Release 3.1.0 (#68)

* Version bump 3.0.0rc2 * Fix master / main branch naming in GH action * Fix typos in README file * Add pypi GH action * Fix PyPI linting errors * Reduce version to 3.0.0rc1 * Add a changelog * Install changelog with package * Change PyPI CD trigger to published release * 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 * Fixed issues #38, #44 and #45 (#46) * Fixed issues #44 and #45 * Fix #48, include review suggestions * Improve/update documentation (#50) * Update CHANGELOG * Extend README * Change framework name in code comment * Remove logging warning * Change file ending in tutorial * Add docstrings, minor formatting * Update CHANGELOG version and setup.py * Update date * Fix #52 (#53) * add check if transcript sequence available from BioMart, cleanup (#58) * Add interface for netMHCpan 4.1 (#59) * add interface for netmhcpan 4.1 * remove duplicate alleles from list * Update supportedAlleles of syfpeithi (#62) Co-authored-by: Christopher Mohr <christopher.mohr@qbic.uni-tuebingen.de> * 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 <gisela.gabernet@gmail.com> Co-authored-by: Christopher Mohr <christopher.mohr@uni-tuebingen.de> Co-authored-by: Jonas Scheid <jonas@u-081-c204.eap.uni-tuebingen.de> Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com> * 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 <christopher.mohr@qbic.uni-tuebingen.de> Co-authored-by: Christopher Mohr <christopher.mohr@uni-tuebingen.de> Co-authored-by: Christopher Mohr <christopher.mohr@qbic.uni-tuebingen.de> * minor doc improvements, cleanup setup.py * bump version Co-authored-by: Leon Kuchenbecker <leon.kuchenbecker@uni-tuebingen.de> Co-authored-by: Jonas Scheid <43858870+jonasscheid@users.noreply.github.com> Co-authored-by: Jonas Scheid <jonas@u-081-c204.eap.uni-tuebingen.de> Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
KohlbacherLab · Jun 15, 2022 · 86586c9 · 86586c9
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diff --git 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
@@ -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
@@ -3,6 +3,22 @@
 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).
 
+## v3.1.0 - 2022-06-15
+
+### `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` [#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`
+
+- [#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
@@ -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/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)
+[![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)
 
@@ -57,8 +61,8 @@ 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
-  - [NetMHCIIpan](https://pubmed.ncbi.nlm.nih.gov/32406916/) 3.0, 3.1, 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, 4.1
   - [PickPocket](https://pubmed.ncbi.nlm.nih.gov/19297351/) 1.1
   - [NetCTLpan](https://pubmed.ncbi.nlm.nih.gov/20379710/) 1.1
 - Epitope Selection
@@ -71,7 +75,7 @@ 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/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/Data/pssms/syfpeithi/mat/A_0300_9.py b/epytope/Data/pssms/syfpeithi/mat/A_0300_9.py
diff --git 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:

diff --git a/epytope/EpitopePrediction/External.py b/epytope/EpitopePrediction/External.py
diff --git 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"
 

diff --git 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:

diff --git 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
@@ -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"
      ]
     }

diff --git 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
@@ -45,7 +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,
@@ -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=[