5]+'*'+x[5:] for x in next(f) if x != ""] + alleles = [x for x in next(f) if x != ""] ranks = defaultdict(defaultdict) rank_pos = 5 offset = 3 header = next(f) - logging.warning("\t".join(header)) if "Aff(nM)" in header: # With option command line option '-ia', which includes prediction score in output file scores = defaultdict(defaultdict) for row in f: @@ -2011,7 +2021,7 @@ class NetMHCII_2_2(AExternalEpitopePrediction): __alleles = frozenset( ['HLA-DRB1*01:01', 'HLA-DRB1*03:01', 'HLA-DRB1*04:01', 'HLA-DRB1*04:04', 'HLA-DRB1*04:05', 'HLA-DRB1*07:01', 'HLA-DRB1*08:02', 'HLA-DRB1*09:01', 'HLA-DRB1*11:01', 'HLA-DRB1*13:02', 'HLA-DRB1*15:01', 'HLA-DRB3*01:01', 'HLA-DRB4*01:01', 'HLA-DRB5*01:01', - 'H2-IAb', 'H2-IAd']) + 'H-2-Iab', 'H-2-Iad']) __version = "2.2" @property @@ -2071,7 +2081,8 @@ def convert_alleles(self, alleles): def parse_external_result(self, file): """ - Parses external results and returns the result + Parses external results and returns the result containing the predictors string representation + of alleles and peptides. :param str file: The file path or the external prediction results :return: A dictionary containing the prediction results @@ -2087,10 +2098,10 @@ def parse_external_result(self, file): if not len(row): continue - if Allele.organism not in row[HLAIndex.NETMHCII_2_2]: + if "HLA" not in row[HLAIndex.NETMHCII_2_2]: continue - allele = Allele(row[HLAIndex.NETMHCII_2_2][:8]+'*'+row[HLAIndex.NETMHCII_2_2][8:10]+':'+row[HLAIndex.NETMHCII_2_2][10:]) - pep = Peptide(row[PeptideIndex.NETMHCII_2_2]) + allele = row[HLAIndex.NETMHCII_2_2] + pep = row[PeptideIndex.NETMHCII_2_2] scores[allele][pep] = float(row[ScoreIndex.NETMHCII_2_2]) result = {allele: {"Score":list(scores.values())[j]} for j, allele in enumerate(scores.keys())} @@ -2126,6 +2137,115 @@ def prepare_input(self, input, file): file.write("\n".join(">pepe_%i\n%s" % (i, p) for i, p in enumerate(input))) +class NetMHCII_2_3(NetMHCII_2_2): + """ + Implements a wrapper for NetMHCII 2.3 + + .. note:: + + Jensen KK, Andreatta M, Marcatili P, Buus S, Greenbaum JA, Yan Z, Sette A, Peters B, and Nielsen M. (2018) + Improved methods for predicting peptide binding affinity to MHC class II molecules. + """ + __supported_length = frozenset([15]) + __name = "netmhcII" + __command = 'netMHCII {peptides} -a {alleles} {options} | grep -v "#" > {out}' + __alleles = frozenset( + ['HLA-DRB1*01:01', 'HLA-DRB1*01:03', 'HLA-DRB1*03:01', 'HLA-DRB1*04:01', 'HLA-DRB1*04:02', +'HLA-DRB1*04:03', 'HLA-DRB1*04:04', 'HLA-DRB1*04:05', 'HLA-DRB1*07:01', 'HLA-DRB1*08:01', +'HLA-DRB1*08:02', 'HLA-DRB1*09:01', 'HLA-DRB1*10:01', 'HLA-DRB1*11:01', 'HLA-DRB1*12:01', +'HLA-DRB1*13:01', 'HLA-DRB1*13:02', 'HLA-DRB1*15:01', 'HLA-DRB1*16:02', 'HLA-DRB3*01:01', +'HLA-DRB3*02:02', 'HLA-DRB3*03:01', 'HLA-DRB4*01:01', 'HLA-DRB4*01:03', 'HLA-DRB5*01:01', +'HLA-DPA1*01:03-DPB1*02:01', 'HLA-DPA1*01:03-DPB1*03:01', 'HLA-DPA1*01:03-DPB1*04:01', +'HLA-DPA1*01:03-DPB1*04:02', 'HLA-DPA1*01:03-DPB1*06:01', 'HLA-DPA1*02:01-DPB1*01:01', 'HLA-DPA1*02:01-DPB1*05:01', 'HLA-DPA1*02:01-DPB1*14:01', +'HLA-DPA1*03:01-DPB1*04:02', 'HLA-DQA1*01:01-DQB1*05:01', 'HLA-DQA1*01:02-DQB1*05:01', 'HLA-DQA1*01:02-DQB1*05:02', 'HLA-DQA1*01:02-DQB1*06:02', +'HLA-DQA1*01:03-DQB1*06:03', 'HLA-DQA1*01:04-DQB1*05:03', 'HLA-DQA1*02:01-DQB1*02:02', 'HLA-DQA1*02:01-DQB1*03:01', 'HLA-DQA1*02:01-DQB1*03:03', +'HLA-DQA1*02:01-DQB1*04:02', 'HLA-DQA1*03:01-DQB1*03:01', 'HLA-DQA1*03:01-DQB1*03:02', 'HLA-DQA1*03:03-DQB1*04:02', 'HLA-DQA1*04:01-DQB1*04:02', +'HLA-DQA1*05:01-DQB1*02:01', 'HLA-DQA1*05:01-DQB1*03:01', 'HLA-DQA1*05:01-DQB1*03:02', 'HLA-DQA1*05:01-DQB1*03:03', 'HLA-DQA1*05:01-DQB1*04:02', +'HLA-DQA1*06:01-DQB1*04:02', 'H-2-Iab', 'H-2-Iad', 'H-2-Iak', 'H-2-Ias', 'H-2-Iau', 'H-2-Iad', 'H-2-Iak']) + __version = "2.3" + + @property + def version(self): + """The version of the predictor""" + return self.__version + + @property + def command(self): + """ + Defines the commandline call for external tool + """ + return self.__command + + @property + def supportedLength(self): + """ + A list of supported :class:`~epytope.Core.Peptide.Peptide` lengths + """ + return self.__supported_length + + @property + def supportedAlleles(self): + """A list of valid :class:`~epytope.Core.Allele.Allele` models""" + return self.__alleles + + @property + def name(self): + """The name of the predictor""" + return self.__name + + def _represent(self, allele): + """ + Internal function transforming an allele object into its representative string + :param allele: The :class:`~epytope.Core.Allele.Allele` for which the internal predictor representation is + needed + :type alleles: :class:`~epytope.Core.Allele.Allele` + :return: str + """ + if isinstance(allele, MouseAllele): + return "H-2-%s%s%s" % (allele.locus, allele.supertype, allele.subtype) + elif isinstance(allele, CombinedAllele): + return '%s-%s%s%s-%s%s%s' % (allele.organism, allele.alpha_locus, allele.alpha_supertype, allele.alpha_subtype, + allele.beta_locus, allele.beta_supertype, allele.beta_subtype) + else: + return "%s_%s%s" % (allele.locus, allele.supertype, allele.subtype) + + + def parse_external_result(self, file): + """ + Parses external results and returns the result containing the predictors string representation + of alleles and peptides. + + :param str file: The file path or the external prediction results + :return: A dictionary containing the prediction results + :rtype: dict + """ + f = csv.reader(open(file, "r"), delimiter='\t') + scores = defaultdict(defaultdict) + ranks = defaultdict(defaultdict) + + for r in f: + if not r: + continue + + row = r[0].split() + if not len(row): + continue + + if all(prefix not in row[HLAIndex.NETMHCII_2_3] for prefix in ['HLA-', 'H-2', 'D']): + continue + + allele = row[HLAIndex.NETMHCII_2_3] + + pep = row[PeptideIndex.NETMHCII_2_3] + scores[allele][pep] = float(row[ScoreIndex.NETMHCII_2_3]) + ranks[allele][pep] = float(row[ScoreIndex.NETMHCII_2_3]) + + + result = {allele: {metric:(list(scores.values())[j] if metric == "Score" else list(ranks.values())[j]) for metric in ["Score", "Rank"]} for j, allele in enumerate(scores.keys())} + + return result + + class NetMHCIIpan_3_0(AExternalEpitopePrediction): """ Implements a wrapper for NetMHCIIpan. @@ -2251,1660 +2371,1660 @@ class NetMHCIIpan_3_0(AExternalEpitopePrediction): 'HLA-DRB4*01:06', 'HLA-DRB4*01:07', 'HLA-DRB4*01:08', 'HLA-DRB5*01:01', 'HLA-DRB5*01:02', 'HLA-DRB5*01:03', 'HLA-DRB5*01:04', 'HLA-DRB5*01:05', 'HLA-DRB5*01:06', 'HLA-DRB5*01:08N', 'HLA-DRB5*01:11', 'HLA-DRB5*01:12', 'HLA-DRB5*01:13', 'HLA-DRB5*01:14', 'HLA-DRB5*02:02', 'HLA-DRB5*02:03', 'HLA-DRB5*02:04', 'HLA-DRB5*02:05', - 'HLA-DPA1*01:03-HLA-DPB1*01:01', 'HLA-DPA1*01:03-HLA-DPB1*02:01', 'HLA-DPA1*01:03-HLA-DPB1*02:02', 'HLA-DPA1*01:03-HLA-DPB1*03:01', - 'HLA-DPA1*01:03-HLA-DPB1*04:01', 'HLA-DPA1*01:03-HLA-DPB1*04:02', 'HLA-DPA1*01:03-HLA-DPB1*05:01', 'HLA-DPA1*01:03-HLA-DPB1*06:01', - 'HLA-DPA1*01:03-HLA-DPB1*08:01', 'HLA-DPA1*01:03-HLA-DPB1*09:01', 'HLA-DPA1*01:03-HLA-DPB1*10:001', 'HLA-DPA1*01:03-HLA-DPB1*10:01', - 'HLA-DPA1*01:03-HLA-DPB1*10:101', 'HLA-DPA1*01:03-HLA-DPB1*10:201', - 'HLA-DPA1*01:03-HLA-DPB1*10:301', 'HLA-DPA1*01:03-HLA-DPB1*10:401', - 'HLA-DPA1*01:03-HLA-DPB1*10:501', 'HLA-DPA1*01:03-HLA-DPB1*10:601', 'HLA-DPA1*01:03-HLA-DPB1*10:701', 'HLA-DPA1*01:03-HLA-DPB1*10:801', - 'HLA-DPA1*01:03-HLA-DPB1*10:901', 'HLA-DPA1*01:03-HLA-DPB1*11:001', - 'HLA-DPA1*01:03-HLA-DPB1*11:01', 'HLA-DPA1*01:03-HLA-DPB1*11:101', 'HLA-DPA1*01:03-HLA-DPB1*11:201', 'HLA-DPA1*01:03-HLA-DPB1*11:301', - 'HLA-DPA1*01:03-HLA-DPB1*11:401', 'HLA-DPA1*01:03-HLA-DPB1*11:501', - 'HLA-DPA1*01:03-HLA-DPB1*11:601', 'HLA-DPA1*01:03-HLA-DPB1*11:701', 'HLA-DPA1*01:03-HLA-DPB1*11:801', 'HLA-DPA1*01:03-HLA-DPB1*11:901', - 'HLA-DPA1*01:03-HLA-DPB1*12:101', 'HLA-DPA1*01:03-HLA-DPB1*12:201', - 'HLA-DPA1*01:03-HLA-DPB1*12:301', 'HLA-DPA1*01:03-HLA-DPB1*12:401', 'HLA-DPA1*01:03-HLA-DPB1*12:501', 'HLA-DPA1*01:03-HLA-DPB1*12:601', - 'HLA-DPA1*01:03-HLA-DPB1*12:701', 'HLA-DPA1*01:03-HLA-DPB1*12:801', - 'HLA-DPA1*01:03-HLA-DPB1*12:901', 'HLA-DPA1*01:03-HLA-DPB1*13:001', 'HLA-DPA1*01:03-HLA-DPB1*13:01', 'HLA-DPA1*01:03-HLA-DPB1*13:101', - 'HLA-DPA1*01:03-HLA-DPB1*13:201', 'HLA-DPA1*01:03-HLA-DPB1*13:301', - 'HLA-DPA1*01:03-HLA-DPB1*13:401', 'HLA-DPA1*01:03-HLA-DPB1*14:01', 'HLA-DPA1*01:03-HLA-DPB1*15:01', 'HLA-DPA1*01:03-HLA-DPB1*16:01', - 'HLA-DPA1*01:03-HLA-DPB1*17:01', 'HLA-DPA1*01:03-HLA-DPB1*18:01', - 'HLA-DPA1*01:03-HLA-DPB1*19:01', 'HLA-DPA1*01:03-HLA-DPB1*20:01', 'HLA-DPA1*01:03-HLA-DPB1*21:01', 'HLA-DPA1*01:03-HLA-DPB1*22:01', - 'HLA-DPA1*01:03-HLA-DPB1*23:01', 'HLA-DPA1*01:03-HLA-DPB1*24:01', - 'HLA-DPA1*01:03-HLA-DPB1*25:01', 'HLA-DPA1*01:03-HLA-DPB1*26:01', 'HLA-DPA1*01:03-HLA-DPB1*27:01', 'HLA-DPA1*01:03-HLA-DPB1*28:01', - 'HLA-DPA1*01:03-HLA-DPB1*29:01', 'HLA-DPA1*01:03-HLA-DPB1*30:01', - 'HLA-DPA1*01:03-HLA-DPB1*31:01', 'HLA-DPA1*01:03-HLA-DPB1*32:01', 'HLA-DPA1*01:03-HLA-DPB1*33:01', 'HLA-DPA1*01:03-HLA-DPB1*34:01', - 'HLA-DPA1*01:03-HLA-DPB1*35:01', 'HLA-DPA1*01:03-HLA-DPB1*36:01', - 'HLA-DPA1*01:03-HLA-DPB1*37:01', 'HLA-DPA1*01:03-HLA-DPB1*38:01', 'HLA-DPA1*01:03-HLA-DPB1*39:01', 'HLA-DPA1*01:03-HLA-DPB1*40:01', - 'HLA-DPA1*01:03-HLA-DPB1*41:01', 'HLA-DPA1*01:03-HLA-DPB1*44:01', - 'HLA-DPA1*01:03-HLA-DPB1*45:01', 'HLA-DPA1*01:03-HLA-DPB1*46:01', 'HLA-DPA1*01:03-HLA-DPB1*47:01', 'HLA-DPA1*01:03-HLA-DPB1*48:01', - 'HLA-DPA1*01:03-HLA-DPB1*49:01', 'HLA-DPA1*01:03-HLA-DPB1*50:01', - 'HLA-DPA1*01:03-HLA-DPB1*51:01', 'HLA-DPA1*01:03-HLA-DPB1*52:01', 'HLA-DPA1*01:03-HLA-DPB1*53:01', 'HLA-DPA1*01:03-HLA-DPB1*54:01', - 'HLA-DPA1*01:03-HLA-DPB1*55:01', 'HLA-DPA1*01:03-HLA-DPB1*56:01', - 'HLA-DPA1*01:03-HLA-DPB1*58:01', 'HLA-DPA1*01:03-HLA-DPB1*59:01', 'HLA-DPA1*01:03-HLA-DPB1*60:01', 'HLA-DPA1*01:03-HLA-DPB1*62:01', - 'HLA-DPA1*01:03-HLA-DPB1*63:01', 'HLA-DPA1*01:03-HLA-DPB1*65:01', - 'HLA-DPA1*01:03-HLA-DPB1*66:01', 'HLA-DPA1*01:03-HLA-DPB1*67:01', 'HLA-DPA1*01:03-HLA-DPB1*68:01', 'HLA-DPA1*01:03-HLA-DPB1*69:01', - 'HLA-DPA1*01:03-HLA-DPB1*70:01', 'HLA-DPA1*01:03-HLA-DPB1*71:01', - 'HLA-DPA1*01:03-HLA-DPB1*72:01', 'HLA-DPA1*01:03-HLA-DPB1*73:01', 'HLA-DPA1*01:03-HLA-DPB1*74:01', 'HLA-DPA1*01:03-HLA-DPB1*75:01', - 'HLA-DPA1*01:03-HLA-DPB1*76:01', 'HLA-DPA1*01:03-HLA-DPB1*77:01', - 'HLA-DPA1*01:03-HLA-DPB1*78:01', 'HLA-DPA1*01:03-HLA-DPB1*79:01', 'HLA-DPA1*01:03-HLA-DPB1*80:01', 'HLA-DPA1*01:03-HLA-DPB1*81:01', - 'HLA-DPA1*01:03-HLA-DPB1*82:01', 'HLA-DPA1*01:03-HLA-DPB1*83:01', - 'HLA-DPA1*01:03-HLA-DPB1*84:01', 'HLA-DPA1*01:03-HLA-DPB1*85:01', 'HLA-DPA1*01:03-HLA-DPB1*86:01', 'HLA-DPA1*01:03-HLA-DPB1*87:01', - 'HLA-DPA1*01:03-HLA-DPB1*88:01', 'HLA-DPA1*01:03-HLA-DPB1*89:01', - 'HLA-DPA1*01:03-HLA-DPB1*90:01', 'HLA-DPA1*01:03-HLA-DPB1*91:01', 'HLA-DPA1*01:03-HLA-DPB1*92:01', 'HLA-DPA1*01:03-HLA-DPB1*93:01', - 'HLA-DPA1*01:03-HLA-DPB1*94:01', 'HLA-DPA1*01:03-HLA-DPB1*95:01', - 'HLA-DPA1*01:03-HLA-DPB1*96:01', 'HLA-DPA1*01:03-HLA-DPB1*97:01', 'HLA-DPA1*01:03-HLA-DPB1*98:01', 'HLA-DPA1*01:03-HLA-DPB1*99:01', - 'HLA-DPA1*01:04-HLA-DPB1*01:01', 'HLA-DPA1*01:04-HLA-DPB1*02:01', - 'HLA-DPA1*01:04-HLA-DPB1*02:02', 'HLA-DPA1*01:04-HLA-DPB1*03:01', 'HLA-DPA1*01:04-HLA-DPB1*04:01', 'HLA-DPA1*01:04-HLA-DPB1*04:02', - 'HLA-DPA1*01:04-HLA-DPB1*05:01', 'HLA-DPA1*01:04-HLA-DPB1*06:01', - 'HLA-DPA1*01:04-HLA-DPB1*08:01', 'HLA-DPA1*01:04-HLA-DPB1*09:01', 'HLA-DPA1*01:04-HLA-DPB1*10:001', 'HLA-DPA1*01:04-HLA-DPB1*10:01', - 'HLA-DPA1*01:04-HLA-DPB1*10:101', 'HLA-DPA1*01:04-HLA-DPB1*10:201', - 'HLA-DPA1*01:04-HLA-DPB1*10:301', 'HLA-DPA1*01:04-HLA-DPB1*10:401', 'HLA-DPA1*01:04-HLA-DPB1*10:501', 'HLA-DPA1*01:04-HLA-DPB1*10:601', - 'HLA-DPA1*01:04-HLA-DPB1*10:701', 'HLA-DPA1*01:04-HLA-DPB1*10:801', - 'HLA-DPA1*01:04-HLA-DPB1*10:901', 'HLA-DPA1*01:04-HLA-DPB1*11:001', 'HLA-DPA1*01:04-HLA-DPB1*11:01', 'HLA-DPA1*01:04-HLA-DPB1*11:101', - 'HLA-DPA1*01:04-HLA-DPB1*11:201', 