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        "author": "Hyeshik Chang, Kamil Slowikowski",
        "author_email": "hyeshik@snu.ac.kr, slowikow@broadinstitute.org",
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        "classifiers": [
            "Development Status :: 4 - Beta",
            "Intended Audience :: Developers",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: MIT License",
            "Operating System :: OS Independent",
            "Programming Language :: C",
            "Programming Language :: Python",
            "Topic :: Scientific/Engineering :: Bio-Informatics",
            "Topic :: Software Development :: Libraries :: Python Modules"
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        "description": "This module allows fast random access to files compressed with bgzip_ and\r\nindexed by tabix_. It includes a C extension with code from klib_. The bgzip\r\nand tabix programs are available here_.\r\n\r\nInstallation\r\n------------\r\n\r\n::\r\n\r\n    pip install --user pytabix\r\n\r\n\r\nSynopsis\r\n--------\r\n\r\nGenomics data is often in a table where each row corresponds to a genomic\r\nregion (start, end) or a position::\r\n\r\n    chrom  pos      snp\r\n    1      1000760  rs75316104\r\n    1      1000894  rs114006445\r\n    1      1000910  rs79750022\r\n    1      1001177  rs4970401\r\n    1      1001256  rs78650406\r\n\r\nWith tabix_, you can quickly retrieve all rows in a genomic region by\r\nspecifying a query with a sequence name, start, and end:\r\n\r\n.. code:: python\r\n\r\n    import tabix\r\n\r\n    # Open a remote or local file.\r\n    url = \"ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20100804/\"\r\n    url += \"ALL.2of4intersection.20100804.genotypes.vcf.gz\"\r\n\r\n    tb = tabix.open(url)\r\n\r\n    # These queries are identical. A query returns an iterator over the results.\r\n    records = tb.query(\"1\", 1000000, 1250000)\r\n    records = tb.queryi(0, 1000000, 1250000)\r\n    records = tb.querys(\"1:1000000-1250000\")\r\n\r\n    # Each record is a list of strings.\r\n    for record in records:\r\n        print record[:3]\r\n\r\n.. code:: python\r\n\r\n    ['1', '1000760', 'rs75316104']\r\n    ['1', '1000760', 'rs75316104']\r\n    ['1', '1000894', 'rs114006445']\r\n    ['1', '1000910', 'rs79750022']\r\n    ['1', '1001177', 'rs4970401']\r\n    ['1', '1001256', 'rs78650406']\r\n\r\n\r\nExample\r\n-------\r\n\r\nLet's say you have a table of gene coordinates:\r\n\r\n.. code:: bash\r\n\r\n    $ zcat example.bed.gz | shuf | head -n5 | column -t\r\n    chr19  53611131   53636172   55786   ZNF415\r\n    chr10  72149121   72150375   221017  CEP57L1P1\r\n    chr4   185009858  185139113  133121  ENPP6\r\n    chrX   132669772  133119672  2719    GPC3\r\n    chr6   134924279  134925376  114182  FAM8A6P\r\n\r\nSort_ it by chromosome, then by start and end positions. Then, use bgzip_ to\r\ndeflate the file into compressed blocks:\r\n\r\n.. code:: bash\r\n\r\n    $ zcat example.bed.gz | sort -k1V -k2n -k3n | bgzip > example.bed.bgz\r\n\r\nThe compressed size is usually slightly larger than that obtained with gzip.\r\n\r\nIndex the file with tabix_:\r\n\r\n.. code:: bash\r\n\r\n    $ tabix -s 1 -b 2 -e 3 example.bed.gz\r\n    \r\n    $ ls\r\n    example.bed.gz  example.bed.bgz  example.bed.bgz.tbi\r\n\r\n.. _bgzip: http://samtools.sourceforge.net/tabix.shtml\r\n.. _tabix: http://samtools.sourceforge.net/tabix.shtml\r\n.. _klib: https://github.com/jmarshall/klib\r\n.. _here: http://sourceforge.net/projects/samtools/files/tabix/\r\n.. _Sort: https://www.gnu.org/software/coreutils/manual/html_node/Details-about-version-sort.html#Details-about-version-sort",
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        "license": "MIT",
        "maintainer": "Kamil Slowikowski",
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