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        "author": "M\u00e5ns Magnusson",
        "author_email": "mans.magnusson@scilifelab.com",
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            "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"
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        "description": "\n# loqusdb [![Build Status][travis-image]][travis-url] \n\nSmall tool to setup a local variant database.\n\nRight now **locusdb** uses [mongodb][mongodb] as backend for \nstoring variants but there should not be a huge difference to use another\ndatabase manager.\n\n## Installation ##\n\n`pip install loqusdb`\n\nor\n\n```\n$git clone https://github.com/moonso/loqusdb\n$cd loqusdb\n$pip install --editable .\n```\n\n## Idea ##\n\nTool to keep track of what variants that have been seen and in what families they have been observed.\nThis is **NOT** a tool to create a true frequency database.\nIt will basically count the number of times we have seen a variant in any individual.\nWe will also keep track of the variants that have been seen in a homozygous or hemizygous state.\n\nVariants are stored by providing a vcf file and a (ped or ped like)family file.\n\nLoqusdb will first check if the vcf file looks ok.\n\nThe tool will then check all variants if they have been observed in any of the individuals in the family.\n\nWhen the variants are added:\n\n- Either the variant exists, in this case we increase the number of observations with one\n- Or this variant has not ben seen before, then the variant is added to database\n\n\n## Command Line Interface ##\n\n```\n$ loqusdb\nUsage: loqusdb [OPTIONS] COMMAND [ARGS]...\n\n  loqusdb: manage a local variant count database.\n\nOptions:\n  -db, --database TEXT   [default: loqusdb]\n  -u, --username TEXT\n  -p, --password TEXT\n  -port, --port INTEGER  Specify the port where to look for the mongo\n                         database.  [default: 27017]\n  -h, --host TEXT        Specify the host where to look for the mongo\n                         database.  [default: localhost]\n  -b, --backend [mongo]  Specify what backend to use.  [default: mongo]\n  -c, --conn_host TEXT   Used for testing.  [default: mongodb://]\n  -l, --logfile PATH     Path to log file. If none logging is printed to\n                         stderr.\n  -v, --verbose\n  --version              Show the version and exit.\n  --help                 Show this message and exit.\n\nCommands:\n  cases     Display cases in database\n  delete    Delete the variants of a family\n  export    Export variants to VCF format\n  index     Add indexes to database\n  load      Load the variants of a family\n  migrate   Migrate an old loqusdb instance\n  variants  Display variants in database\n  wipe      Wipe a loqusdb instance\n```\n\n\n## Database ##\n\n### Mongo ###\n\nThe collections looks like:\n\n**Case**\n\n```python\n{\n    'case_id': 'case_id',\n    'vcf_path': 'path_to_vcf'\n}\n```\n\n**Variant**\n\n```python\n{\n    '_id': 'variant_id',\n    'chrom': 'CHROM',\n    'start': postition,\n    'end': end postition,\n    'ref': reference base(s),\n    'alt': alternative base(s),\n    'homozygote': number_of_homozygotes,\n    'hemizygote': number_of_hemizygotes,\n    'observations': number_of_observations,\n    'families': ['family_id', ...]\n}\n```\n\n[travis-url]: https://travis-ci.org/moonso/loqusdb?branch=master\n[travis-image]: https://img.shields.io/travis/moonso/loqusdb/master.svg?style=flat-square\n[mongodb]: https://www.mongodb.org\n\n\n",
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