'HLA-DPA1*01:04-HLA-DPB1*11:301', - 'HLA-DPA1*01:04-HLA-DPB1*11:401', 'HLA-DPA1*01:04-HLA-DPB1*11:501', 'HLA-DPA1*01:04-HLA-DPB1*11:601', 'HLA-DPA1*01:04-HLA-DPB1*11:701', - 'HLA-DPA1*01:04-HLA-DPB1*11:801', 'HLA-DPA1*01:04-HLA-DPB1*11:901', - 'HLA-DPA1*01:04-HLA-DPB1*12:101', 'HLA-DPA1*01:04-HLA-DPB1*12:201', 'HLA-DPA1*01:04-HLA-DPB1*12:301', 'HLA-DPA1*01:04-HLA-DPB1*12:401', - 'HLA-DPA1*01:04-HLA-DPB1*12:501', 'HLA-DPA1*01:04-HLA-DPB1*12:601', - 'HLA-DPA1*01:04-HLA-DPB1*12:701', 'HLA-DPA1*01:04-HLA-DPB1*12:801', 'HLA-DPA1*01:04-HLA-DPB1*12:901', 'HLA-DPA1*01:04-HLA-DPB1*13:001', - 'HLA-DPA1*01:04-HLA-DPB1*13:01', 'HLA-DPA1*01:04-HLA-DPB1*13:101', - 'HLA-DPA1*01:04-HLA-DPB1*13:201', 'HLA-DPA1*01:04-HLA-DPB1*13:301', 'HLA-DPA1*01:04-HLA-DPB1*13:401', 'HLA-DPA1*01:04-HLA-DPB1*14:01', - 'HLA-DPA1*01:04-HLA-DPB1*15:01', 'HLA-DPA1*01:04-HLA-DPB1*16:01', - 'HLA-DPA1*01:04-HLA-DPB1*17:01', 'HLA-DPA1*01:04-HLA-DPB1*18:01', 'HLA-DPA1*01:04-HLA-DPB1*19:01', 'HLA-DPA1*01:04-HLA-DPB1*20:01', - 'HLA-DPA1*01:04-HLA-DPB1*21:01', 'HLA-DPA1*01:04-HLA-DPB1*22:01', - 'HLA-DPA1*01:04-HLA-DPB1*23:01', 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'HLA-DQA1*06:01-DQB1*03:20', + 'HLA-DQA1*06:01-DQB1*03:21', 'HLA-DQA1*06:01-DQB1*03:22', + 'HLA-DQA1*06:01-DQB1*03:23', 'HLA-DQA1*06:01-DQB1*03:24', 'HLA-DQA1*06:01-DQB1*03:25', 'HLA-DQA1*06:01-DQB1*03:26', + 'HLA-DQA1*06:01-DQB1*03:27', 'HLA-DQA1*06:01-DQB1*03:28', + 'HLA-DQA1*06:01-DQB1*03:29', 'HLA-DQA1*06:01-DQB1*03:30', 'HLA-DQA1*06:01-DQB1*03:31', 'HLA-DQA1*06:01-DQB1*03:32', + 'HLA-DQA1*06:01-DQB1*03:33', 'HLA-DQA1*06:01-DQB1*03:34', + 'HLA-DQA1*06:01-DQB1*03:35', 'HLA-DQA1*06:01-DQB1*03:36', 'HLA-DQA1*06:01-DQB1*03:37', 'HLA-DQA1*06:01-DQB1*03:38', + 'HLA-DQA1*06:01-DQB1*04:01', 'HLA-DQA1*06:01-DQB1*04:02', + 'HLA-DQA1*06:01-DQB1*04:03', 'HLA-DQA1*06:01-DQB1*04:04', 'HLA-DQA1*06:01-DQB1*04:05', 'HLA-DQA1*06:01-DQB1*04:06', + 'HLA-DQA1*06:01-DQB1*04:07', 'HLA-DQA1*06:01-DQB1*04:08', + 'HLA-DQA1*06:01-DQB1*05:01', 'HLA-DQA1*06:01-DQB1*05:02', 'HLA-DQA1*06:01-DQB1*05:03', 'HLA-DQA1*06:01-DQB1*05:05', + 'HLA-DQA1*06:01-DQB1*05:06', 'HLA-DQA1*06:01-DQB1*05:07', + 'HLA-DQA1*06:01-DQB1*05:08', 'HLA-DQA1*06:01-DQB1*05:09', 'HLA-DQA1*06:01-DQB1*05:10', 'HLA-DQA1*06:01-DQB1*05:11', + 'HLA-DQA1*06:01-DQB1*05:12', 'HLA-DQA1*06:01-DQB1*05:13', + 'HLA-DQA1*06:01-DQB1*05:14', 'HLA-DQA1*06:01-DQB1*06:01', 'HLA-DQA1*06:01-DQB1*06:02', 'HLA-DQA1*06:01-DQB1*06:03', + 'HLA-DQA1*06:01-DQB1*06:04', 'HLA-DQA1*06:01-DQB1*06:07', + 'HLA-DQA1*06:01-DQB1*06:08', 'HLA-DQA1*06:01-DQB1*06:09', 'HLA-DQA1*06:01-DQB1*06:10', 'HLA-DQA1*06:01-DQB1*06:11', + 'HLA-DQA1*06:01-DQB1*06:12', 'HLA-DQA1*06:01-DQB1*06:14', + 'HLA-DQA1*06:01-DQB1*06:15', 'HLA-DQA1*06:01-DQB1*06:16', 'HLA-DQA1*06:01-DQB1*06:17', 'HLA-DQA1*06:01-DQB1*06:18', + 'HLA-DQA1*06:01-DQB1*06:19', 'HLA-DQA1*06:01-DQB1*06:21', + 'HLA-DQA1*06:01-DQB1*06:22', 'HLA-DQA1*06:01-DQB1*06:23', 'HLA-DQA1*06:01-DQB1*06:24', 'HLA-DQA1*06:01-DQB1*06:25', + 'HLA-DQA1*06:01-DQB1*06:27', 'HLA-DQA1*06:01-DQB1*06:28', + 'HLA-DQA1*06:01-DQB1*06:29', 'HLA-DQA1*06:01-DQB1*06:30', 'HLA-DQA1*06:01-DQB1*06:31', 'HLA-DQA1*06:01-DQB1*06:32', + 'HLA-DQA1*06:01-DQB1*06:33', 'HLA-DQA1*06:01-DQB1*06:34', + 'HLA-DQA1*06:01-DQB1*06:35', 'HLA-DQA1*06:01-DQB1*06:36', 'HLA-DQA1*06:01-DQB1*06:37', 'HLA-DQA1*06:01-DQB1*06:38', + 'HLA-DQA1*06:01-DQB1*06:39', 'HLA-DQA1*06:01-DQB1*06:40', + 'HLA-DQA1*06:01-DQB1*06:41', 'HLA-DQA1*06:01-DQB1*06:42', 'HLA-DQA1*06:01-DQB1*06:43', 'HLA-DQA1*06:01-DQB1*06:44', + 'HLA-DQA1*06:02-DQB1*02:01', 'HLA-DQA1*06:02-DQB1*02:02', + 'HLA-DQA1*06:02-DQB1*02:03', 'HLA-DQA1*06:02-DQB1*02:04', 'HLA-DQA1*06:02-DQB1*02:05', 'HLA-DQA1*06:02-DQB1*02:06', + 'HLA-DQA1*06:02-DQB1*03:01', 'HLA-DQA1*06:02-DQB1*03:02', + 'HLA-DQA1*06:02-DQB1*03:03', 'HLA-DQA1*06:02-DQB1*03:04', 'HLA-DQA1*06:02-DQB1*03:05', 'HLA-DQA1*06:02-DQB1*03:06', + 'HLA-DQA1*06:02-DQB1*03:07', 'HLA-DQA1*06:02-DQB1*03:08', + 'HLA-DQA1*06:02-DQB1*03:09', 'HLA-DQA1*06:02-DQB1*03:10', 'HLA-DQA1*06:02-DQB1*03:11', 'HLA-DQA1*06:02-DQB1*03:12', + 'HLA-DQA1*06:02-DQB1*03:13', 'HLA-DQA1*06:02-DQB1*03:14', + 'HLA-DQA1*06:02-DQB1*03:15', 'HLA-DQA1*06:02-DQB1*03:16', 'HLA-DQA1*06:02-DQB1*03:17', 'HLA-DQA1*06:02-DQB1*03:18', + 'HLA-DQA1*06:02-DQB1*03:19', 'HLA-DQA1*06:02-DQB1*03:20', + 'HLA-DQA1*06:02-DQB1*03:21', 'HLA-DQA1*06:02-DQB1*03:22', 'HLA-DQA1*06:02-DQB1*03:23', 'HLA-DQA1*06:02-DQB1*03:24', + 'HLA-DQA1*06:02-DQB1*03:25', 'HLA-DQA1*06:02-DQB1*03:26', + 'HLA-DQA1*06:02-DQB1*03:27', 'HLA-DQA1*06:02-DQB1*03:28', 'HLA-DQA1*06:02-DQB1*03:29', 'HLA-DQA1*06:02-DQB1*03:30', + 'HLA-DQA1*06:02-DQB1*03:31', 'HLA-DQA1*06:02-DQB1*03:32', + 'HLA-DQA1*06:02-DQB1*03:33', 'HLA-DQA1*06:02-DQB1*03:34', 'HLA-DQA1*06:02-DQB1*03:35', 'HLA-DQA1*06:02-DQB1*03:36', + 'HLA-DQA1*06:02-DQB1*03:37', 'HLA-DQA1*06:02-DQB1*03:38', + 'HLA-DQA1*06:02-DQB1*04:01', 'HLA-DQA1*06:02-DQB1*04:02', 'HLA-DQA1*06:02-DQB1*04:03', 'HLA-DQA1*06:02-DQB1*04:04', + 'HLA-DQA1*06:02-DQB1*04:05', 'HLA-DQA1*06:02-DQB1*04:06', + 'HLA-DQA1*06:02-DQB1*04:07', 'HLA-DQA1*06:02-DQB1*04:08', 'HLA-DQA1*06:02-DQB1*05:01', 'HLA-DQA1*06:02-DQB1*05:02', + 'HLA-DQA1*06:02-DQB1*05:03', 'HLA-DQA1*06:02-DQB1*05:05', + 'HLA-DQA1*06:02-DQB1*05:06', 'HLA-DQA1*06:02-DQB1*05:07', 'HLA-DQA1*06:02-DQB1*05:08', 'HLA-DQA1*06:02-DQB1*05:09', + 'HLA-DQA1*06:02-DQB1*05:10', 'HLA-DQA1*06:02-DQB1*05:11', + 'HLA-DQA1*06:02-DQB1*05:12', 'HLA-DQA1*06:02-DQB1*05:13', 'HLA-DQA1*06:02-DQB1*05:14', 'HLA-DQA1*06:02-DQB1*06:01', + 'HLA-DQA1*06:02-DQB1*06:02', 'HLA-DQA1*06:02-DQB1*06:03', + 'HLA-DQA1*06:02-DQB1*06:04', 'HLA-DQA1*06:02-DQB1*06:07', 'HLA-DQA1*06:02-DQB1*06:08', 'HLA-DQA1*06:02-DQB1*06:09', + 'HLA-DQA1*06:02-DQB1*06:10', 'HLA-DQA1*06:02-DQB1*06:11', + 'HLA-DQA1*06:02-DQB1*06:12', 'HLA-DQA1*06:02-DQB1*06:14', 'HLA-DQA1*06:02-DQB1*06:15', 'HLA-DQA1*06:02-DQB1*06:16', + 'HLA-DQA1*06:02-DQB1*06:17', 'HLA-DQA1*06:02-DQB1*06:18', + 'HLA-DQA1*06:02-DQB1*06:19', 'HLA-DQA1*06:02-DQB1*06:21', 'HLA-DQA1*06:02-DQB1*06:22', 'HLA-DQA1*06:02-DQB1*06:23', + 'HLA-DQA1*06:02-DQB1*06:24', 'HLA-DQA1*06:02-DQB1*06:25', + 'HLA-DQA1*06:02-DQB1*06:27', 'HLA-DQA1*06:02-DQB1*06:28', 'HLA-DQA1*06:02-DQB1*06:29', 'HLA-DQA1*06:02-DQB1*06:30', + 'HLA-DQA1*06:02-DQB1*06:31', 'HLA-DQA1*06:02-DQB1*06:32', + 'HLA-DQA1*06:02-DQB1*06:33', 'HLA-DQA1*06:02-DQB1*06:34', 'HLA-DQA1*06:02-DQB1*06:35', 'HLA-DQA1*06:02-DQB1*06:36', + 'HLA-DQA1*06:02-DQB1*06:37', 'HLA-DQA1*06:02-DQB1*06:38', + 'HLA-DQA1*06:02-DQB1*06:39', 'HLA-DQA1*06:02-DQB1*06:40', 'HLA-DQA1*06:02-DQB1*06:41', 'HLA-DQA1*06:02-DQB1*06:42', + 'HLA-DQA1*06:02-DQB1*06:43', 'HLA-DQA1*06:02-DQB1*06:44', + 'H-2-Iab', 'H-2-Iad']) __version = "3.0" @property @@ -3945,7 +4065,7 @@ def _represent(self, allele): :return: str """ if isinstance(allele, MouseAllele): - return "H-2-%s%s%s" % (allele.locus, allele.supertype, allele.subtype) + return "H-2-%s%s%s" % (allele.locus, allele.supertype.upper(), allele.subtype) elif isinstance(allele, CombinedAllele): return "HLA-%s%s%s-%s%s%s" % (allele.alpha_locus, allele.alpha_supertype, allele.alpha_subtype, allele.beta_locus, allele.beta_supertype, allele.beta_subtype) @@ -3967,20 +4087,43 @@ def convert_alleles(self, alleles): def parse_external_result(self, file): """ - Parses external results and returns the result + Parses external results and returns the result containing the predictors string representation + of alleles and peptides. :param str file: The file path or the external prediction results :return: A dictionary containing the prediction results :rtype: dict """ + def parse_allele_from_external_result(alleles_str_out): + """ + Parses allele string from external result to allele string representation of input + + :param str allele_str_out: The allele string representation from the external result output + :return: str allele_str_in: The allele string representation from the external result input + :rtype: str + """ + alleles_str_in = [] + for allele_str_out in alleles_str_out: + if allele_str_out.startswith('HLA-'): + allele_str_in = allele_str_out.replace('*','').replace(':','') + elif allele_str_out.startswith('D'): + allele_str_in = allele_str_out.replace('*','_').replace(':','') + else: + allele_str_in = allele_str_out + alleles_str_in.append(allele_str_in) + + return(alleles_str_in) + f = csv.reader(open(file, "r"), delimiter='\t') scores = defaultdict(defaultdict) ranks = defaultdict(defaultdict) - # NetMHCiipan 3.1 inherits from NetMHCiipan 3.0 thus has a slighty different allele nomenclature - alleles = [Allele('HLA-'+x) for x in set([x for x in next(f) if x != ""])] + alleles = [x for x in set([x for x in next(f) if x != ""])] + # Convert output representation of allele to input representation of allele, because they differ + alleles = parse_allele_from_external_result(alleles) + next(f) for row in f: - pep_seq = Peptide(row[PeptideIndex.NETMHCIIPAN_3_0]) + pep_seq = row[PeptideIndex.NETMHCIIPAN_3_0] for i, a in enumerate(alleles): scores[a][pep_seq] = float(row[ScoreIndex.NETMHCIIPAN_3_0 + i * Offset.NETMHCIIPAN_3_0]) ranks[a][pep_seq] = float(row[RankIndex.NETMHCIIPAN_3_0 + i * Offset.NETMHCIIPAN_3_0]) @@ -4143,1660 +4286,1660 @@ class NetMHCIIpan_3_1(NetMHCIIpan_3_0): 'HLA-DRB4*01:06', 'HLA-DRB4*01:07', 'HLA-DRB4*01:08', 'HLA-DRB5*01:01', 'HLA-DRB5*01:02', 'HLA-DRB5*01:03', 'HLA-DRB5*01:04', 'HLA-DRB5*01:05', 'HLA-DRB5*01:06', 'HLA-DRB5*01:08N', 'HLA-DRB5*01:11', 'HLA-DRB5*01:12', 'HLA-DRB5*01:13', 'HLA-DRB5*01:14', 'HLA-DRB5*02:02', 'HLA-DRB5*02:03', 'HLA-DRB5*02:04', 'HLA-DRB5*02:05', - 'HLA-DPA1*01:03-HLA-DPB1*01:01', 'HLA-DPA1*01:03-HLA-DPB1*02:01', 'HLA-DPA1*01:03-HLA-DPB1*02:02', 'HLA-DPA1*01:03-HLA-DPB1*03:01', - 'HLA-DPA1*01:03-HLA-DPB1*04:01', 'HLA-DPA1*01:03-HLA-DPB1*04:02', 'HLA-DPA1*01:03-HLA-DPB1*05:01', 'HLA-DPA1*01:03-HLA-DPB1*06:01', - 'HLA-DPA1*01:03-HLA-DPB1*08:01', 'HLA-DPA1*01:03-HLA-DPB1*09:01', 'HLA-DPA1*01:03-HLA-DPB1*10:001', 'HLA-DPA1*01:03-HLA-DPB1*10:01', - 'HLA-DPA1*01:03-HLA-DPB1*10:101', 'HLA-DPA1*01:03-HLA-DPB1*10:201', - 'HLA-DPA1*01:03-HLA-DPB1*10:301', 'HLA-DPA1*01:03-HLA-DPB1*10:401', - 'HLA-DPA1*01:03-HLA-DPB1*10:501', 'HLA-DPA1*01:03-HLA-DPB1*10:601', 'HLA-DPA1*01:03-HLA-DPB1*10:701', 'HLA-DPA1*01:03-HLA-DPB1*10:801', - 'HLA-DPA1*01:03-HLA-DPB1*10:901', 'HLA-DPA1*01:03-HLA-DPB1*11:001', - 'HLA-DPA1*01:03-HLA-DPB1*11:01', 'HLA-DPA1*01:03-HLA-DPB1*11:101', 'HLA-DPA1*01:03-HLA-DPB1*11:201', 'HLA-DPA1*01:03-HLA-DPB1*11:301', - 'HLA-DPA1*01:03-HLA-DPB1*11:401', 'HLA-DPA1*01:03-HLA-DPB1*11:501', - 'HLA-DPA1*01:03-HLA-DPB1*11:601', 'HLA-DPA1*01:03-HLA-DPB1*11:701', 'HLA-DPA1*01:03-HLA-DPB1*11:801', 'HLA-DPA1*01:03-HLA-DPB1*11:901', - 'HLA-DPA1*01:03-HLA-DPB1*12:101', 'HLA-DPA1*01:03-HLA-DPB1*12:201', - 'HLA-DPA1*01:03-HLA-DPB1*12:301', 'HLA-DPA1*01:03-HLA-DPB1*12:401', 'HLA-DPA1*01:03-HLA-DPB1*12:501', 'HLA-DPA1*01:03-HLA-DPB1*12:601', - 'HLA-DPA1*01:03-HLA-DPB1*12:701', 'HLA-DPA1*01:03-HLA-DPB1*12:801', - 'HLA-DPA1*01:03-HLA-DPB1*12:901', 'HLA-DPA1*01:03-HLA-DPB1*13:001', 'HLA-DPA1*01:03-HLA-DPB1*13:01', 'HLA-DPA1*01:03-HLA-DPB1*13:101', - 'HLA-DPA1*01:03-HLA-DPB1*13:201', 'HLA-DPA1*01:03-HLA-DPB1*13:301', - 'HLA-DPA1*01:03-HLA-DPB1*13:401', 'HLA-DPA1*01:03-HLA-DPB1*14:01', 'HLA-DPA1*01:03-HLA-DPB1*15:01', 'HLA-DPA1*01:03-HLA-DPB1*16:01', - 'HLA-DPA1*01:03-HLA-DPB1*17:01', 'HLA-DPA1*01:03-HLA-DPB1*18:01', - 'HLA-DPA1*01:03-HLA-DPB1*19:01', 'HLA-DPA1*01:03-HLA-DPB1*20:01', 'HLA-DPA1*01:03-HLA-DPB1*21:01', 'HLA-DPA1*01:03-HLA-DPB1*22:01', - 'HLA-DPA1*01:03-HLA-DPB1*23:01', 'HLA-DPA1*01:03-HLA-DPB1*24:01', - 'HLA-DPA1*01:03-HLA-DPB1*25:01', 'HLA-DPA1*01:03-HLA-DPB1*26:01', 'HLA-DPA1*01:03-HLA-DPB1*27:01', 'HLA-DPA1*01:03-HLA-DPB1*28:01', - 'HLA-DPA1*01:03-HLA-DPB1*29:01', 'HLA-DPA1*01:03-HLA-DPB1*30:01', - 'HLA-DPA1*01:03-HLA-DPB1*31:01', 'HLA-DPA1*01:03-HLA-DPB1*32:01', 'HLA-DPA1*01:03-HLA-DPB1*33:01', 'HLA-DPA1*01:03-HLA-DPB1*34:01', - 'HLA-DPA1*01:03-HLA-DPB1*35:01', 'HLA-DPA1*01:03-HLA-DPB1*36:01', - 