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        "author": "Shareef M. Dabdoub",
        "author_email": "dabdoub.2@osu.edu",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 5 - Production/Stable",
            "Environment :: Console",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: Apache Software License",
            "Operating System :: OS Independent",
            "Programming Language :: Python",
            "Programming Language :: Python :: 2",
            "Programming Language :: Python :: 3",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
        ],
        "description": "clark-biom\n===========\n.. image:: https://img.shields.io/travis/smdabdoub/clark-biom.svg?style=plastic\n    :target: https://travis-ci.org/smdabdoub/clark-biom\n    :alt: Travis CI build status\n\nCreate BIOM-format tables (http://biom-format.org) from CLARK output \n(http://clark.cs.ucr.edu/) for use with downstream tools such as\nPhyloToAST (http://phylotoast.org).\n\nInstallation\n------------\n\n>From PyPI:\n\n.. code-block:: bash\n\n    $ pip install clark-biom\n\n>From GitHub:\n\n.. code-block:: bash\n\n    $ pip install git+http://github.com/smdabdoub/clark-biom.git\n\n>From source:\n\n.. code-block:: bash\n\n    $ python setup.py install\n\n\nRequirements\n------------\n\n- biom-format >= 2.1.5\n- h5py >= 2.5.0 [optional]\n\nDocumentation\n-------------\n\nThe program takes as input, one or more files output from CLARK's \nestimate_abundance tool. Each file is parsed and the counts for each OTU \n(operational taxonomic unit) are recorded, along with database ID (e.g. NCBI), \nand lineage. The extracted data are then stored in a BIOM table where each count\nis linked to the Sample and OTU it belongs to. Sample IDs are extracted from the\ninput filenames (everything up to the '.' preceeding the extension).\n\nThe BIOM format currently has two major versions. Version 1.0 uses the \nJSON (JavaScript Object Notation) format as a base. Version 2.x uses the\nHDF5 (Hierarchical Data Format v5) as a base. The output format can be\nspecified with the --fmt option. Note that a tab-separated (tsv) output\nformat is also available. The resulting file will not contain most of the\nmetadata, but can be opened by spreadsheet programs.\n\nVersion 2 of the BIOM format is used by default for output, but requires the\nPython library 'h5py'. If the library is not installed, clark-biom will \nautomatically switch to using version 1.0. Note that the output can \noptionally be compressed with gzip (--gzip) for version 1.0 and TSV files. \nVersion 2 files are automatically compressed.\n\nCurrently the taxonomy for each OTU ID is stored as row metadata in the BIOM\ntable using the seven-level format used by QIIME and metaphlan: k__K, p__P, ... \ns__S. If you would like another format supported, please file an issue or send a\npull request (note the contribution guidelines).\n::\n\n    usage: clark-biom.py [-h] [-o OUTPUT_FP] [--fmt {hdf5,json,tsv}] [--gzip]\n                         [--version] [-v]\n                         clark_abd_tbl [clark_abd_tbl ...]\n\nUsage examples\n--------------\n\n1. Basic usage with default parameters::\n\n    $ clark-biom S1.txt S2.txt\n\n  This produces a compressed BIOM 2.1 file: table.biom\n  with sample IDs: S1, S2.\n\n2. BIOM v1.0 output::\n\n    $ clark-biom S1.txt S2.txt --fmt json\n\n  Produces a BIOM 1.0 file: table.biom\n\n3. Compressed TSV output::\n\n    $ clark-biom S1.txt S2.txt --fmt tsv --gzip -o table.tsv\n\n  Produces a TSV file: table.tsv.gz\n\n\nProgram arguments\n-----------------\n\npositional arguments::\n\n    clark_abd_tbls          Abundance table files from estimate_abundance.sh\n\noptional arguments::\n\n      -o OUTPUT_FP, --output_fp OUTPUT_FP\n                            Path to the BIOM-format file. By default, the table\n                            will be in the HDF5 BIOM 2.x format. Users can \n                            output to a different format using the --fmt option.\n                            The output can also be gzipped using the --gzip \n                            option. Default path is: ./table.biom\n      --fmt {hdf5,json,tsv}\n                            Set the output format of the BIOM table. Default is\n                            HDF5.\n      --gzip                Compress the output BIOM table with gzip. HDF5 BIOM\n                            (v2.x) files are internally compressed by default,\n                            so this option is ignored when specifying --fmt \n                            hdf5.\n      --version             Print program's version number and exit\n      -v, --verbose         Print status messages during program execution.\n      -h, --help            Print this help message and exit\n\n\n\n\n",
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        "keywords": "CLARK,BIOM,metagenomics,bioinformatics,taxonomy,taxonomic-classification",
        "license": "MIT",
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        "name": "clark-biom",
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