Update MartsAdapter #69
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jonasscheid
reviewed
Aug 22, 2022
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Not sure why the requests to I will run it again tomorrow. Maybe it's a problem on their side. |
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I added a retry strategy for the |
ggabernet
reviewed
Sep 8, 2022
Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
christopher-mohr
added a commit
that referenced
this pull request
Nov 9, 2022
* 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 * Update MartsAdapter (#69) * Rewrite, extend, cleanup MartsAdapter, adapt tests * add requests and beautifulsoup4 dependency * prevent too long requests, avoid server request for each attribute * add gene to test object * fix enum ref * adapt MartsAdapter in other test * add function for getting gene names, add tests * change method name, add test * add lxml as dependency * workaround for pandas read_xml, remove dependency * add missing all() * fix test * add retry strategy for GET requests * Update epytope/IO/MartsAdapter.py Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com> * add default biomart url Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com> * Outsource supported alleles (#63) * Draft for outsourcing supported alleles * Further outsourcing of netmhc alleles * Finish outsourcing external alleles * Outsource alleles from pssm and ann predictors * Correct minor erroneous hla nomenclatures of smmpmbec * Change allele imports by importing frozensets * Add __allele_import_name to classes to increase readability * Refactor: convert_alleles is now classmethod in pssm * Incorporate feedback * Update __init__.py * Update uniprot adapter (#71) * remove HLAtyping and distance2self tests, update CHANGELOG * fix reading sequences in uniprot adapter * add test for uniprot adapter * remove HLAtyping and distance2self tests, update CHANGELOG (#70) * Fix netmhcii4.0 parser (#73) * fix netmhciipan4.0 issue * update changelog * Add function for peptides to check if created by variant (#74) * remove HLAtyping and distance2self tests, update CHANGELOG * add Peptide functon to determine if peptide originates from a variant * fix peptide call, update CHANGELOG * Improve function to check peptide origin (#75) * remove HLAtyping and distance2self tests, update CHANGELOG * add Peptide functon to determine if peptide originates from a variant * fix peptide call, update CHANGELOG * improve method for variant-peptide check * minor CHANGELOG change * change peptide to self * update setup.py and CHANGELOG * Fix errorneous supported alleles (#78) * Draft for outsourcing supported alleles * Further outsourcing of netmhc alleles * Finish outsourcing external alleles * Outsource alleles from pssm and ann predictors * Correct minor erroneous hla nomenclatures of smmpmbec * Change allele imports by importing frozensets * Add __allele_import_name to classes to increase readability * Refactor: convert_alleles is now classmethod in pssm * Incorporate feedback * Fix parsing error and sort allele list * Adjust variable naming 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>
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This rewrites parts of the MartsAdapter and extends it to add new functionality and to make it more flexible in its use.
The main changes are the following:
requestsinstead ofurllibElementTreeto createXMLqueriesPandasfor fetching resultsGRCh37releaseget_variant_idsandget_all_variant_idsResolves #57.