'HLA-DPA1*01:03-HLA-DPB1*37:01', 'HLA-DPA1*01:03-HLA-DPB1*38:01', 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'HLA-DPA1*01:03-DPB1*13:01', 'HLA-DPA1*01:03-DPB1*13:101', + 'HLA-DPA1*01:03-DPB1*13:201', 'HLA-DPA1*01:03-DPB1*13:301', + 'HLA-DPA1*01:03-DPB1*13:401', 'HLA-DPA1*01:03-DPB1*14:01', 'HLA-DPA1*01:03-DPB1*15:01', 'HLA-DPA1*01:03-DPB1*16:01', + 'HLA-DPA1*01:03-DPB1*17:01', 'HLA-DPA1*01:03-DPB1*18:01', + 'HLA-DPA1*01:03-DPB1*19:01', 'HLA-DPA1*01:03-DPB1*20:01', 'HLA-DPA1*01:03-DPB1*21:01', 'HLA-DPA1*01:03-DPB1*22:01', + 'HLA-DPA1*01:03-DPB1*23:01', 'HLA-DPA1*01:03-DPB1*24:01', + 'HLA-DPA1*01:03-DPB1*25:01', 'HLA-DPA1*01:03-DPB1*26:01', 'HLA-DPA1*01:03-DPB1*27:01', 'HLA-DPA1*01:03-DPB1*28:01', + 'HLA-DPA1*01:03-DPB1*29:01', 'HLA-DPA1*01:03-DPB1*30:01', + 'HLA-DPA1*01:03-DPB1*31:01', 'HLA-DPA1*01:03-DPB1*32:01', 'HLA-DPA1*01:03-DPB1*33:01', 'HLA-DPA1*01:03-DPB1*34:01', + 'HLA-DPA1*01:03-DPB1*35:01', 'HLA-DPA1*01:03-DPB1*36:01', + 'HLA-DPA1*01:03-DPB1*37:01', 'HLA-DPA1*01:03-DPB1*38:01', 'HLA-DPA1*01:03-DPB1*39:01', 'HLA-DPA1*01:03-DPB1*40:01', + 'HLA-DPA1*01:03-DPB1*41:01', 'HLA-DPA1*01:03-DPB1*44:01', + 'HLA-DPA1*01:03-DPB1*45:01', 'HLA-DPA1*01:03-DPB1*46:01', 'HLA-DPA1*01:03-DPB1*47:01', 'HLA-DPA1*01:03-DPB1*48:01', + 'HLA-DPA1*01:03-DPB1*49:01', 'HLA-DPA1*01:03-DPB1*50:01', + 'HLA-DPA1*01:03-DPB1*51:01', 'HLA-DPA1*01:03-DPB1*52:01', 'HLA-DPA1*01:03-DPB1*53:01', 'HLA-DPA1*01:03-DPB1*54:01', + 'HLA-DPA1*01:03-DPB1*55:01', 'HLA-DPA1*01:03-DPB1*56:01', + 'HLA-DPA1*01:03-DPB1*58:01', 'HLA-DPA1*01:03-DPB1*59:01', 'HLA-DPA1*01:03-DPB1*60:01', 'HLA-DPA1*01:03-DPB1*62:01', + 'HLA-DPA1*01:03-DPB1*63:01', 'HLA-DPA1*01:03-DPB1*65:01', + 'HLA-DPA1*01:03-DPB1*66:01', 'HLA-DPA1*01:03-DPB1*67:01', 'HLA-DPA1*01:03-DPB1*68:01', 'HLA-DPA1*01:03-DPB1*69:01', + 'HLA-DPA1*01:03-DPB1*70:01', 'HLA-DPA1*01:03-DPB1*71:01', + 'HLA-DPA1*01:03-DPB1*72:01', 'HLA-DPA1*01:03-DPB1*73:01', 'HLA-DPA1*01:03-DPB1*74:01', 'HLA-DPA1*01:03-DPB1*75:01', + 'HLA-DPA1*01:03-DPB1*76:01', 'HLA-DPA1*01:03-DPB1*77:01', + 'HLA-DPA1*01:03-DPB1*78:01', 'HLA-DPA1*01:03-DPB1*79:01', 'HLA-DPA1*01:03-DPB1*80:01', 'HLA-DPA1*01:03-DPB1*81:01', + 'HLA-DPA1*01:03-DPB1*82:01', 'HLA-DPA1*01:03-DPB1*83:01', + 'HLA-DPA1*01:03-DPB1*84:01', 'HLA-DPA1*01:03-DPB1*85:01', 'HLA-DPA1*01:03-DPB1*86:01', 'HLA-DPA1*01:03-DPB1*87:01', + 'HLA-DPA1*01:03-DPB1*88:01', 'HLA-DPA1*01:03-DPB1*89:01', + 'HLA-DPA1*01:03-DPB1*90:01', 'HLA-DPA1*01:03-DPB1*91:01', 'HLA-DPA1*01:03-DPB1*92:01', 'HLA-DPA1*01:03-DPB1*93:01', + 'HLA-DPA1*01:03-DPB1*94:01', 'HLA-DPA1*01:03-DPB1*95:01', + 'HLA-DPA1*01:03-DPB1*96:01', 'HLA-DPA1*01:03-DPB1*97:01', 'HLA-DPA1*01:03-DPB1*98:01', 'HLA-DPA1*01:03-DPB1*99:01', + 'HLA-DPA1*01:04-DPB1*01:01', 'HLA-DPA1*01:04-DPB1*02:01', + 'HLA-DPA1*01:04-DPB1*02:02', 'HLA-DPA1*01:04-DPB1*03:01', 'HLA-DPA1*01:04-DPB1*04:01', 'HLA-DPA1*01:04-DPB1*04:02', + 'HLA-DPA1*01:04-DPB1*05:01', 'HLA-DPA1*01:04-DPB1*06:01', + 'HLA-DPA1*01:04-DPB1*08:01', 'HLA-DPA1*01:04-DPB1*09:01', 'HLA-DPA1*01:04-DPB1*10:001', 'HLA-DPA1*01:04-DPB1*10:01', + 'HLA-DPA1*01:04-DPB1*10:101', 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'HLA-DPA1*01:04-DPB1*13:301', 'HLA-DPA1*01:04-DPB1*13:401', 'HLA-DPA1*01:04-DPB1*14:01', + 'HLA-DPA1*01:04-DPB1*15:01', 'HLA-DPA1*01:04-DPB1*16:01', + 'HLA-DPA1*01:04-DPB1*17:01', 'HLA-DPA1*01:04-DPB1*18:01', 'HLA-DPA1*01:04-DPB1*19:01', 'HLA-DPA1*01:04-DPB1*20:01', + 'HLA-DPA1*01:04-DPB1*21:01', 'HLA-DPA1*01:04-DPB1*22:01', + 'HLA-DPA1*01:04-DPB1*23:01', 'HLA-DPA1*01:04-DPB1*24:01', 'HLA-DPA1*01:04-DPB1*25:01', 'HLA-DPA1*01:04-DPB1*26:01', + 'HLA-DPA1*01:04-DPB1*27:01', 'HLA-DPA1*01:04-DPB1*28:01', + 'HLA-DPA1*01:04-DPB1*29:01', 'HLA-DPA1*01:04-DPB1*30:01', 'HLA-DPA1*01:04-DPB1*31:01', 'HLA-DPA1*01:04-DPB1*32:01', + 'HLA-DPA1*01:04-DPB1*33:01', 'HLA-DPA1*01:04-DPB1*34:01', + 'HLA-DPA1*01:04-DPB1*35:01', 'HLA-DPA1*01:04-DPB1*36:01', 'HLA-DPA1*01:04-DPB1*37:01', 'HLA-DPA1*01:04-DPB1*38:01', + 'HLA-DPA1*01:04-DPB1*39:01', 'HLA-DPA1*01:04-DPB1*40:01', + 'HLA-DPA1*01:04-DPB1*41:01', 'HLA-DPA1*01:04-DPB1*44:01', 'HLA-DPA1*01:04-DPB1*45:01', 'HLA-DPA1*01:04-DPB1*46:01', + 'HLA-DPA1*01:04-DPB1*47:01', 'HLA-DPA1*01:04-DPB1*48:01', + 'HLA-DPA1*01:04-DPB1*49:01', 'HLA-DPA1*01:04-DPB1*50:01', 'HLA-DPA1*01:04-DPB1*51:01', 'HLA-DPA1*01:04-DPB1*52:01', + 'HLA-DPA1*01:04-DPB1*53:01', 'HLA-DPA1*01:04-DPB1*54:01', + 'HLA-DPA1*01:04-DPB1*55:01', 'HLA-DPA1*01:04-DPB1*56:01', 'HLA-DPA1*01:04-DPB1*58:01', 'HLA-DPA1*01:04-DPB1*59:01', + 'HLA-DPA1*01:04-DPB1*60:01', 'HLA-DPA1*01:04-DPB1*62:01', + 'HLA-DPA1*01:04-DPB1*63:01', 'HLA-DPA1*01:04-DPB1*65:01', 'HLA-DPA1*01:04-DPB1*66:01', 'HLA-DPA1*01:04-DPB1*67:01', + 'HLA-DPA1*01:04-DPB1*68:01', 'HLA-DPA1*01:04-DPB1*69:01', + 'HLA-DPA1*01:04-DPB1*70:01', 'HLA-DPA1*01:04-DPB1*71:01', 'HLA-DPA1*01:04-DPB1*72:01', 'HLA-DPA1*01:04-DPB1*73:01', + 'HLA-DPA1*01:04-DPB1*74:01', 'HLA-DPA1*01:04-DPB1*75:01', + 'HLA-DPA1*01:04-DPB1*76:01', 'HLA-DPA1*01:04-DPB1*77:01', 'HLA-DPA1*01:04-DPB1*78:01', 'HLA-DPA1*01:04-DPB1*79:01', + 'HLA-DPA1*01:04-DPB1*80:01', 'HLA-DPA1*01:04-DPB1*81:01', + 'HLA-DPA1*01:04-DPB1*82:01', 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'HLA-DQA1*06:02-DQB1*05:09', + 'HLA-DQA1*06:02-DQB1*05:10', 'HLA-DQA1*06:02-DQB1*05:11', + 'HLA-DQA1*06:02-DQB1*05:12', 'HLA-DQA1*06:02-DQB1*05:13', 'HLA-DQA1*06:02-DQB1*05:14', 'HLA-DQA1*06:02-DQB1*06:01', + 'HLA-DQA1*06:02-DQB1*06:02', 'HLA-DQA1*06:02-DQB1*06:03', + 'HLA-DQA1*06:02-DQB1*06:04', 'HLA-DQA1*06:02-DQB1*06:07', 'HLA-DQA1*06:02-DQB1*06:08', 'HLA-DQA1*06:02-DQB1*06:09', + 'HLA-DQA1*06:02-DQB1*06:10', 'HLA-DQA1*06:02-DQB1*06:11', + 'HLA-DQA1*06:02-DQB1*06:12', 'HLA-DQA1*06:02-DQB1*06:14', 'HLA-DQA1*06:02-DQB1*06:15', 'HLA-DQA1*06:02-DQB1*06:16', + 'HLA-DQA1*06:02-DQB1*06:17', 'HLA-DQA1*06:02-DQB1*06:18', + 'HLA-DQA1*06:02-DQB1*06:19', 'HLA-DQA1*06:02-DQB1*06:21', 'HLA-DQA1*06:02-DQB1*06:22', 'HLA-DQA1*06:02-DQB1*06:23', + 'HLA-DQA1*06:02-DQB1*06:24', 'HLA-DQA1*06:02-DQB1*06:25', + 'HLA-DQA1*06:02-DQB1*06:27', 'HLA-DQA1*06:02-DQB1*06:28', 'HLA-DQA1*06:02-DQB1*06:29', 'HLA-DQA1*06:02-DQB1*06:30', + 'HLA-DQA1*06:02-DQB1*06:31', 'HLA-DQA1*06:02-DQB1*06:32', + 'HLA-DQA1*06:02-DQB1*06:33', 'HLA-DQA1*06:02-DQB1*06:34', 'HLA-DQA1*06:02-DQB1*06:35', 'HLA-DQA1*06:02-DQB1*06:36', + 'HLA-DQA1*06:02-DQB1*06:37', 'HLA-DQA1*06:02-DQB1*06:38', + 'HLA-DQA1*06:02-DQB1*06:39', 'HLA-DQA1*06:02-DQB1*06:40', 'HLA-DQA1*06:02-DQB1*06:41', 'HLA-DQA1*06:02-DQB1*06:42', + 'HLA-DQA1*06:02-DQB1*06:43', 'HLA-DQA1*06:02-DQB1*06:44', + 'H-2-Iad', 'H-2-Iab']) __version = "3.1" @@ -5831,7 +5974,8 @@ def name(self): def parse_external_result(self, file): """ - Parses external results and returns the result + Parses external results and returns the result containing the predictors string representation + of alleles and peptides. :param str file: The file path or the external prediction results :return: A dictionary containing the prediction results @@ -5840,11 +5984,11 @@ def parse_external_result(self, file): f = csv.reader(open(file, "r"), delimiter='\t') scores = defaultdict(defaultdict) ranks = defaultdict(defaultdict) - # NetMHCiipan 3.1 inherits from NetMHCiipan 3.0 thus has a slighty different allele nomenclature - alleles = [Allele('HLA-'+x[:7].replace("_","*")+':'+x[7:]) for x in set([x for x in next(f) if x != ""])] + alleles = [x for x in set([x for x in next(f) if x != ""])] + next(f) for row in f: - pep_seq = Peptide(row[PeptideIndex.NETMHCIIPAN_3_1]) + pep_seq = row[PeptideIndex.NETMHCIIPAN_3_1] for i, a in enumerate(alleles): scores[a][pep_seq] = float(row[ScoreIndex.NETMHCIIPAN_3_1 + i * Offset.NETMHCIIPAN_3_1]) ranks[a][pep_seq] = float(row[RankIndex.NETMHCIIPAN_3_1 + i * Offset.NETMHCIIPAN_3_1]) @@ -5853,6 +5997,1201 @@ def parse_external_result(self, file): return result +class NetMHCIIpan_4_0(NetMHCIIpan_3_1): + """ + Implementation of NetMHCIIpan 4.0 adapter. + + .. note:: + + Reynisson B, Barra C, Kaabinejadian S, Hildebrand WH, Peters B, Nielsen M (2020). Improved prediction of MHC II antigen presentation + through integration and motif deconvolution of mass spectrometry MHC eluted ligand data. + Immunogenetics, 1-10. + """ + + __supported_length = frozenset([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20]) + __name = "netmhcIIpan" + __command = "netMHCIIpan -f {peptides} -inptype 1 -a {alleles} {options} -xls -xlsfile {out}" + __alleles = frozenset(['HLA-DRB1*01:01', 'HLA-DRB1*01:02', 'HLA-DRB1*01:03', 'HLA-DRB1*01:04', 'HLA-DRB1*01:05', +'HLA-DRB1*01:06', 'HLA-DRB1*01:07', 'HLA-DRB1*01:08', 'HLA-DRB1*01:09', 'HLA-DRB1*01:10', +'HLA-DRB1*01:11', 'HLA-DRB1*01:12', 'HLA-DRB1*01:13', 'HLA-DRB1*01:14', 'HLA-DRB1*01:15', +'HLA-DRB1*01:16', 'HLA-DRB1*01:17', 'HLA-DRB1*01:18', 'HLA-DRB1*01:19', 'HLA-DRB1*01:20', +'HLA-DRB1*01:21', 'HLA-DRB1*01:22', 'HLA-DRB1*01:23', 'HLA-DRB1*01:24', 'HLA-DRB1*01:25', +'HLA-DRB1*01:26', 'HLA-DRB1*01:27', 'HLA-DRB1*01:28', 'HLA-DRB1*01:29', 'HLA-DRB1*01:30', +'HLA-DRB1*01:31', 'HLA-DRB1*01:32', 'HLA-DRB1*03:01', 'HLA-DRB1*03:02', 'HLA-DRB1*03:03', +'HLA-DRB1*03:04', 'HLA-DRB1*03:05', 'HLA-DRB1*03:06', 'HLA-DRB1*03:07', 'HLA-DRB1*03:08', +'HLA-DRB1*03:10', 'HLA-DRB1*03:11', 'HLA-DRB1*03:13', 'HLA-DRB1*03:14', 'HLA-DRB1*03:15', +'HLA-DRB1*03:17', 'HLA-DRB1*03:18', 'HLA-DRB1*03:19', 'HLA-DRB1*03:20', 'HLA-DRB1*03:21', +'HLA-DRB1*03:22', 'HLA-DRB1*03:23', 'HLA-DRB1*03:24', 'HLA-DRB1*03:25', 'HLA-DRB1*03:26', +'HLA-DRB1*03:27', 'HLA-DRB1*03:28', 'HLA-DRB1*03:29', 'HLA-DRB1*03:30', 'HLA-DRB1*03:31', +'HLA-DRB1*03:32', 'HLA-DRB1*03:33', 'HLA-DRB1*03:34', 'HLA-DRB1*03:35', 'HLA-DRB1*03:36', +'HLA-DRB1*03:37', 'HLA-DRB1*03:38', 'HLA-DRB1*03:39', 'HLA-DRB1*03:40', 'HLA-DRB1*03:41', +'HLA-DRB1*03:42', 'HLA-DRB1*03:43', 'HLA-DRB1*03:44', 'HLA-DRB1*03:45', 'HLA-DRB1*03:46', +'HLA-DRB1*03:47', 'HLA-DRB1*03:48', 'HLA-DRB1*03:49', 'HLA-DRB1*03:50', 'HLA-DRB1*03:51', +'HLA-DRB1*03:52', 'HLA-DRB1*03:53', 'HLA-DRB1*03:54', 'HLA-DRB1*03:55', 'HLA-DRB1*04:01', +'HLA-DRB1*04:02', 'HLA-DRB1*04:03', 'HLA-DRB1*04:04', 'HLA-DRB1*04:05', 'HLA-DRB1*04:06', +'HLA-DRB1*04:07', 'HLA-DRB1*04:08', 'HLA-DRB1*04:09', 'HLA-DRB1*04:10', 'HLA-DRB1*04:11', +'HLA-DRB1*04:12', 'HLA-DRB1*04:13', 'HLA-DRB1*04:14', 'HLA-DRB1*04:15', 'HLA-DRB1*04:16', +'HLA-DRB1*04:17', 'HLA-DRB1*04:18', 'HLA-DRB1*04:19', 'HLA-DRB1*04:21', 'HLA-DRB1*04:22', +'HLA-DRB1*04:23', 'HLA-DRB1*04:24', 'HLA-DRB1*04:26', 'HLA-DRB1*04:27', 'HLA-DRB1*04:28', +'HLA-DRB1*04:29', 'HLA-DRB1*04:30', 'HLA-DRB1*04:31', 'HLA-DRB1*04:33', 'HLA-DRB1*04:34', +'HLA-DRB1*04:35', 'HLA-DRB1*04:36', 'HLA-DRB1*04:37', 'HLA-DRB1*04:38', 'HLA-DRB1*04:39', +'HLA-DRB1*04:40', 'HLA-DRB1*04:41', 'HLA-DRB1*04:42', 'HLA-DRB1*04:43', 'HLA-DRB1*04:44', +'HLA-DRB1*04:45', 'HLA-DRB1*04:46', 'HLA-DRB1*04:47', 'HLA-DRB1*04:48', 'HLA-DRB1*04:49', +'HLA-DRB1*04:50', 'HLA-DRB1*04:51', 'HLA-DRB1*04:52', 'HLA-DRB1*04:53', 'HLA-DRB1*04:54', +'HLA-DRB1*04:55', 'HLA-DRB1*04:56', 'HLA-DRB1*04:57', 'HLA-DRB1*04:58', 'HLA-DRB1*04:59', +'HLA-DRB1*04:60', 'HLA-DRB1*04:61', 'HLA-DRB1*04:62', 'HLA-DRB1*04:63', 'HLA-DRB1*04:64', +'HLA-DRB1*04:65', 'HLA-DRB1*04:66', 'HLA-DRB1*04:67', 'HLA-DRB1*04:68', 'HLA-DRB1*04:69', +'HLA-DRB1*04:70', 'HLA-DRB1*04:71', 'HLA-DRB1*04:72', 'HLA-DRB1*04:73', 'HLA-DRB1*04:74', +'HLA-DRB1*04:75', 'HLA-DRB1*04:76', 'HLA-DRB1*04:77', 'HLA-DRB1*04:78', 'HLA-DRB1*04:79', +'HLA-DRB1*04:80', 'HLA-DRB1*04:82', 'HLA-DRB1*04:83', 'HLA-DRB1*04:84', 'HLA-DRB1*04:85', +'HLA-DRB1*04:86', 'HLA-DRB1*04:87', 'HLA-DRB1*04:88', 'HLA-DRB1*04:89', 'HLA-DRB1*04:91', +'HLA-DRB1*07:01', 'HLA-DRB1*07:03', 'HLA-DRB1*07:04', 'HLA-DRB1*07:05', 'HLA-DRB1*07:06', +'HLA-DRB1*07:07', 'HLA-DRB1*07:08', 'HLA-DRB1*07:09', 'HLA-DRB1*07:11', 'HLA-DRB1*07:12', +'HLA-DRB1*07:13', 'HLA-DRB1*07:14', 'HLA-DRB1*07:15', 'HLA-DRB1*07:16', 'HLA-DRB1*07:17', +'HLA-DRB1*07:19', 'HLA-DRB1*08:01', 'HLA-DRB1*08:02', 'HLA-DRB1*08:03', 'HLA-DRB1*08:04', +'HLA-DRB1*08:05', 'HLA-DRB1*08:06', 