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        "author": "Saket Choudhary",
        "author_email": "saketkc@gmail.com",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 4 - Beta",
            "Intended Audience :: Developers",
            "License :: OSI Approved :: ISC License (ISCL)",
            "Natural Language :: English",
            "Operating System :: MacOS",
            "Operating System :: POSIX",
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            "Programming Language :: Python :: 2",
            "Programming Language :: Python :: 2.6",
            "Programming Language :: Python :: 2.7",
            "Programming Language :: Python :: 3.3",
            "Programming Language :: Python :: 3.5",
            "Topic :: Scientific/Engineering :: Bio-Informatics",
            "Topic :: Scientific/Engineering :: Visualization"
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        "description": "==========================================\nMoCA: Tool for MOtif Conservation Analysis\n==========================================\n\n.. image:: https://img.shields.io/pypi/v/moca.svg\n        :target: https://pypi.python.org/pypi/moca/\n\n.. image:: https://img.shields.io/travis/saketkc/moca.svg\n        :target: https://travis-ci.org/saketkc/moca\n\n.. image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg\n        :target: https://bioconda.github.io/recipes/moca/README.html\n\n.. image:: https://coveralls.io/repos/github/saketkc/moca/badge.svg?branch=master\n        :target: https://coveralls.io/github/saketkc/moca?branch=master\n\n.. image:: https://landscape.io/github/saketkc/moca/master/landscape.svg?style=flat\n        :target: https://landscape.io/github/saketkc/moca/master\n\n.. image:: https://requires.io/github/saketkc/moca/requirements.svg?branch=master\n        :target: https://requires.io/github/saketkc/moca/requirements/?branch=master\n\n\nLICENSE\n-------\nISC\n\n\n\nInstallation\n------------\n\n\nRequirements\n~~~~~~~~~~~~\n\n* pybedtools\n* biopython\n* pandas\n* scipy\n* statsmodels\n* pybigwig\n* seaborn\n* MEME==4.10.2\n\nNOTE: MoCA also relies on `fasta-shuffle-letters` that was introduced in MEME `4.11.0`\nhence if you are using `4.10.2` make sure the `fasta-shuffle-letters` is the updated one.\n\nFor a sample script see `travis/install_meme.sh`\n\nUsing Conda\n~~~~~~~~~~~\n``moca`` is most compatible with the `conda`_ environment.\n\n::\n\n    $ conda config --add channels bioconda\n    $ conda install moca\n\n\nUsing pip\n~~~~~~~~~\n\n::\n\n   $ pip install moca\n\n\nFor development\n~~~~~~~~~~~~~~~\n\n::\n\n    $ git clone https://github.com:saketkc/moca.git\n    $ cd moca\n    $ conda env create -f environment.yml python=2.7\n    $ source activate mocadev\n    $ python setup.py install\n\n\n\nWorkflow\n--------\n\nMoCA makes use of PhyloP/PhastCons/GERP scores to assess the quality of a\nmotif, the hypothesis being a 'true motif' would evolve slower as compared\nto its surrounding(flanking sequences).\n\n.. image:: https://raw.githubusercontent.com/saketkc/moca_web/master/docs/abstract/workflow.png\n\n\nUsage\n-----\n\n::\n\n    $ moca\n    Usage: moca [OPTIONS] COMMAND [ARGS]...\n\n      moca: Motif Conservation Analysis\n\n    Options:\n      --version  Show the version and exit.\n      --help     Show this message and exit.\n\n    Commands:\n      find_motifs  Run meme to locate motifs and create...\n      plot         Create stacked conservation plots\n\n\n\nMotif analysis using MEME\n~~~~~~~~~~~~~~~~~~~~~~~~~\n\nMoCA can perform motif analysis for you given a bedfile containing\nChIP-Seq peaks.\n\nGenome builds and MEME binary locations are specified through a configuraton file.\nA sample configuration file is available: `tests/data/application.cfg` and should be\nself-explanatory.