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        "author": "Alex Rubinsteyn",
        "author_email": "alex.rubinsteyn@mssm.edu",
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            "Environment :: Console",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: Apache Software License",
            "Operating System :: OS Independent",
            "Programming Language :: Python",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "[![Build Status](https://travis-ci.org/openvax/mhctools.svg?branch=master)](https://travis-ci.org/openvax/mhctools) [![Coverage Status](https://coveralls.io/repos/openvax/mhctools/badge.svg?branch=master)](https://coveralls.io/r/openvax/mhctools?branch=master)\n<a href=\"https://pypi.python.org/pypi/mhctools/\">\n    <img src=\"https://img.shields.io/pypi/v/mhctools.svg?maxAge=1000\" alt=\"PyPI\" />\n</a>\n<!-- \n<a href='https://mhctools.readthedocs.io/en/latest/?badge=latest'>\n    <img src='https://readthedocs.org/projects/mhctools/badge/?version=latest' alt='Documentation Status' />\n</a>\n--> \n<!-- \n[![DOI](https://zenodo.org/badge/18834/openvax/mhctools.svg)](https://zenodo.org/badge/latestdoi/18834/openvax/mhctools)\n-->\n\n# mhctools\nPython interface to running command-line and web-based MHC binding predictors.\n\n## Commandline examples\n\n### Prediction for user-supplied peptide sequences\n```sh\nmhctools --sequence SIINFEKL SIINFEKLQ --mhc-predictor netmhc --mhc-alleles A0201\n```\n\n### Automatically extract peptides as subsequences of specified length\n```sh\nmhctools --sequence AAAQQQSIINFEKL --extract-subsequences --mhc-peptide-lengths 8-10 --mhc-predictor mhcflurry --mhc-alleles A0201\n```\n\n## Python usage\n\n```python\nfrom mhctools import NetMHCpan\n# Run NetMHCpan for alleles HLA-A*01:01 and HLA-A*02:01\npredictor = NetMHCpan(alleles=[\"A*02:01\", \"hla-a0101\"])\n\n# scan the short proteins 1L2Y and 1L3Y for epitopes\nprotein_sequences = {\n  \"1L2Y\": \"NLYIQWLKDGGPSSGRPPPS\",\n  \"1L3Y\": \"ECDTINCERYNGQVCGGPGRGLCFCGKCRCHPGFEGSACQA\"\n}\n\nbinding_predictions = predictor.predict_subsequences(protein_sequences, peptide_lengths=[9])\n\n# flatten binding predictions into a Pandas DataFrame\ndf = binding_predictions.to_dataframe()\n\n# epitope collection is sorted by percentile rank\n# of binding predictions\nfor binding_prediction in binding_predictions:\n    if binding_prediction.affinity < 100:\n        print(\"Strong binder: %s\" % (binding_prediction,))\n```\n\n## API\n\nThe following MHC binding predictors are available in `mhctools`:\n* `MHCflurry`: open source predictor installed by default with `mhctools`, requires the user run `mhcflurry-downloads fetch` first to download MHCflurry models\n* `NetMHC3`: requires locally installed version of [NetMHC 3.x](http://www.cbs.dtu.dk/services/NetMHC-3.4/)\n* `NetMHC4`: requires locally installed version of [NetMHC 4.x](http://www.cbs.dtu.dk/services/NetMHC/)\n* `NetMHC`: a wrapper function to automatically use `NetMHC3` or `NetMHC4` depending on what's installed.\n* `NetMHCpan`: requires locally installed version of [NetMHCpan](http://www.cbs.dtu.dk/services/NetMHCpan/)\n* `NetMHCIIpan`: requires locally installed version of [NetMHCIIpan](http://www.cbs.dtu.dk/services/NetMHCIIpan/)\n* `NetMHCcons`: requires locally installed version of [NetMHCcons](http://www.cbs.dtu.dk/services/NetMHCcons/)\n* `IedbMhcClass1`: Uses IEDB's REST API for class I binding predictions.\n* `IedbMhcClass2`: Uses IEDB's REST API for class II binding predictions.\n* `RandomBindingPredictor`: Creates binding predictions with random IC50 and percentile rank values.\n\nEvery binding predictor is constructed with an `alleles` argument specifying the HLA type for which to make predictions. Predictions are generated by calling the `predict` method with a dictionary mapping sequence IDs or names to amino acid sequences.\n\nAdditionally there is a module for running the [NetChop](http://www.cbs.dtu.dk/services/NetChop)  proteosomal cleavage predictor:\n* `NetChop`: requires locally installed version of [NetChop-3.1](http://www.cbs.dtu.dk/services/NetChop/)",
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