'HLA-DRB1*08:07', 'HLA-DRB1*08:08', 'HLA-DRB1*08:09', +'HLA-DRB1*08:10', 'HLA-DRB1*08:11', 'HLA-DRB1*08:12', 'HLA-DRB1*08:13', 'HLA-DRB1*08:14', +'HLA-DRB1*08:15', 'HLA-DRB1*08:16', 'HLA-DRB1*08:18', 'HLA-DRB1*08:19', 'HLA-DRB1*08:20', +'HLA-DRB1*08:21', 'HLA-DRB1*08:22', 'HLA-DRB1*08:23', 'HLA-DRB1*08:24', 'HLA-DRB1*08:25', +'HLA-DRB1*08:26', 'HLA-DRB1*08:27', 'HLA-DRB1*08:28', 'HLA-DRB1*08:29', 'HLA-DRB1*08:30', +'HLA-DRB1*08:31', 'HLA-DRB1*08:32', 'HLA-DRB1*08:33', 'HLA-DRB1*08:34', 'HLA-DRB1*08:35', +'HLA-DRB1*08:36', 'HLA-DRB1*08:37', 'HLA-DRB1*08:38', 'HLA-DRB1*08:39', 'HLA-DRB1*08:40', +'HLA-DRB1*09:01', 'HLA-DRB1*09:02', 'HLA-DRB1*09:03', 'HLA-DRB1*09:04', 'HLA-DRB1*09:05', +'HLA-DRB1*09:06', 'HLA-DRB1*09:07', 'HLA-DRB1*09:08', 'HLA-DRB1*09:09', 'HLA-DRB1*10:01', +'HLA-DRB1*10:02', 'HLA-DRB1*10:03', 'HLA-DRB1*11:01', 'HLA-DRB1*11:02', 'HLA-DRB1*11:03', +'HLA-DRB1*11:04', 'HLA-DRB1*11:05', 'HLA-DRB1*11:06', 'HLA-DRB1*11:07', 'HLA-DRB1*11:08', +'HLA-DRB1*11:09', 'HLA-DRB1*11:10', 'HLA-DRB1*11:11', 'HLA-DRB1*11:12', 'HLA-DRB1*11:13', +'HLA-DRB1*11:14', 'HLA-DRB1*11:15', 'HLA-DRB1*11:16', 'HLA-DRB1*11:17', 'HLA-DRB1*11:18', +'HLA-DRB1*11:19', 'HLA-DRB1*11:20', 'HLA-DRB1*11:21', 'HLA-DRB1*11:24', 'HLA-DRB1*11:25', +'HLA-DRB1*11:27', 'HLA-DRB1*11:28', 'HLA-DRB1*11:29', 'HLA-DRB1*11:30', 'HLA-DRB1*11:31', +'HLA-DRB1*11:32', 'HLA-DRB1*11:33', 'HLA-DRB1*11:34', 'HLA-DRB1*11:35', 'HLA-DRB1*11:36', +'HLA-DRB1*11:37', 'HLA-DRB1*11:38', 'HLA-DRB1*11:39', 'HLA-DRB1*11:41', 'HLA-DRB1*11:42', +'HLA-DRB1*11:43', 'HLA-DRB1*11:44', 'HLA-DRB1*11:45', 'HLA-DRB1*11:46', 'HLA-DRB1*11:47', +'HLA-DRB1*11:48', 'HLA-DRB1*11:49', 'HLA-DRB1*11:50', 'HLA-DRB1*11:51', 'HLA-DRB1*11:52', +'HLA-DRB1*11:53', 'HLA-DRB1*11:54', 'HLA-DRB1*11:55', 'HLA-DRB1*11:56', 'HLA-DRB1*11:57', +'HLA-DRB1*11:58', 'HLA-DRB1*11:59', 'HLA-DRB1*11:60', 'HLA-DRB1*11:61', 'HLA-DRB1*11:62', +'HLA-DRB1*11:63', 'HLA-DRB1*11:64', 'HLA-DRB1*11:65', 'HLA-DRB1*11:66', 'HLA-DRB1*11:67', +'HLA-DRB1*11:68', 'HLA-DRB1*11:69', 'HLA-DRB1*11:70', 'HLA-DRB1*11:72', 'HLA-DRB1*11:73', +'HLA-DRB1*11:74', 'HLA-DRB1*11:75', 'HLA-DRB1*11:76', 'HLA-DRB1*11:77', 'HLA-DRB1*11:78', +'HLA-DRB1*11:79', 'HLA-DRB1*11:80', 'HLA-DRB1*11:81', 'HLA-DRB1*11:82', 'HLA-DRB1*11:83', +'HLA-DRB1*11:84', 'HLA-DRB1*11:85', 'HLA-DRB1*11:86', 'HLA-DRB1*11:87', 'HLA-DRB1*11:88', +'HLA-DRB1*11:89', 'HLA-DRB1*11:90', 'HLA-DRB1*11:91', 'HLA-DRB1*11:92', 'HLA-DRB1*11:93', +'HLA-DRB1*11:94', 'HLA-DRB1*11:95', 'HLA-DRB1*11:96', 'HLA-DRB1*12:01', 'HLA-DRB1*12:02', +'HLA-DRB1*12:03', 'HLA-DRB1*12:04', 'HLA-DRB1*12:05', 'HLA-DRB1*12:06', 'HLA-DRB1*12:07', +'HLA-DRB1*12:08', 'HLA-DRB1*12:09', 'HLA-DRB1*12:10', 'HLA-DRB1*12:11', 'HLA-DRB1*12:12', +'HLA-DRB1*12:13', 'HLA-DRB1*12:14', 'HLA-DRB1*12:15', 'HLA-DRB1*12:16', 'HLA-DRB1*12:17', +'HLA-DRB1*12:18', 'HLA-DRB1*12:19', 'HLA-DRB1*12:20', 'HLA-DRB1*12:21', 'HLA-DRB1*12:22', +'HLA-DRB1*12:23', 'HLA-DRB1*13:01', 'HLA-DRB1*13:02', 'HLA-DRB1*13:03', 'HLA-DRB1*13:04', +'HLA-DRB1*13:05', 'HLA-DRB1*13:06', 'HLA-DRB1*13:07', 'HLA-DRB1*13:08', 'HLA-DRB1*13:09', +'HLA-DRB1*13:10', 'HLA-DRB1*13:100', 'HLA-DRB1*13:101', 'HLA-DRB1*13:11', 'HLA-DRB1*13:12', +'HLA-DRB1*13:13', 'HLA-DRB1*13:14', 'HLA-DRB1*13:15', 'HLA-DRB1*13:16', 'HLA-DRB1*13:17', +'HLA-DRB1*13:18', 'HLA-DRB1*13:19', 'HLA-DRB1*13:20', 'HLA-DRB1*13:21', 'HLA-DRB1*13:22', +'HLA-DRB1*13:23', 'HLA-DRB1*13:24', 'HLA-DRB1*13:26', 'HLA-DRB1*13:27', 'HLA-DRB1*13:29', +'HLA-DRB1*13:30', 'HLA-DRB1*13:31', 'HLA-DRB1*13:32', 'HLA-DRB1*13:33', 'HLA-DRB1*13:34', +'HLA-DRB1*13:35', 'HLA-DRB1*13:36', 'HLA-DRB1*13:37', 'HLA-DRB1*13:38', 'HLA-DRB1*13:39', +'HLA-DRB1*13:41', 'HLA-DRB1*13:42', 'HLA-DRB1*13:43', 'HLA-DRB1*13:44', 'HLA-DRB1*13:46', +'HLA-DRB1*13:47', 'HLA-DRB1*13:48', 'HLA-DRB1*13:49', 'HLA-DRB1*13:50', 'HLA-DRB1*13:51', +'HLA-DRB1*13:52', 'HLA-DRB1*13:53', 'HLA-DRB1*13:54', 'HLA-DRB1*13:55', 'HLA-DRB1*13:56', +'HLA-DRB1*13:57', 'HLA-DRB1*13:58', 'HLA-DRB1*13:59', 'HLA-DRB1*13:60', 'HLA-DRB1*13:61', +'HLA-DRB1*13:62', 'HLA-DRB1*13:63', 'HLA-DRB1*13:64', 'HLA-DRB1*13:65', 'HLA-DRB1*13:66', +'HLA-DRB1*13:67', 'HLA-DRB1*13:68', 'HLA-DRB1*13:69', 'HLA-DRB1*13:70', 'HLA-DRB1*13:71', +'HLA-DRB1*13:72', 'HLA-DRB1*13:73', 'HLA-DRB1*13:74', 'HLA-DRB1*13:75', 'HLA-DRB1*13:76', +'HLA-DRB1*13:77', 'HLA-DRB1*13:78', 'HLA-DRB1*13:79', 'HLA-DRB1*13:80', 'HLA-DRB1*13:81', +'HLA-DRB1*13:82', 'HLA-DRB1*13:83', 'HLA-DRB1*13:84', 'HLA-DRB1*13:85', 'HLA-DRB1*13:86', +'HLA-DRB1*13:87', 'HLA-DRB1*13:88', 'HLA-DRB1*13:89', 'HLA-DRB1*13:90', 'HLA-DRB1*13:91', +'HLA-DRB1*13:92', 'HLA-DRB1*13:93', 'HLA-DRB1*13:94', 'HLA-DRB1*13:95', 'HLA-DRB1*13:96', +'HLA-DRB1*13:97', 'HLA-DRB1*13:98', 'HLA-DRB1*13:99', 'HLA-DRB1*14:01', 'HLA-DRB1*14:02', +'HLA-DRB1*14:03', 'HLA-DRB1*14:04', 'HLA-DRB1*14:05', 'HLA-DRB1*14:06', 'HLA-DRB1*14:07', +'HLA-DRB1*14:08', 'HLA-DRB1*14:09', 'HLA-DRB1*14:10', 'HLA-DRB1*14:11', 'HLA-DRB1*14:12', +'HLA-DRB1*14:13', 'HLA-DRB1*14:14', 'HLA-DRB1*14:15', 'HLA-DRB1*14:16', 'HLA-DRB1*14:17', +'HLA-DRB1*14:18', 'HLA-DRB1*14:19', 'HLA-DRB1*14:20', 'HLA-DRB1*14:21', 'HLA-DRB1*14:22', 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'HLA-DQA1*06:02-DQB1*06:42', 'HLA-DQA1*06:02-DQB1*06:43', 'HLA-DQA1*06:02-DQB1*06:44', +'H-2-Iab', 'H-2-Iad', 'H-2-Iak', 'H-2-Iaq', 'H-2-Ias', +'H-2-Iau', 'H-2-Iad', 'H-2-Iak']) + + __version = "4.0" + + @property + def version(self): + """The version of the predictor""" + return self.__version + + @property + def command(self): + """ + Defines the commandline call for external tool + """ + return self.__command + + @property + def supportedLength(self): + """ + A list of supported :class:`~epytope.Core.Peptide.Peptide` lengths + """ + return self.__supported_length + + @property + def supportedAlleles(self): + """A list of valid :class:`~epytope.Core.Allele.Allele` models""" + return self.__alleles + + @property + def name(self): + """The name of the predictor""" + return self.__name + + def parse_external_result(self, file): + """ + Parses external results and returns the result containing the predictors string representation + of alleles and peptides. + + :param str file: The file path or the external prediction results + :return: A dictionary containing the prediction results + :rtype: dict + """ + f = csv.reader(open(file, "r"), delimiter='\t') + scores = defaultdict(defaultdict) + ranks = defaultdict(defaultdict) + alleles = [x for x in set([x for x in next(f) if x != ""])] + next(f) + for row in f: + pep_seq = row[PeptideIndex.NETMHCIIPAN_4_0] + for i, a in enumerate(alleles): + scores[a][pep_seq] = float(row[ScoreIndex.NETMHCIIPAN_4_0 + i * Offset.NETMHCIIPAN_4_0]) + ranks[a][pep_seq] = float(row[RankIndex.NETMHCIIPAN_4_0 + i * Offset.NETMHCIIPAN_4_0]) + # Create dictionary with hierarchy: {'Allele1': {'Score': {'Pep1': Score1, 'Pep2': Score2,..}, 'Rank': {'Pep1': RankScore1, 'Pep2': RankScore2,..}}, 'Allele2':...} + result = {allele: {metric:(list(scores.values())[j] if metric == "Score" else list(ranks.values())[j]) for metric in ["Score", "Rank"]} for j, allele in enumerate(alleles)} + + return result class PickPocket_1_1(AExternalEpitopePrediction): """ @@ -6525,7 +7864,8 @@ def convert_alleles(self, alleles): def parse_external_result(self, file): """ - Parses external results and returns the result + Parses external results and returns the result containing the predictors string representation + of alleles and peptides. :param str file: The file path or the external prediction results :return: A dictionary containing the prediction results @@ -6538,9 +7878,12 @@ def parse_external_result(self, file): if row[0] in ["#", "-"] or row.strip() == "" or "pos" in row: continue else: - allele, pep, score = Allele(row.split()[HLAIndex.PICKPOCKET_1_1]), Peptide(row.split()[PeptideIndex.PICKPOCKET_1_1]), float(row.split()[ScoreIndex.PICKPOCKET_1_1]) + allele = row.split()[HLAIndex.PICKPOCKET_1_1].replace('*','') + pep = row.split()[PeptideIndex.PICKPOCKET_1_1] + score = float(row.split()[ScoreIndex.PICKPOCKET_1_1]) if allele not in alleles: alleles.append(allele) + scores[allele][pep] = score result = {allele: {"Score": list(scores.values())[j]} for j, allele in enumerate(alleles)} @@ -6982,7 +8325,8 @@ def supportedLength(self): def parse_external_result(self, file): """ - Parses external results and returns the result + Parses external results and returns the result containing the predictors string representation + of alleles and peptides. :param str file: The file path or the external prediction results :return: A dictionary containing the prediction results @@ -6998,7 +8342,10 @@ def parse_external_result(self, file): if not row[0].isdigit(): continue - epitope, allele, comb_score = Peptide(row[PeptideIndex.NETCTLPAN_1_1]), Allele(row[HLAIndex.NETCTLPAN_1_1]), float(row[ScoreIndex.NETCTLPAN_1_1]) + epitope = row[PeptideIndex.NETCTLPAN_1_1] + # Allele input representation differs from output representation. Needs to be in input representation to parse the output properly + allele = row[HLAIndex.NETCTLPAN_1_1].replace('*','') + comb_score = float(row[ScoreIndex.NETCTLPAN_1_1]) if allele not in alleles: alleles.append(allele) @@ -7049,8 +8396,10 @@ class PeptideIndex(IntEnum): NETMHCPAN_4_0 = 1 NETMHCSTABPAN_1_0 = 1 NETMHCII_2_2 = 2 + NETMHCII_2_3 = 2 NETMHCIIPAN_3_0 = 1 NETMHCIIPAN_3_1 = 1 + NETMHCIIPAN_4_0 = 1 PICKPOCKET_1_1 = 2 NETCTLPAN_1_1 = 3 @@ -7066,8 +8415,10 @@ class ScoreIndex(IntEnum): NETMHCPAN_4_0 = 5 NETMHCSTABPAN_1_0 = 6 NETMHCII_2_2 = 4 + NETMHCII_2_3 = 5 NETMHCIIPAN_3_0 = 3 NETMHCIIPAN_3_1 = 3 + NETMHCIIPAN_4_0 = 3 PICKPOCKET_1_1 = 4 NETCTLPAN_1_1 = 7 @@ -7079,8 +8430,10 @@ class RankIndex(IntEnum): NETMHCPAN_3_0 = 6 NETMHCPAN_4_0 = 7 NETMHCSTABPAN_1_0 = 5 + NETMHCII_2_3 = 7 NETMHCIIPAN_3_0 = 5 NETMHCIIPAN_3_1 = 5 + NETMHCIIPAN_4_0 = 5 class Offset(IntEnum): """ @@ -7094,11 +8447,14 @@ class Offset(IntEnum): NETMHCSTABPAN_1_0_W_SCORE = 8 NETMHCSTABPAN_1_0_WO_SCORE = 3 NETMHCIIPAN_3_0 = 3 + NETMHCIIPAN_3_1 = 3 + NETMHCIIPAN_4_0 = 1 class HLAIndex(IntEnum): """ Specifies the HLA-allele index in the parsed output of the predictor """ NETMHCII_2_2 = 0 + NETMHCII_2_3 = 0 PICKPOCKET_1_1 = 1 NETCTLPAN_1_1 = 2 From 028fc31ab9d9927af61ef0bf5560cbbb7f7c4244 Mon Sep 17 00:00:00 2001 From: Christopher Mohr Date: Wed, 5 Jan 2022 12:58:19 +0100 Subject: [PATCH 12/25] Improve/update documentation (#50) * Update CHANGELOG * Extend README * Change framework name in code comment --- CHANGELOG.md | 35 +++++++++++++------- README.md | 80 +++++++++++++++++++++++++++++++-------------- epytope/IO/Utils.py | 2 +- 3 files changed, 79 insertions(+), 38 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4e064037..187ad3f9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,20 +5,31 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## v3.0.0dev - [date] -Initial release of epytope. Epytope is the successor project of FRED-2, which was renamed to a more versioning friendly base name. +Initial release of `epytope`. `epytope` is the successor project of `FRED-2`, which was renamed to a more versioning friendly base name. ### `Added` -- [#1](https://github.com/KohlbacherLab/epytope/pull/1) - Switch CI/CD from Travis to GitHub Actions - [#6](https://github.com/KohlbacherLab/epytope/pull/6) - Add CI for external tools -- [#9](https://github.com/KohlbacherLab/epytope/pull/9) - Initial Python 2 to Python 3 conversion based on 2to3conv -- [#11](https://github.com/KohlbacherLab/epytope/pull/11) - Fix python version matrix in CI, remove versions that fail -- [#16](https://github.com/KohlbacherLab/epytope/pull/16) - Fix epitope prediction 2to3 bugs and tests -- [#17](https://github.com/KohlbacherLab/epytope/pull/17) - Fix Invalid subprocess handling and mhcflurry polluting stdout -- [#18](https://github.com/KohlbacherLab/epytope/pull/18) - Fix external (NetMHC tool family) epitope prediction error and tempfile handling -- [#20](https://github.com/KohlbacherLab/epytope/pull/20) - Use logging module rather than print calls across the library -- [#23](https://github.com/KohlbacherLab/epytope/pull/23) - Rename the package from FRED-2 to epytope -- [#24](https://github.com/KohlbacherLab/epytope/pull/24) - Add keras dependency -- [#25](https://github.com/KohlbacherLab/epytope/pull/25) - Refactor CI to use more pip and less conda +- [#24](https://github.com/KohlbacherLab/epytope/pull/24) - Add `keras` dependency - [#26](https://github.com/KohlbacherLab/epytope/pull/26) - Add a license file -- [#31](https://github.com/KohlbacherLab/epytope/pull/31) - Add deployment to PyPI +- [#31](https://github.com/KohlbacherLab/epytope/pull/31) - Add deployment to `PyPI` +- [#42](https://github.com/KohlbacherLab/epytope/pull/42) - Add new `Syfpeithi` matrices +- [#46](https://github.com/KohlbacherLab/epytope/pull/46) - Add support for `NetMHCII 2.3` and `NetMHCIIpan 4.0` + +### `Changed` + +- [#1](https://github.com/KohlbacherLab/epytope/pull/1) - Switch CI/CD from Travis to GitHub Actions +- [#9](https://github.com/KohlbacherLab/epytope/pull/9) - Initial `Python 2` to `Python 3` conversion based on 2to3conv +- [#20](https://github.com/KohlbacherLab/epytope/pull/20) - Use logging module rather than print calls across the library +- [#23](https://github.com/KohlbacherLab/epytope/pull/23) - Rename the package from `FRED-2` to `epytope` +- [#25](https://github.com/KohlbacherLab/epytope/pull/25) - Refactor CI to use more `pip` and less `conda` +- [#42](https://github.com/KohlbacherLab/epytope/pull/42) - Extend `EpitopePredictionResult` structure to store `rank`-based scores + +### `Fixed` + +- [#11](https://github.com/KohlbacherLab/epytope/pull/11) - Fix `Python` version matrix in CI, remove versions that fail +- [#16](https://github.com/KohlbacherLab/epytope/pull/16) - Fix epitope prediction 2to3 bugs and tests +- [#17](https://github.com/KohlbacherLab/epytope/pull/17) - Fix Invalid subprocess handling and `mhcflurry` polluting stdout +- [#18](https://github.com/KohlbacherLab/epytope/pull/18) - Fix external (`NetMHC` tool family) epitope prediction error and temp file handling +- [#46](https://github.com/KohlbacherLab/epytope/pull/46) - Fix issues with MHC class-II `CombinedAlleles` [#45](https://github.com/KohlbacherLab/epytope/issues/45) +- [#46](https://github.com/KohlbacherLab/epytope/pull/46) - Do not override `Allele` objects [#38](https://github.com/KohlbacherLab/epytope/issues/38) diff --git a/README.md b/README.md index 77c2ade9..3172b4fe 100644 --- a/README.md +++ b/README.md @@ -1,28 +1,29 @@ +# epytope - An Immunoinformatics Framework for Python + +![PyPi](https://github.com/KohlbacherLab/epytope/actions/workflows/pypi-publish.yml/badge.svg) +![Tests](https://github.com/KohlbacherLab/epytope/actions/workflows/python-test-conda.yml/badge.svg) +![Tests external](https://github.com/KohlbacherLab/epytope/actions/workflows/python-test-conda-external.yml/badge.svg) +[![License](https://img.shields.io/badge/License-BSD_3--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause) [![Anaconda-Server Badge](https://anaconda.org/bioconda/fred2/badges/installer/conda.svg)](https://conda.anaconda.org/bioconda) -epytope - An Immunoinformatics Framework for Python ---------------------------------------------------- Copyright 2014 by Benjamin Schuber, Mathias Walzer, Philipp Brachvogel, Andras Szolek, Christopher Mohr, and Oliver Kohlbacher +**epytope** is a framework for T-cell epitope detection, and vaccine design. It offers consistent, easy, and simultaneous access to well established prediction methods of computational immunology. **epytope** can handle polymorphic proteins and offers analysis tools to select, assemble, and design linker sequences for string-of-beads epitope-based vaccines. It is implemented in Python in a modular way and can easily be extended by user defined methods. -Epytope is a framework for T-cell epitope detection, and vaccine design. It offers consistent, easy, and simultaneous access to well established prediction methods of computational immunology. Epytope can handle polymorphic proteins and offers analysis tools to select, assemble, and design linker sequences for string-of-beads epitope-based vaccines. It is implemented in Python in a modular way and can easily be extended by user defined methods. - +## Copyright -Copyright ----------- epytope is released under the three clause BSD licence. -Installation ------------- +## Installation use the following commands: - $ pip install git+https://github.com/KohlbacherLab/epytope + pip install git+https://github.com/KohlbacherLab/epytope + +## Dependencies -Dependencies ------------- +### Python Packages -**Python Packages** - pandas - pyomo>=4.0 - svmlight @@ -30,22 +31,51 @@ Dependencies - Biopython - pyVCF -**Third-Party Software (not installed through pip)** - - NetMHC predictor family (NetMHC(pan)-(I/II), NetChop, NetCTL) (http://www.cbs.dtu.dk/services/software.php) - - PickPocket (http://www.cbs.dtu.dk/services/software.php) - - Integer Linear Programming Solver (recommended CBC: https://projects.coin-or.org/Cbc) +### Third-Party Software (not installed through pip) -Please pay attention to the different licensing of third party tools. - -Getting Started ---------------- +- NetMHC predictor family (NetMHC(pan)-(I/II), NetChop, NetCTL) () +- PickPocket () +- Integer Linear Programming Solver (recommended CBC: ) -Users and developers should start by reading our [wiki](https://github.com/KohlbacherLab/epytope/wiki) and [IPython tutorials](https://github.com/KohlbacherLab/epytope/tree/master/epytope/tutorials). -A reference documentation is also available [online](http://fred2.readthedocs.org/en/latest/). +Please pay attention to the different licensing of third party tools. -How to Cite ------------ -Please cite: +## Framework summary + +Currently **epytope** provides implementations of several prediction methods or interfaces to external prediction tools. + +- Cleavage Prediction + - Proteasomal cleavage matrix-based prediction by [Dönnes et al.](https://pubmed.ncbi.nlm.nih.gov/15987883/) + - ProteaSMM by [Tenzer et al.](https://pubmed.ncbi.nlm.nih.gov/15868101/) + - [NetChop](https://pubmed.ncbi.nlm.nih.gov/15744535/) 3.1 +- Epitope Assembly + - Approach by [Toussaint et al.](https://pubmed.ncbi.nlm.nih.gov/21875632/) + - Bi-objective extension of approach by [Toussaint et al.](https://pubmed.ncbi.nlm.nih.gov/21875632/) + - Assembly with spacers by [Schubert et al.](https://pubmed.ncbi.nlm.nih.gov/26813686/) +- Epitope Prediction + - [SYFPEITHI](https://link.springer.com/article/10.1007/s002510050595) + - [MHCNuggets](https://pubmed.ncbi.nlm.nih.gov/31871119/) 2.0, 2.3.2 + - [MHCflurry](https://pubmed.ncbi.nlm.nih.gov/29960884/) 1.2.2, 1.4.3 + - [NetMHC](https://pubmed.ncbi.nlm.nih.gov/26515819/) 3.0, 3.4, 4.0 + - [NetMHCII](https://pubmed.ncbi.nlm.nih.gov/29315598/) 2.2, 2.3 + - [NetMHCpan](https://pubmed.ncbi.nlm.nih.gov/28978689/) 2.4, 2.8, 3.0, 4.0 + - [NetMHCIIpan](https://pubmed.ncbi.nlm.nih.gov/32406916/) 3.0, 3.1, 4.0 + - [PickPocket](https://pubmed.ncbi.nlm.nih.gov/19297351/) 1.1 + - [NetCTLpan](https://pubmed.ncbi.nlm.nih.gov/20379710/) 1.1 +- Epitope Selection + - [OptiTope](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703925/) +- Stability Prediction + - [NetMHCstabpan](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4976001/) 1.0 +- TAPP Prediction + - TAP prediction model by [Doytchinova et al.](https://pubmed.ncbi.nlm.nih.gov/15557175/) + - [SMMTAP](https://pubmed.ncbi.nlm.nih.gov/12902473/) + +## Getting Started + +Users and developers should start by reading our [wiki](https://github.com/KohlbacherLab/epytope/wiki) and [IPython tutorials](https://github.com/KohlbacherLab/epytope/tree/master/epytope/tutorials). A reference documentation is also available [online](http://fred2.readthedocs.org/en/latest/). + +## How to Cite + +Please cite [Schubert, B., Walzer, M., Brachvogel, H-P., Sozolek, A., Mohr, C., and Kohlbacher, O. (2016). FRED 2 - An Immunoinformatics Framework for Python. Bioinformatics 2016; doi: 10.1093/bioinformatics/btw113](http://bioinformatics.oxfordjournals.org/content/early/2016/02/26/bioinformatics.btw113.short?rss=1) diff --git a/epytope/IO/Utils.py b/epytope/IO/Utils.py index 15d30fd5..81fd0ccb 100644 --- a/epytope/IO/Utils.py +++ b/epytope/IO/Utils.py @@ -1,4 +1,4 @@ -# This code is part of the Fred2 distribution and governed by its +# This code is part of the epytope distribution and governed by its # license. Please see the LICENSE file that should have been included # as part of this package. """ From 0b6e75de4991a5c909333d9cf266dccce6727953 Mon Sep 17 00:00:00 2001 From: Christopher Mohr Date: Mon, 17 Jan 2022 08:26:40 +0100 Subject: [PATCH 13/25] Remove logging warning --- epytope/EpitopeAssembly/EpitopeAssembly.py | 1 - 1 file changed, 1 deletion(-) diff --git a/epytope/EpitopeAssembly/EpitopeAssembly.py b/epytope/EpitopeAssembly/EpitopeAssembly.py index 8aa9be94..d0239d4b 100644 --- a/epytope/EpitopeAssembly/EpitopeAssembly.py +++ b/epytope/EpitopeAssembly/EpitopeAssembly.py @@ -353,7 +353,6 @@ def __init__(self, peptides, cl_pred, ep_pred, alleles, threshold, comparator, l for index,row in epi_pred.iterrows(): nof_epis = int(sum(comparator(row[a],threshold.get(a.name, 0)) for a in _alleles)) - logging.warning(index.proteins.values()) for protein in index.proteins.values(): start, stop = fragments[protein] ep_edge_matrix[start,stop] += len(index.proteinPos[protein.transcript_id])*nof_epis From 46927ada22e76e8ee69cfdaebd0de30211ef0fae Mon Sep 17 00:00:00 2001 From: Christopher Mohr Date: Mon, 17 Jan 2022 08:31:15 +0100 Subject: [PATCH 14/25] Change file ending in tutorial --- epytope/tutorials/EpitopePrediction.ipynb | 6 +++--- epytope/tutorials/data/{test.csv => test.tsv} | 0 2 files changed, 3 insertions(+), 3 deletions(-) rename epytope/tutorials/data/{test.csv => test.tsv} (100%) diff --git a/epytope/tutorials/EpitopePrediction.ipynb b/epytope/tutorials/EpitopePrediction.ipynb index 7c302b28..fb174c82 100644 --- a/epytope/tutorials/EpitopePrediction.ipynb +++ b/epytope/tutorials/EpitopePrediction.ipynb @@ -564,7 +564,7 @@ "
