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    "info": {
        "author": "Shareef M. Dabdoub",
        "author_email": "dabdoub.2@osu.edu",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 4 - Beta",
            "Environment :: Console",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: MIT License",
            "Operating System :: OS Independent",
            "Programming Language :: Python",
            "Programming Language :: Python :: 2",
            "Programming Language :: Python :: 3",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
        ],
        "description": "kraken-biom\r\n===========\r\nCreate BIOM-format tables (http://biom-format.org) from Kraken output \r\n(http://ccb.jhu.edu/software/kraken/).\r\n\r\nInstallation\r\n------------\r\nFrom PyPI:\r\n\r\n.. code-block:: bash\r\n\r\n    $ pip install kraken-biom\r\n\r\nFrom GitHub:\r\n\r\n.. code-block:: bash\r\n\r\n    $ pip install git+http://github.com/smdabdoub/kraken-biom.git\r\n\r\nFrom source:\r\n\r\n.. code-block:: bash\r\n\r\n    $ python setup.py install\r\n\r\n\r\nRequirements\r\n------------\r\n\r\n- biom-format >= 2.1.5\r\n\r\nDocumentation\r\n-------------\r\n\r\nThe program takes as input, one or more files output from the kraken-report\r\ntool. Each file is parsed and the counts for each OTU (operational taxonomic\r\nunit) are recorded, along with database ID (e.g. NCBI), and lineage. The\r\nextracted data are then stored in a BIOM table where each count is linked\r\nto the Sample and OTU it belongs to. Sample IDs are extracted from the input\r\nfilenames (everything up to the '.').\r\n\r\nOTUs are defined by the --max and --min arguments. By default these are\r\nset to Order and Species respectively. This means that counts assigned\r\ndirectly to an Order, Family, or Genus are recorded under the associated\r\nOTU ID, and counts assigned at or below the Species level are assigned to\r\nthe OTU ID for the species. Setting a minimum rank below Species is not yet\r\navailable.\r\n\r\nThe BIOM format currently has two major versions. Version 1.0 uses the \r\nJSON (JavaScript Object Notation) format as a base. Version 2.x uses the\r\nHDF5 (Hierarchical Data Format v5) as a base. The output format can be\r\nspecified with the --fmt option. Note that a tab-separated (tsv) output\r\nformat is also available. The resulting file will not contain most of the\r\nmetadata, but can be opened by spreadsheet programs.\r\n\r\nVersion 2 of the BIOM format is used by default for output, but requires the\r\nPython library 'h5py'. If the library is not installed, kraken-biom will \r\nautomatically switch to using version 1.0. Note that the output can \r\noptionally be compressed with gzip (--gzip) for version 1.0 and TSV files. \r\nVersion 2 files are automatically compressed.\r\n\r\nCurrently the taxonomy for each OTU ID is stored as row metadata in the BIOM\r\ntable using the standard seven-level QIIME format: k__K; p__P; ... s__S. If\r\nyou would like another format supported, please file an issue or send a pull\r\nrequest (note the contribution guidelines).\r\n::\r\n\r\n    usage: kraken-biom.py [-h] [--max {D,P,C,O,F,G,S}] [--min {D,P,C,O,F,G,S}]\r\n                          [-o OUTPUT_FP] [--fmt {hdf5,json,tsv}] [--gzip]\r\n                          [--version] [-v]\r\n                          kraken_reports [kraken_reports ...]\r\n\r\nUsage examples\r\n--------------\r\n\r\n1. Basic usage with default parameters::\r\n\r\n    $ kraken-biom.py S1.txt S2.txt\r\n\r\n  This produces a compressed BIOM 2.1 file: table.biom\r\n\r\n2. BIOM v1.0 output::\r\n\r\n    $ kraken-biom.py S1.txt S2.txt --fmt json\r\n\r\n  Produces a BIOM 1.0 file: table.biom\r\n\r\n3. Compressed TSV output::\r\n\r\n    $ kraken-biom.py S1.txt S2.txt --fmt tsv --gzip -o table.tsv\r\n\r\n  Produces a TSV file: table.tsv.gz\r\n\r\n4. Change the max and min OTU levels to Class and Genus::\r\n\r\n    $ kraken-biom.py S1.txt S2.txt --max C --min G\r\n\r\n\r\nProgram arguments\r\n-----------------\r\n\r\npositional arguments::\r\n\r\n    kraken_reports        Results files from the kraken-report tool.\r\n\r\noptional arguments::\r\n    \r\n      -h, --help            show this help message and exit\r\n      --max {D,P,C,O,F,G,S}\r\n                            Assigned reads will be recorded only if they are at or\r\n                            below max rank. Default: O.\r\n      --min {D,P,C,O,F,G,S}\r\n                            Reads assigned at and below min rank will be recorded\r\n                            as being assigned to the min rank level. Default: S.\r\n      -o OUTPUT_FP, --output_fp OUTPUT_FP\r\n                            Path to the BIOM-format file. By default, the table\r\n                            will be in the HDF5 BIOM 2.x format. Users can output\r\n                            to a different format using the --fmt option. The\r\n                            output can also be gzipped using the --gzip option.\r\n                            Default path is: ./table.biom\r\n      --fmt {hdf5,json,tsv}\r\n                            Set the output format of the BIOM table. Default is\r\n                            HDF5.\r\n      --gzip                Compress the output BIOM table with gzip. HDF5 BIOM\r\n                            (v2.x) files are internally compressed by default, so\r\n                            this option is not needed when specifying --fmt hdf5.\r\n      --version             show program's version number and exit\r\n      -v, --verbose         Prints status messages during program execution.",
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        "keywords": "kraken,BIOM,metagenomics,bioinformatics,taxonomy",
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