{
    "info": {
        "author": "Tavi Nathanson",
        "author_email": "tavi {dot} nathanson {at} gmail {dot} com",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 3 - Alpha",
            "Environment :: Console",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: Apache Software License",
            "Operating System :: OS Independent",
            "Programming Language :: Python",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
        ],
        "description": "[![Build Status](https://travis-ci.org/hammerlab/topeology.svg?branch=master)](https://travis-ci.org/hammerlab/topeology) [![Coverage Status](https://coveralls.io/repos/hammerlab/topeology/badge.svg?branch=master&service=github)](https://coveralls.io/github/hammerlab/topeology?branch=master)\n\n# Topeology\n\nTopeology compares neoepitope sequences with epitopes from [IEDB](http://www.iedb.org/).\n\n## Example\n\nFrom the command line:\n\n```sh\ntopeology --input epitopes.csv --epitope-lengths 8 9 10 11 > scores.csv\n```\n\nIn Python:\n\n```python\nfrom topeology import compare\noutput_dataframe = compare('epitopes.csv')\n```\n\nInput looks like:\n\n| sample      | epitope\n| ------      | -------\n| 001         | AAALPGKCGV\n\nOutput looks like:\n\n| sample      | epitope        | iedb_epitope    | score\n| ------      | -------        | ------------    | -----\n| 001         | AAALPGKCGV     | EFKEFAAGRR      | 2.38\n\n## Installation\n\nYou can install topeology using [pip]:\n\n```sh\npip install topeology\n```\n\nCurrently, topeology use [seq-align] to quickly compare sequences, wrapped in a C extension. It will be\ninstalled if [seq-align] is installed; otherwise, topeology reverts to using another scorer.\n\nTo install topeology with this extension:\n- Follow [seq-align]'s installation instructions, and then set `SEQ_ALIGN_PATH` to the installation\n  directory.\n- Install topeology via [pip]. If topeology is already installed, run `pip install topeology --upgrade --no-deps --force-reinstall`.\n\n## Methodology\n\nTopeology uses Smith-Waterman alignment to align each neoepitope with each IEDB epitope of the\nsame length, and returns the resultant epitope-epitope scores. Only position 3 to the penultimate\namino acid are considered.\n\nThis software uses the following libraries for Smith-Waterman alignment:\n\n- [seq-align]\n- [Complete-Striped-Smith-Waterman-Library](https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library)\n\n[seq-align]: https://github.com/noporpoise/seq-align\n[pip]: https://pip.pypa.io/en/latest/quickstart.html",
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