\n", "The predictor all return a data table like object (DataFrame) storing the peptide and allele objects, as well as the predicted results. Because it is a inherited pandas DataFrame we can do all sorts of nifty thinks. \n", "\n", - "For example exporting the results to csv:" + "For example exporting the results to tsv:" ] }, { @@ -573,7 +573,7 @@ "metadata": {}, "outputs": [], "source": [ - "results.to_csv('./data/test.csv', sep='\\t')" + "results.to_csv('./data/test.tsv', sep='\\t')" ] }, { @@ -602,7 +602,7 @@ }, { "data": { - "image/png": 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\n", 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", 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" ] diff --git a/epytope/tutorials/data/test.csv b/epytope/tutorials/data/test.tsv similarity index 100% rename from epytope/tutorials/data/test.csv rename to epytope/tutorials/data/test.tsv From 480ebcfa44c1ed3dbccbd345a2a2958b34ebaf9f Mon Sep 17 00:00:00 2001 From: Christopher Mohr Date: Mon, 24 Jan 2022 08:53:19 +0100 Subject: [PATCH 15/25] Add docstrings, minor formatting --- epytope/Core/Result.py | 18 ++++++++++++------ 1 file changed, 12 insertions(+), 6 deletions(-) diff --git a/epytope/Core/Result.py b/epytope/Core/Result.py index 4b738438..eabb271c 100644 --- a/epytope/Core/Result.py +++ b/epytope/Core/Result.py @@ -33,7 +33,7 @@ def filter_result(self, expressions): """ Filter result based on a list of expressions - :param list((str,comparator,float)) expressions: A list of triples consisting of (method_name, comparator,threshold) + :param list((str, comparator, float)) expressions: A list of triples consisting of (method_name, comparator, threshold) :return: A new filtered AResult object :rtype: :class:`~epytope.Core.Result.AResult` """ @@ -83,7 +83,7 @@ def filter_result(self, expressions, scoretype='Score'): (method_name, comparator, threshold) and a str of the methods scoretype to be filtered. The expression is applied to each row. If any of the columns fulfill the criteria the row remains. - :param list((str,comparator,float)) expression: A list of triples consisting of (method_name, comparator, threshold) + :param list((str, comparator, float)) expressions: A list of triples consisting of (method_name, comparator, threshold) :param str scoretype: Indicates which scoretype of the specified method should be filtered :return: Filtered result object @@ -136,7 +136,13 @@ def merge_results(self, others): def from_dict(d, peps, method): """ - Create EpitopePredictionResult object from dictionary holding scores for alleles, peptides and a specified method + Create :class:`~epytope.Core.Result.EpitopePredictionResult` object from dictionary holding scores for alleles, peptides and a specified method + + :param d: dict with following structure: {allele: {scoretype: {peptide: score}}} + :param peps: list of :class:`~epytope.Core.Peptide.Peptide` + :param method: str specifying the prediction method + :return: A new :class:`~epytope.Core.Result.EpitopePredictionResult` object + :rtype: :class:`~epytope.Core.Result.EpitopePredictionResult` """ scoreType = numpy.asarray([list(m.keys()) for m in [metrics for a, metrics in d.items()]]).flatten() alleles = numpy.asarray([numpy.repeat(a, len(set(scoreType))) for a in d]).flatten() @@ -198,7 +204,7 @@ def filter_result(self, expressions): of a list of triple with (method_name, comparator, threshold). The expression is applied to each row. If any of the columns fulfill the criteria the row remains. - :param list((str,comparator,float)) expressions: A list of triples consisting of (method_name, comparator, + :param list((str, comparator, float)) expressions: A list of triples consisting of (method_name, comparator, threshold) :return: A new filtered result object :rtype: :class:`~epytope.Core.Result.CleavageSitePredictionResult` @@ -291,7 +297,7 @@ def filter_result(self, expressions): (method_name, comparator, threshold). The expression is applied to each row. If any of the columns fulfill the criteria the row remains. - :param list((str,comparator,float)) expressions: A list of triples consisting of (method_name, comparator, + :param list((str, comparator, float)) expressions: A list of triples consisting of (method_name, comparator, threshold) :return: A new filtered result object :rtype: :class:`~epytope.Core.Result.CleavageFragmentPredictionResult` @@ -349,7 +355,7 @@ def filter_result(self, expressions): of a list of triple with (method_name, comparator, threshold). The expression is applied to each row. If any of the columns fulfill the criteria the row remains. - :param list((str,comparator,float)) expressions: A list of triples consisting of (method_name, comparator, + :param list((str, comparator, float)) expressions: A list of triples consisting of (method_name, comparator, threshold) :return: A new filtered result object :rtype: :class:`~epytope.Core.Result.TAPPredictionResult` From 1fa8b117698a73474b0cfd36d1b8659c864480e9 Mon Sep 17 00:00:00 2001 From: Christopher Mohr Date: Wed, 26 Jan 2022 16:30:41 +0100 Subject: [PATCH 16/25] Update CHANGELOG version and setup.py --- CHANGELOG.md | 2 +- setup.py | 14 +++++++++----- 2 files changed, 10 insertions(+), 6 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 187ad3f9..b6b1a7a3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v3.0.0dev - [date] +## v3.0.0 - 2022-01-24 Initial release of `epytope`. `epytope` is the successor project of `FRED-2`, which was renamed to a more versioning friendly base name. diff --git a/setup.py b/setup.py index ec07b34f..1aa49bed 100644 --- a/setup.py +++ b/setup.py @@ -45,7 +45,7 @@ name='epytope', # Version: - version='3.0.0rc1', + version='3.0.0', description='A Framework for Epitope Detection and Vaccine Design', long_description=long_description, @@ -55,8 +55,12 @@ url='https://github.com/KohlbacherLab/epytope', # Author details - author='Benjamin Schubert, Mathias Walzer', - author_email='schubert@informatik.uni-tuebingen.de, walzer@informatik.uni-tuebingen.de', + author='Benjamin Schubert, Mathias Walzer, Christopher Mohr, Leon Kuchenbecker', + author_email='benjamin.schubert@helmholtz-muenchen.de, walzer@ebi.ac.uk, christopher.mohr@uni-tuebingen.de, leon.kuchenbecker@uni-tuebingen.de ', + + # maintainer details + maintainer='Christopher Mohr', + maintainer_email='christopher.mohr@uni-tuebingen.de', # Choose your license license='BSD', @@ -67,7 +71,7 @@ # 3 - Alpha # 4 - Beta # 5 - Production/Stable - 'Development Status :: 4 - Beta', + 'Development Status :: 5 - Production/Stable', # Indicate who your project is intended for 'Intended Audience :: Science/Research', @@ -80,7 +84,7 @@ ], # What epytope relates to: - keywords='epitope prediction MHC vaccine', + keywords='epitope prediction vaccine design HLA MHC', # Specify packages via find_packages() and exclude the tests and # documentation: From 5bd74a8a9bafb659df2e5a95b5228a3bc8d766a7 Mon Sep 17 00:00:00 2001 From: Christopher Mohr Date: Wed, 26 Jan 2022 16:39:21 +0100 Subject: [PATCH 17/25] Update date --- CHANGELOG.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index b6b1a7a3..8e930f17 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,9 +3,9 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v3.0.0 - 2022-01-24 +## v3.0.0 - 2022-01-26 -Initial release of `epytope`. `epytope` is the successor project of `FRED-2`, which was renamed to a more versioning friendly base name. +Initial release of `epytope`. `epytope` is the successor project of [`FRED2`](https://github.com/FRED-2/Fred2), which was renamed to a more versioning friendly base name. ### `Added` From 070f664267f5bda936e7e12d792f9301123cbdd2 Mon Sep 17 00:00:00 2001 From: Jonas Scheid <43858870+jonasscheid@users.noreply.github.com> Date: Tue, 15 Mar 2022 10:00:22 +0100 Subject: [PATCH 18/25] Fix #52 (#53) --- epytope/EpitopePrediction/ANN.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/epytope/EpitopePrediction/ANN.py b/epytope/EpitopePrediction/ANN.py index b3b7ba1e..cc8e4030 100644 --- a/epytope/EpitopePrediction/ANN.py +++ b/epytope/EpitopePrediction/ANN.py @@ -249,7 +249,7 @@ def predict(self, peptides, alleles=None, binary=False, **kwargs): # create EpitopePredictionResult object. This is a multi-indexed DataFrame # with Allele, Method and Score type as multi-columns and peptides as rows - df_result = EpitopePredictionResult.from_dict(result, pep_groups, self.name) + df_result = EpitopePredictionResult.from_dict(result, peptide_objects.values(), self.name) return df_result @@ -534,7 +534,7 @@ def predict(self, peptides, alleles=None, binary=False, **kwargs): # create EpitopePredictionResult object. This is a multi-indexed DataFrame # with Allele, Method and Score type as multi-columns and peptides as rows - df_result = EpitopePredictionResult.from_dict(result, pep_groups, self.name) + df_result = EpitopePredictionResult.from_dict(result, peptide_objects.values(), self.name) return df_result except BadSignatureException: @@ -804,7 +804,7 @@ def predict(self, peptides, alleles=None, binary=False, **kwargs): # create EpitopePredictionResult object. This is a multi-indexed DataFrame # with Allele, Method and Score type as multi-columns and peptides as rows - df_result = EpitopePredictionResult.from_dict(result, pep_groups, self.name) + df_result = EpitopePredictionResult.from_dict(result, peptide_objects.values(), self.name) return df_result except BadSignatureException: From 26edb0413b9e1e069e86a8b47f6e6958fd2e5ace Mon Sep 17 00:00:00 2001 From: Christopher Mohr Date: Wed, 25 May 2022 08:58:11 +0200 Subject: [PATCH 19/25] add check if transcript sequence available from BioMart, cleanup (#58) --- epytope/Core/Generator.py | 5 +++-- epytope/IO/MartsAdapter.py | 13 +++++++------ 2 files changed, 10 insertions(+), 8 deletions(-) diff --git a/epytope/Core/Generator.py b/epytope/Core/Generator.py index 0fd83850..64549b74 100644 --- a/epytope/Core/Generator.py +++ b/epytope/Core/Generator.py @@ -12,6 +12,7 @@ """ +import logging import warnings from itertools import chain @@ -243,7 +244,7 @@ def _generate_combinations(tId, vs, seq, usedVs, offset, isReverse): #print tId query = dbadapter.get_transcript_information(tId, type=id_type, _db=db) if query is None: - warnings.warn("Transcript with ID %s not found in DB"%tId) + logging.warning("Transcript with ID %s not found in DB or sequence unavailable"%tId) continue tSeq = query[EAdapterFields.SEQ] @@ -349,7 +350,7 @@ def _generate_combinations(tId, vs, seq, usedVs, offset, isReverse=False): for tId, vs in transToVar.items(): query = dbadapter.get_transcript_information(tId, type=id_type, _db=db) if query is None: - warnings.warn("Transcript with ID %s not found in DB"%tId) + logging.warning("Transcript with ID %s not found in DB or sequence unavailable"%tId) continue tSeq = query[EAdapterFields.SEQ] diff --git a/epytope/IO/MartsAdapter.py b/epytope/IO/MartsAdapter.py index 47e34390..4f9f7969 100755 --- a/epytope/IO/MartsAdapter.py +++ b/epytope/IO/MartsAdapter.py @@ -100,13 +100,11 @@ def get_product_sequence(self, product_id, **kwargs): + self.biomart_attribute%("external_gene_name") \ + self.biomart_tail - # logging.warn(rq_n) tsvreader = csv.DictReader((urllib.request.urlopen(self.biomart_url + urllib.parse.quote(rq_n))).read().decode('utf-8').splitlines(), dialect='excel-tab') tsvselect = [x for x in tsvreader] if not tsvselect: logging.warning("There seems to be no Proteinsequence for " + str(product_id)) - #print self.biomart_url+rq_n return None self.sequence_proxy[product_id] = tsvselect[0]["Peptide"][:-1] if tsvselect[0]["Peptide"].endswith('*')\ else tsvselect[0]["Peptide"] @@ -157,8 +155,10 @@ def get_transcript_sequence(self, transcript_id, **kwargs): urllib.parse.quote(rq_n))).read().decode('utf-8').splitlines(), dialect='excel-tab') tsvselect = [x for x in tsvreader] if not tsvselect: - logging.warning("There seems to be no transcript sequence for " + str(transcript_id)) - #print self.biomart_url+rq_n + logging.warning("No transcript sequence available for " + str(transcript_id)) + return None + elif 'Sequence unavailable' in tsvselect[0]['Coding sequence']: + logging.warning("No transcript sequence available for " + str(transcript_id)) return None self.sequence_proxy[transcript_id] = tsvselect[0]['Coding sequence'] @@ -210,6 +210,9 @@ def get_transcript_information(self, transcript_id, **kwargs): if not tsvselect: logging.warning("No Information on transcript %s"%transcript_id) return None + elif 'Sequence unavailable' in tsvselect[0]['Coding sequence']: + logging.warning("No transcript sequence available for " + str(transcript_id)) + return None self.ids_proxy[transcript_id] = {EAdapterFields.SEQ: tsvselect[0]['Coding sequence'], EAdapterFields.GENE: tsvselect[0].get('Associated Gene Name', ""), @@ -596,8 +599,6 @@ def get_variant_ids(self, **kwargs): + self.biomart_attribute%("refseq_peptide") rq_n += self.biomart_attribute%("uniprot_swissprot") + self.biomart_tail - # logging.warning(rq_n) - tsvreader = csv.DictReader((urllib.request.urlopen(self.biomart_url + urllib.parse.quote(rq_n)).read()).decode('utf-8').splitlines(), dialect='excel-tab') if ensemble_only: From 34fe63be0ce65cccf2e0c7f07d1ccf388e4469bb Mon Sep 17 00:00:00 2001 From: Christopher Mohr Date: Wed, 25 May 2022 10:10:20 +0200 Subject: [PATCH 20/25] Add interface for netMHCpan 4.1 (#59) * add interface for netmhcpan 4.1 * remove duplicate alleles from list --- epytope/EpitopePrediction/External.py | 46 ++++++++++++++++++++++++++- 1 file changed, 45 insertions(+), 1 deletion(-) diff --git a/epytope/EpitopePrediction/External.py b/epytope/EpitopePrediction/External.py index 8d93edcc..11f2f6af 100755 --- a/epytope/EpitopePrediction/External.py +++ b/epytope/EpitopePrediction/External.py @@ -1476,7 +1476,6 @@ def parse_external_result(self, file): return result - class NetMHCpan_4_0(NetMHCpan_3_0): """ Implements the NetMHC binding version 4.0 @@ -1517,6 +1516,47 @@ def parse_external_result(self, file): +class NetMHCpan_4_1(NetMHCpan_4_0): + """ + Implements the NetMHC binding version 4.1 + Supported MHC alleles currently only restricted to HLA alleles. + """ + __version = "4.1" + __command = "netMHCpan -p {peptides} -a {alleles} {options} -xls -xlsfile {out}" + @property + def version(self): + return self.