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    "info": {
        "author": "M\u00e5ns Magnusson",
        "author_email": "mans.magnusson@scilifelab.com",
        "bugtrack_url": null,
        "classifiers": [
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: MIT License",
            "Operating System :: MacOS :: MacOS X",
            "Operating System :: Unix",
            "Programming Language :: Python",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.6",
            "Programming Language :: Python :: Implementation :: CPython",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
        ],
        "description": "\n# Stranger [![Build Status][travis-image]][travis-url] [![Coverage Status][coveralls-image]][coveralls-url] [![PyPI Version][pypi-img]][pypi-url]\nAnnotates output files from [ExpansionHunter][hunter] with the pathologic implications of the repeat sizes.\n\n## Installation\n\n```\ngit clone github.com/moonso/stranger\ncd stranger\npip install --editable .\n```\n\n## Usage\n\n```\nstranger --help\nUsage: stranger [OPTIONS] VCF\n\n  Annotate str variants with str status\n\nOptions:\n  -f, --repeats-file PATH         Path to a file with repeat definitions. See\n                                  README for explanation  [default: /Users/man\n                                  smagnusson/Projects/stranger/stranger/resour\n                                  ces/repeatexpansionsloci.tsv]\n  --version\n  --loglevel [DEBUG|INFO|WARNING|ERROR|CRITICAL]\n                                  Set the level of log output.  [default:\n                                  INFO]\n  --help                          Show this message and exit.\n\n```\n\n\n## Repeat definitions\n\nThe repeats are called with Expansion Hunter as mentioned earlier. Expansion Hunter will annotate the number of times that a repeat has been seen in the bam files of each individual and what repeat id the variant has.\nStranger will annotate the level of pathogenecity for the repeat number. The intervals that comes with the package are manually collected from the literature since there is no source where this information can be collected.\nThere is a repeat definitions file that comes with Stranger in `stranger/resources/repeatexpansionsloci.tsv`. This is a tsv formated file on the following format:\n\n| hgnc_id | hgnc_symbol | repid | ru | normal_max | pathologic_min | disease |\n| ------- | ------- | ------- | ------- | ------- | ------- | ------- |\n| 10548 | ATXN1 | ATXN1 | CAG | 35 | 45 | SCA1 |\n| 10555 | ATXN2 | ATXN2 | CAG | 31 | 39 | SCA2 |\n| 7106 | ATXN3 | ATXN3 | CAG | 44 | 60 | SCA3 |\n| 1388 | CACNA1A | CACNA1A | CAG | 18 | 20 | SCA6 |\n| 10560 | ATXN7 | ATXN7 | CAG | 19 | 37 | SCA7 |\n| 10561 | ATXN8OS | ATXN8OS | CAG | 50 | 80 | SCA8 |\n| 10549 | ATXN10 | ATXN10 | ATTCT | 32 | 800 | SCA10 |\n| 9305 | PPP2R2B | PPP2R2B | CAG | 35 | 49 | SCA12 |\n| 11588 | TBP | TBP | CAG | 31 | 49 | SCA17 |\n| 3951 | FXN | FXN | CAG | 35 | 51 | FRDA |\n| 4851 | HTT | HTT | CCG | 36 | 37 | Huntington |\n| 3775 | FMR1 | FMR1 | CGG | 65 | 200 | FragileX |\n| 3776 | AFF2 | AFF2 | CCG | 25 | 200 | FRAXE |\n| 13164 | CNBP | CNBP | CCTG | 30 | 75 | DM2 |\n| 2933 | DMPK | DMPK | CAG | 37 | 50 | DM1 |\n| 3033 | ATN1 | ATN1 | CAG | 34 | 49 | DRPLA |\n| 15911 | NOP56 | NOP56 | GGCCTG | 14 | 650 | SCA36 |\n| 28337 | C9ORF72 | C9ORF72 | GGCCCC | 25 | 40 | FTDALS1 |\n| 8565 | PABPN1 | PABPN1 | GCG | 6 | 10 | OPMD |\n| 2482 | CSTB | CSTB | CGCGGGGCGGGG | 3 | 30 | EPM1 |\n| 1541 | CBL | CBL | CGG | 79 | 100 | FRAX11B |\n| 14203 | JPH3 | JPH3 | CTG | 28 | 40 | HDL2 |\n| 644 | AR | AR | CAG | 35 | 38 | SBMA |\n\nThe file is structured like a SCOUT gene panel, with STR specific columns.\n\n| Column | Content |\n| ------- | ------- |\n| HGNC_ID | HGNC identifier for the repeat or most associated gene. |\n| HGNC_SYMBOL |HGNC symbol for the repeat or most associated gene. |\n| REPID | ExpansionHunter repeat ID. |\n| RU | Basic repeat unit, as seen in ExpansionHunter. Unused. |\n| Normal_Max | (#copies) Longest repeat expected for normal individual; higher are marked pre- or full-mutation | \n| Pathologic_Min | (#copies) Shortest repeat expected for pathology. This and higher is annotated as full-mutation. |\n| Disease | Associated disease. |\n\nAs a default the file that follows the distribution is used but the users can create their own file.\nHeader line(s) should be preceded with a `#`. \n\n\n[hunter]: https://github.com/Illumina/ExpansionHunter\n\n[travis-url]: https://travis-ci.com/moonso/stranger\n[travis-image]: https://travis-ci.com/moonso/stranger.svg?branch=master\n[pypi-img]: https://img.shields.io/pypi/v/stranger.svg?style=flat-square\n[pypi-url]: https://pypi.python.org/pypi/stranger/\n[coveralls-url]: https://coveralls.io/github/moonso/stranger\n[coveralls-image]: https://coveralls.io/repos/github/moonso/stranger/badge.svg?branch=master\n\n\n\n",
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