__version + + @property + def command(self): + return self.__command + + __alleles = 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+ + def parse_external_result(self, file): + """ + Parses external results and returns the result containing the predictors string representation + of alleles and peptides. + + :param str file: The file path or the external prediction results + :return: A dictionary containing the prediction results + :rtype: dict + """ + f = csv.reader(open(file, "r"), delimiter = '\t') + scores = defaultdict(defaultdict) + ranks = defaultdict(defaultdict) + alleles = [x for x in next(f) if x != ""] + next(f, None) # Avoid header column, only access raw and rank scores + for row in f: + pep_seq = row[PeptideIndex.NETMHCPAN_4_1] + for i, a in enumerate(alleles): + scores[a][pep_seq] = float(row[ScoreIndex.NETMHCPAN_4_1 + i * Offset.NETMHCPAN_4_1]) + ranks[a][pep_seq] = float(row[RankIndex.NETMHCPAN_4_1 + i * Offset.NETMHCPAN_4_1]) + # Create dictionary with hierarchy: {'Allele1': {'Score': {'Pep1': Score1, 'Pep2': Score2,..}, 'Rank': {'Pep1': RankScore1, 'Pep2': RankScore2,..}}, 'Allele2':...} + result = {allele: {metric:(list(scores.values())[j] if metric == "Score" else list(ranks.values())[j]) for metric in ["Score", "Rank"]} for j, allele in enumerate(alleles)} + return result + + class NetMHCstabpan_1_0(AExternalEpitopePrediction): """ Implements a wrapper to NetMHCstabpan 1.0 @@ -8394,6 +8434,7 @@ class PeptideIndex(IntEnum): NETMHCPAN_2_8 = 1 NETMHCPAN_3_0 = 1 NETMHCPAN_4_0 = 1 + NETMHCPAN_4_1 = 1 NETMHCSTABPAN_1_0 = 1 NETMHCII_2_2 = 2 NETMHCII_2_3 = 2 @@ -8413,6 +8454,7 @@ class ScoreIndex(IntEnum): NETMHCPAN_2_8 = 3 NETMHCPAN_3_0 = 4 NETMHCPAN_4_0 = 5 + NETMHCPAN_4_1 = 5 NETMHCSTABPAN_1_0 = 6 NETMHCII_2_2 = 4 NETMHCII_2_3 = 5 @@ -8429,6 +8471,7 @@ class RankIndex(IntEnum): NETMHCPAN_2_8 = 5 NETMHCPAN_3_0 = 6 NETMHCPAN_4_0 = 7 + NETMHCPAN_4_1 = 6 NETMHCSTABPAN_1_0 = 5 NETMHCII_2_3 = 7 NETMHCIIPAN_3_0 = 5 @@ -8444,6 +8487,7 @@ class Offset(IntEnum): NETMHCPAN_2_8 = 3 NETMHCPAN_3_0 = 4 NETMHCPAN_4_0 = 5 + NETMHCPAN_4_1 = 4 NETMHCSTABPAN_1_0_W_SCORE = 8 NETMHCSTABPAN_1_0_WO_SCORE = 3 NETMHCIIPAN_3_0 = 3 From 252a65cf946862399abe2ac40d8c0ff6c8c48e06 Mon Sep 17 00:00:00 2001 From: Jonas Scheid <43858870+jonasscheid@users.noreply.github.com> Date: Fri, 27 May 2022 09:47:27 +0200 Subject: [PATCH 21/25] Update supportedAlleles of syfpeithi (#62) Co-authored-by: Christopher Mohr --- epytope/Data/pssms/syfpeithi/mat/A_0300_9.py | 1 - epytope/EpitopePrediction/PSSM.py | 8 ++------ 2 files changed, 2 insertions(+), 7 deletions(-) delete mode 100644 epytope/Data/pssms/syfpeithi/mat/A_0300_9.py diff --git a/epytope/Data/pssms/syfpeithi/mat/A_0300_9.py b/epytope/Data/pssms/syfpeithi/mat/A_0300_9.py deleted file mode 100644 index 3f3d87a3..00000000 --- a/epytope/Data/pssms/syfpeithi/mat/A_0300_9.py +++ /dev/null @@ -1 +0,0 @@ -A_0300_9 = {0: {'A': 4, 'C': 0, 'D': 4, 'E': 4, 'F': 0, 'G': 4, 'H': 0, 'I': 0, 'K': 4, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 4, 'S': 4, 'T': 4, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 1: {'A': 10, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 10, 'K': 0, 'L': 10, 'M': 10, 'N': 0, 'P': 0, 'Q': 10, 'R': 0, 'S': 10, 'T': 10, 'V': 10, 'W': 0, 'Y': 0, 'X': 0}, 2: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 3: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 4: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 5: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 6: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 7: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 0, 'G': 0, 'H': 0, 'I': 0, 'K': 0, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 0, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 0, 'X': 0}, 8: {'A': 0, 'C': 0, 'D': 0, 'E': 0, 'F': 10, 'G': 0, 'H': 10, 'I': 0, 'K': 10, 'L': 0, 'M': 0, 'N': 0, 'P': 0, 'Q': 0, 'R': 10, 'S': 0, 'T': 0, 'V': 0, 'W': 0, 'Y': 10, 'X': 0}} \ No newline at end of file diff --git a/epytope/EpitopePrediction/PSSM.py b/epytope/EpitopePrediction/PSSM.py index 24a2df11..b6a2f9be 100644 --- a/epytope/EpitopePrediction/PSSM.py +++ b/epytope/EpitopePrediction/PSSM.py @@ -114,12 +114,8 @@ class Syfpeithi(APSSMEpitopePrediction): SYFPEITHI: database for MHC ligands and peptide motifs. Immunogenetics, 50(3-4), 213-219. """ __alleles = frozenset( - ['HLA-B*15:10', 'HLA-B*41:01', 'HLA-B*37:01', 'HLA-B*27:05', 'HLA-B*38:01', 'HLA-A*02:01', 'HLA-B*47:01', - 'HLA-A*26:01', 'HLA-B*37:01', 'HLA-DRB1*11:01', 'HLA-B*50:01', 'HLA-B*07:02', 'HLA-A*68:01', 'HLA-A*24:02', - 'HLA-DRB1*15:01', 'HLA-B*15:01', 'HLA-B*45:01', 'HLA-A*11:01', 'HLA-A*03:01', 'HLA-B*40:01', 'HLA-DRB1*03:01', - 'HLA-B*39:01', 'HLA-DRB1*01:01', 'HLA-B*51:01', 'HLA-B*39:02', 'HLA-B*08:01', 'HLA-B*18:01', 'HLA-B*44:02', - 'HLA-B*49:01', 'HLA-DRB1*07:01', 'HLA-B*14:02', 'HLA-A*01:01']) - __supported_length = frozenset([8, 9, 10, 11]) + ['HLA-A*01:01','HLA-A*02:01','HLA-A*03:01','HLA-A*11:01','HLA-A*24:02','HLA-A*26:01','HLA-A*31:01','HLA-A*32:01','HLA-A*33:01','HLA-A*66:01','HLA-A*68:01','HLA-B*07:02','HLA-B*08:01','HLA-B*13:02','HLA-B*14:02','HLA-B*15:01','HLA-B*15:16','HLA-B*18:01','HLA-B*27:05','HLA-B*27:09','HLA-B*35:01','HLA-B*37:01','HLA-B*38:01','HLA-B*39:01','HLA-B*39:02','HLA-B*40:01','HLA-B*40:02','HLA-B*41:01','HLA-B*44:02','HLA-B*45:01','HLA-B*47:01','HLA-B*49:01','HLA-B*50:01','HLA-B*51:01','HLA-B*53:01','HLA-B*57:01','HLA-B*58:01','HLA-B*58:02','HLA-C*01:02','HLA-C*02:02','HLA-C*03:03','HLA-C*03:04','HLA-C*04:01','HLA-C*05:01','HLA-C*06:01','HLA-C*06:02','HLA-C*07:01','HLA-C*07:02','HLA-C*08:02','HLA-C*12:03','HLA-C*14:02','HLA-C*15:02','HLA-C*16:01','HLA-C*17:01','HLA-DRB1*01:01','HLA-DRB1*03:01','HLA-DRB1*07:01','HLA-DRB1*11:01','HLA-DRB1*15:01','HLA-G*01:01','H-2-Db','H-2-Kb','H-2-Kd','H-2-Ld']) + __supported_length = frozenset([8, 9, 10, 11, 12, 13]) __name = "syfpeithi" __version = "1.0" From 577802ef8978fe62da07cbc74c319acdba2dbbd0 Mon Sep 17 00:00:00 2001 From: Jonas Scheid <43858870+jonasscheid@users.noreply.github.com> Date: Tue, 14 Jun 2022 09:10:02 +0200 Subject: [PATCH 22/25] Fix protobuf version for tests, prepare docs for 3.1.0 release (#64) * Prepare docs for new release * minor changes/additions docs * check if fixing protobuf version resolves testing errors * check if changing github actions workflow resolves testing issue * allow lower versions of protobuf * Update epytope/doc/conf.py Co-authored-by: Gisela Gabernet Co-authored-by: Christopher Mohr Co-authored-by: Jonas Scheid Co-authored-by: Gisela Gabernet --- .github/workflows/python-test-conda-external.yml | 2 +- .github/workflows/python-test-conda.yml | 2 +- CHANGELOG.md | 15 +++++++++++++++ README.md | 6 +++--- epytope/doc/conf.py | 2 +- epytope/tutorials/GeneratorUsage.ipynb | 4 ++-- 6 files changed, 23 insertions(+), 8 deletions(-) diff --git a/.github/workflows/python-test-conda-external.yml b/.github/workflows/python-test-conda-external.yml index fbc3b89c..9d269e80 100644 --- a/.github/workflows/python-test-conda-external.yml +++ b/.github/workflows/python-test-conda-external.yml @@ -40,7 +40,7 @@ jobs: echo "PATH=$PATH" - name: Set up Python ${{ matrix.python-version }} run: | - $CONDA/bin/conda create -p /tmp/condaenv python==${{ matrix.python-version }}'.*' setuptools"==52.0" + $CONDA/bin/conda create -p /tmp/condaenv python==${{ matrix.python-version }}'.*' setuptools"==52.0" protobuf"<=3.20.1" - name: Activate conda environment run: | echo "/tmp/condaenv/bin" >> $GITHUB_PATH diff --git a/.github/workflows/python-test-conda.yml b/.github/workflows/python-test-conda.yml index cadb590d..583990d0 100644 --- a/.github/workflows/python-test-conda.yml +++ b/.github/workflows/python-test-conda.yml @@ -22,7 +22,7 @@ jobs: echo "CONDA_PKGS_DIRS=/tmp/condapkgs" >> $GITHUB_ENV - name: Set up Python ${{ matrix.python-version }} run: | - $CONDA/bin/conda create -p /tmp/condaenv python==${{ matrix.python-version }}'.*' setuptools"==52.0" + $CONDA/bin/conda create -p /tmp/condaenv python==${{ matrix.python-version }}'.*' setuptools"==52.0" protobuf"<=3.20.1" - name: Activate conda environment run: | echo "/tmp/condaenv/bin" >> $GITHUB_PATH diff --git a/CHANGELOG.md b/CHANGELOG.md index 8e930f17..489eb2c1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,21 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## v3.1.0dev - 2022-06-01 + +### `Added` + +- [#58](https://github.com/KohlbacherLab/epytope/pull/58) - Add check for `BioMart` transcript sequence availability [#55](https://github.com/KohlbacherLab/epytope/issues/55) +- [#59](https://github.com/KohlbacherLab/epytope/pull/59) - Add interface for `NetMHCpan 4.1` + +### `Changed` + +- [#62](https://github.com/KohlbacherLab/epytope/pull/62) - Update the supported alleles of `syfpeithi` [#60](https://github.com/KohlbacherLab/epytope/issues/60) + +### `Fixed` + +- [#53](https://github.com/KohlbacherLab/epytope/pull/53) - Fix `ANN` predictor results [#52](https://github.com/KohlbacherLab/epytope/issues/52) + ## v3.0.0 - 2022-01-26 Initial release of `epytope`. `epytope` is the successor project of [`FRED2`](https://github.com/FRED-2/Fred2), which was renamed to a more versioning friendly base name. diff --git a/README.md b/README.md index 3172b4fe..0a83c092 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,7 @@ ![Tests](https://github.com/KohlbacherLab/epytope/actions/workflows/python-test-conda.yml/badge.svg) ![Tests external](https://github.com/KohlbacherLab/epytope/actions/workflows/python-test-conda-external.yml/badge.svg) [![License](https://img.shields.io/badge/License-BSD_3--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause) -[![Anaconda-Server Badge](https://anaconda.org/bioconda/fred2/badges/installer/conda.svg)](https://conda.anaconda.org/bioconda) +[![Anaconda-Server Badge](https://anaconda.org/bioconda/epytope/badges/installer/conda.svg)](https://conda.anaconda.org/bioconda) Copyright 2014 by Benjamin Schuber, Mathias Walzer, Philipp Brachvogel, Andras Szolek, Christopher Mohr, and Oliver Kohlbacher @@ -57,7 +57,7 @@ Currently **epytope** provides implementations of several prediction methods or - [MHCflurry](https://pubmed.ncbi.nlm.nih.gov/29960884/) 1.2.2, 1.4.3 - [NetMHC](https://pubmed.ncbi.nlm.nih.gov/26515819/) 3.0, 3.4, 4.0 - [NetMHCII](https://pubmed.ncbi.nlm.nih.gov/29315598/) 2.2, 2.3 - - [NetMHCpan](https://pubmed.ncbi.nlm.nih.gov/28978689/) 2.4, 2.8, 3.0, 4.0 + - [NetMHCpan](https://pubmed.ncbi.nlm.nih.gov/28978689/) 2.4, 2.8, 3.0, 4.0, 4.1 - [NetMHCIIpan](https://pubmed.ncbi.nlm.nih.gov/32406916/) 3.0, 3.1, 4.0 - [PickPocket](https://pubmed.ncbi.nlm.nih.gov/19297351/) 1.1 - [NetCTLpan](https://pubmed.ncbi.nlm.nih.gov/20379710/) 1.1 @@ -71,7 +71,7 @@ Currently **epytope** provides implementations of several prediction methods or ## Getting Started -Users and developers should start by reading our [wiki](https://github.com/KohlbacherLab/epytope/wiki) and [IPython tutorials](https://github.com/KohlbacherLab/epytope/tree/master/epytope/tutorials). A reference documentation is also available [online](http://fred2.readthedocs.org/en/latest/). +Users and developers should start by reading our [wiki](https://github.com/KohlbacherLab/epytope/wiki) and [IPython tutorials](https://github.com/KohlbacherLab/epytope/tree/master/epytope/tutorials). A reference documentation is also available [online](http://epytope.readthedocs.org/en/latest/). ## How to Cite diff --git a/epytope/doc/conf.py b/epytope/doc/conf.py index a0660037..6bc3568e 100644 --- a/epytope/doc/conf.py +++ b/epytope/doc/conf.py @@ -269,7 +269,7 @@ def __getattr__(cls, name): # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). man_pages = [ - (master_doc, 'fred2', 'epytope Documentation', + (master_doc, 'epytope', 'epytope Documentation', [author], 1) ] diff --git a/epytope/tutorials/GeneratorUsage.ipynb b/epytope/tutorials/GeneratorUsage.ipynb index 21ddecf1..f8fd135f 100644 --- a/epytope/tutorials/GeneratorUsage.ipynb +++ b/epytope/tutorials/GeneratorUsage.ipynb @@ -192,7 +192,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "/Users/antonia/PycharmProjects/Kfred/epytope/Core/Generator.py:57: UserWarning: For NM_001190266 bp does not match ref of assigned variant Variant(g.234183368A>G). Pos 645, var ref A, seq ref C \n", + "epytope/Core/Generator.py:57: UserWarning: For NM_001190266 bp does not match ref of assigned variant Variant(g.234183368A>G). Pos 645, var ref A, seq ref C \n", " seq[pos]))\n" ] }, @@ -277,7 +277,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "/Users/antonia/opt/miniconda3/envs/epy/lib/python3.7/site-packages/Bio/Seq.py:2338: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future.\n", + "/opt/miniconda3/envs/epy/lib/python3.7/site-packages/Bio/Seq.py:2338: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future.\n", " BiopythonWarning,\n" ] } From 60062c19cf86709659b802c12b2680720be5d08d Mon Sep 17 00:00:00 2001 From: Jonas Scheid <43858870+jonasscheid@users.noreply.github.com> Date: Tue, 14 Jun 2022 10:18:11 +0200 Subject: [PATCH 23/25] Add netMHCIIpan 4.1 interface (#66) * add netmhciipan 4.1 interface * remove logging * remove __name method * update changelog * Update CHANGELOG.md Co-authored-by: Christopher Mohr Co-authored-by: Christopher Mohr Co-authored-by: Christopher Mohr --- CHANGELOG.md | 3 +- epytope/EpitopePrediction/External.py | 52 +++++++++++++++++++++++++-- 2 files changed, 52 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 489eb2c1..09789ebd 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,7 +8,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Added` - [#58](https://github.com/KohlbacherLab/epytope/pull/58) - Add check for `BioMart` transcript sequence availability [#55](https://github.com/KohlbacherLab/epytope/issues/55) -- [#59](https://github.com/KohlbacherLab/epytope/pull/59) - Add interface for `NetMHCpan 4.1` +- [#59](https://github.com/KohlbacherLab/epytope/pull/59) - Add interface for `NetMHCpan 4.1` [#56](https://github.com/KohlbacherLab/epytope/issues/56) +- [#66](https://github.com/KohlbacherLab/epytope/pull/66) - Add interface for `NetMHCIIpan 4.1` [#65](https://github.com/KohlbacherLab/epytope/issues/65) ### `Changed` diff --git a/epytope/EpitopePrediction/External.py b/epytope/EpitopePrediction/External.py index 11f2f6af..1049254c 100755 --- a/epytope/EpitopePrediction/External.py +++ b/epytope/EpitopePrediction/External.py @@ -7233,6 +7233,50 @@ def parse_external_result(self, file): return result +class NetMHCIIpan_4_1(NetMHCIIpan_4_0): + """ + Implementation of NetMHCIIpan 4.1 adapter. + """ + + __command = "netMHCIIpan -f {peptides} -inptype 1 -a {alleles} {options} -xls -xlsfile {out}" + __version = "4.1" + + @property + def version(self): + """The version of the predictor""" + return self.__version + + @property + def command(self): + """ + Defines the commandline call for external tool + """ + return self.__command + + def parse_external_result(self, file): + """ + Parses external results and returns the result containing the predictors string representation + of alleles and peptides. + + :param str file: The file path or the external prediction results + :return: A dictionary containing the prediction results + :rtype: dict + """ + f = csv.reader(open(file, "r"), delimiter='\t') + scores = defaultdict(defaultdict) + ranks = defaultdict(defaultdict) + alleles = [x for x in set([x for x in next(f) if x != ""])] + next(f) + for row in f: + pep_seq = row[PeptideIndex.NETMHCIIPAN_4_1] + for i, a in enumerate(alleles): + scores[a][pep_seq] = float(row[ScoreIndex.NETMHCIIPAN_4_1 + i * Offset.NETMHCIIPAN_4_1]) + ranks[a][pep_seq] = float(row[RankIndex.NETMHCIIPAN_4_1 + i * Offset.NETMHCIIPAN_4_1]) + # Create dictionary with hierarchy: {'Allele1': {'Score': {'Pep1': Score1, 'Pep2': Score2,..}, 'Rank': {'Pep1': RankScore1, 'Pep2': RankScore2,..}}, 'Allele2':...} + result = {allele: {metric:(list(scores.values())[j] if metric == "Score" else list(ranks.values())[j]) for metric in ["Score", "Rank"]} for j, allele in enumerate(alleles)} + + return result + class PickPocket_1_1(AExternalEpitopePrediction): """ Implementation of PickPocket adapter. @@ -8441,6 +8485,7 @@ class PeptideIndex(IntEnum): NETMHCIIPAN_3_0 = 1 NETMHCIIPAN_3_1 = 1 NETMHCIIPAN_4_0 = 1 + NETMHCIIPAN_4_1 = 1 PICKPOCKET_1_1 = 2 NETCTLPAN_1_1 = 3 @@ -8460,7 +8505,8 @@ class ScoreIndex(IntEnum): NETMHCII_2_3 = 5 NETMHCIIPAN_3_0 = 3 NETMHCIIPAN_3_1 = 3 - NETMHCIIPAN_4_0 = 3 + NETMHCIIPAN_4_0 = 4 + NETMHCIIPAN_4_1 = 5 PICKPOCKET_1_1 = 4 NETCTLPAN_1_1 = 7 @@ -8477,6 +8523,7 @@ class RankIndex(IntEnum): NETMHCIIPAN_3_0 = 5 NETMHCIIPAN_3_1 = 5 NETMHCIIPAN_4_0 = 5 + NETMHCIIPAN_4_1 = 6 class Offset(IntEnum): """ @@ -8492,7 +8539,8 @@ class Offset(IntEnum): NETMHCSTABPAN_1_0_WO_SCORE = 3 NETMHCIIPAN_3_0 = 3 NETMHCIIPAN_3_1 = 3 - NETMHCIIPAN_4_0 = 1 + NETMHCIIPAN_4_0 = 0 + NETMHCIIPAN_4_1 = 3 class HLAIndex(IntEnum): """ From 0800bb6506aa73619dd14258a07c51cbef0c4159 Mon Sep 17 00:00:00 2001 From: Christopher Mohr Date: Tue, 14 Jun 2022 14:36:08 +0200 Subject: [PATCH 24/25] minor doc improvements, cleanup setup.py --- README.md | 14 +++++++++----- setup.py | 31 +------------------------------ 2 files changed, 10 insertions(+), 35 deletions(-) diff --git a/README.md b/README.md index 0a83c092..e2e4b870 100644 --- a/README.md +++ b/README.md @@ -3,16 +3,19 @@ ![PyPi](https://github.com/KohlbacherLab/epytope/actions/workflows/pypi-publish.yml/badge.svg) ![Tests](https://github.com/KohlbacherLab/epytope/actions/workflows/python-test-conda.yml/badge.svg) ![Tests external](https://github.com/KohlbacherLab/epytope/actions/workflows/python-test-conda-external.yml/badge.svg) +[![Anaconda-Server Badge](https://anaconda.org/bioconda/epytope/badges/version.svg)](https://anaconda.org/bioconda/epytope) +[![Anaconda-Server Badge](https://anaconda.org/bioconda/epytope/badges/latest_release_date.svg)](https://anaconda.org/bioconda/epytope) [![License](https://img.shields.io/badge/License-BSD_3--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause) [![Anaconda-Server Badge](https://anaconda.org/bioconda/epytope/badges/installer/conda.svg)](https://conda.anaconda.org/bioconda) +[![Anaconda-Server Badge](https://anaconda.org/bioconda/epytope/badges/downloads.svg)](https://anaconda.org/bioconda/epytope) -Copyright 2014 by Benjamin Schuber, Mathias Walzer, Philipp Brachvogel, Andras Szolek, Christopher Mohr, and Oliver Kohlbacher +Copyright 2014 by Benjamin Schuber, Mathias Walzer, Philipp Brachvogel, Andras Szolek, Christopher Mohr, and Oliver Kohlbacher **epytope** is a framework for T-cell epitope detection, and vaccine design. It offers consistent, easy, and simultaneous access to well established prediction methods of computational immunology. **epytope** can handle polymorphic proteins and offers analysis tools to select, assemble, and design linker sequences for string-of-beads epitope-based vaccines. It is implemented in Python in a modular way and can easily be extended by user defined methods. ## Copyright -epytope is released under the three clause BSD licence. +epytope is released under the three clause BSD license. ## Installation @@ -27,9 +30,10 @@ use the following commands: - pandas - pyomo>=4.0 - svmlight -- MySQL-python>=1.2.4 -- Biopython +- PyMySQL +- biopython - pyVCF +- h5py<=2.10.0 ### Third-Party Software (not installed through pip) @@ -58,7 +62,7 @@ Currently **epytope** provides implementations of several prediction methods or - [NetMHC](https://pubmed.ncbi.nlm.nih.gov/26515819/) 3.0, 3.4, 4.0 - [NetMHCII](https://pubmed.ncbi.nlm.nih.gov/29315598/) 2.2, 2.3 - [NetMHCpan](https://pubmed.ncbi.nlm.nih.gov/28978689/) 2.4, 2.8, 3.0, 4.0, 4.1 - - [NetMHCIIpan](https://pubmed.ncbi.nlm.nih.gov/32406916/) 3.0, 3.1, 4.0 + - [NetMHCIIpan](https://pubmed.ncbi.nlm.nih.gov/32406916/) 3.0, 3.1, 4.0, 4.1 - [PickPocket](https://pubmed.ncbi.nlm.nih.gov/19297351/) 1.1 - [NetCTLpan](https://pubmed.ncbi.nlm.nih.gov/20379710/) 1.1 - Epitope Selection diff --git a/setup.py b/setup.py index 1aa49bed..c7d44005 100644 --- a/setup.py +++ b/setup.py @@ -6,33 +6,9 @@ here = path.abspath(path.dirname(__file__)) -#d2s_src_dir = path.join(path.join('epytope', 'Distance2Self'), 'src') -#d2s_module = Extension('epytope.d2s', -# define_macros=[('MAJOR_VERSION', '1'), -# ('MINOR_VERSION', '0')], -# include_dirs=[d2s_src_dir], -# libraries=['boost_serialization', 'boost_python'], -# #library_dirs = ['/usr/local/lib'], -# depends=[path.join(d2s_src_dir, 'distance2self.hpp')], -# sources=[path.join(d2s_src_dir, 'distance2self.cpp')]) - - -#data_files = list() -# directories = glob.glob('epytope/Data/svms/*/') -# for directory in directories: -# files = glob.glob(directory + '*') -# data_files.append((directory, files)) -#directories = glob.glob('epytope/Data/examples/') -#for directory in directories: -# files = glob.glob(directory + '*') -# data_files.append((directory, files)) -# -# d2s_files = glob.glob(d2s_dir + "src/" + '*') -#data_files.append((d2s_dir + "src/", d2s_files)) - #for packaging files must be in a package (with init) and listed in package_data # package-externals can be included with data_files, -# and there is a bug in patternmatching http://bugs.python.org/issue19286 +# and there is a bug in patter nmatching http://bugs.python.org/issue19286 # install unclear for data_files # Read the contents of the README.md file for use as long_description @@ -89,7 +65,6 @@ # Specify packages via find_packages() and exclude the tests and # documentation: packages=find_packages(), - #packages=find_packages(exclude=['epytope.test', 'epytope.doc', 'epytope.tutorials']), # If there are data files included in your packages that need to be # installed, specify them here. If using Python 2.6 or less, then these @@ -100,7 +75,6 @@ 'epytope.Data.svms.svmtap': ['*'], 'epytope.Data.svms.svmhc': ['*'], 'epytope.Data.svms.unitope': ['*'], - #'epytope.Distance2Self': ['src/*'], #does not get installed, because the src folder is no package folder - compiles ok }, data_files = [ @@ -124,9 +98,6 @@ # ], #}, - #ext_modules=[helloworld_module], - #ext_modules=[d2s_module], - # Run-time dependencies. (will be installed by pip when epytope is installed) # TODO: find alternative for SMVlight scikitlearn install_requires=[ From 1df2196d6ed9dafb16e97e51f6bb62e5bd7fce44 Mon Sep 17 00:00:00 2001 From: Christopher Mohr Date: Wed, 15 Jun 2022 10:26:40 +0200 Subject: [PATCH 25/25] bump version --- CHANGELOG.md | 2 +- setup.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 09789ebd..bc0fcd5a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v3.1.0dev - 2022-06-01 +## v3.1.0 - 2022-06-15 ### `Added` diff --git a/setup.py b/setup.py index c7d44005..6a320345 100644 --- a/setup.py +++ b/setup.py @@ -21,7 +21,7 @@ name='epytope', # Version: - version='3.0.0', + version='3.1.0', description='A Framework for Epitope Detection and Vaccine Design', long_description=long_description,