\n\nmoca find_motifs\n~~~~~~~~~~~~~~~~\n\n\n::\n\n    $ moca find_motifs -h\n    Usage: moca find_motifs [OPTIONS]\n\n      Run meme to locate motifs and create conservation stacked plots\n\n    Options:\n      -i, --bedfile TEXT            Bed file input  [required]\n      -o, --oc TEXT                 Output Directory  [required]\n      -c, --configuration TEXT      Configuration file  [required]\n      --slop-length INTEGER         Flanking sequence length  [required]\n      --flank-motif INTEGER         Length of sequence flanking motif  [required]\n      --n-motif INTEGER             Number of motifs\n      -t, --cores INTEGER           Number of parallel MEME jobs  [required]\n      -g, -gb, --genome-build TEXT  Key denoting genome build to use in\n                                    configuration file  [required]\n      --show-progress               Print progress\n      -h, --help                    Show this message and exit.\n\n\nmoca plot\n~~~~~~~~~\n\n\n::\n\n    $ moca plot -h\n    Usage: moca plot [OPTIONS]\n\n      Create stacked conservation plots\n\n    Options:\n      --meme-dir, --meme_dir TEXT     MEME output directory  [required]\n      --centrimo-dir, --centrimo_dir TEXT\n                                      Centrimo output directory  [required]\n      --fimo-dir-sample, --fimo_dir_sample TEXT\n                                      Sample fimo.txt  [required]\n      --fimo-dir-control, --fimo_dir_control TEXT\n                                      Control fimo.txt  [required]\n      --name TEXT                     Plot title\n      --flank-motif INTEGER           Length of sequence flanking motif\n                                      [required]\n      --motif INTEGER                 Motif number\n      -o, --oc TEXT                   Output Directory  [required]\n      -c, --configuration TEXT        Configuration file  [required]\n      --show-progress                 Print progress\n      -g, -gb, --genome-build TEXT    Key denoting genome build to use in\n                                      configuration file  [required]\n      -h, --help                      Show this message and exit.\n\n\nExample\n-------\n\nMost users will require using the command line version only:\n\n::\n\n    $ moca find_motifs -i encode_test_data/ENCFF002DAR.bed\\\n        -c tests/data/application.cfg -g hg19 --show-progress\n\n\n\nCreating plots if you already have run MEME and Centrimo:\n\n::\n\n    $ moca plot -c tests/data/application.cfg -g hg19\\\n        --meme-dir moca_output/meme_out\\\n        --centrimo-dir moca_output/centrimo_out\\\n        --fimo-dir-sample moca_output/meme_out/fimo_out_1\\\n        --fimo-dir-control moca_output/meme_out/fimo_random_1\\\n        --name ENCODEID\n\n\n.. image:: http://www.saket-choudhary.me/moca/_static/img/ENCFF002CEL.png\n\n\nThere is also a structured API available,\nhowever it might be missing examples and documentation at places.\n\nAPI Documentation\n-----------------\n\nhttp://saketkc.github.io/moca/\n\n\n\nTests\n-----\n``moca`` is mostly extensively tested. See `code-coverage`_. \n\nRun tests locally\n\n::\n\n    $ ./runtests.sh\n\n\nCredits\n---------\n\nThis package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.\n\n.. _`MoCA0.1.0`: https://github.com/saketkc/moca_web\n.. _Cookiecutter: https://github.com/audreyr/cookiecutter\n.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage\n.. _`conda`: http://conda.pydata.org/docs/using/using.html\n.. _`code-coverage`: https://coveralls.io/github/saketkc/moca?branch=master\n\n\n=======\nHistory\n=======\n0.4.1 (2017-02-16)\n------------------\n* Added $\\delta$ options for sample vs control ttest\n* Removed unused requirements: ipaddress\n* Fixed meme runner to plot\n\n0.3.3 (2016-10-03)\n------------------\n* Removed pycairo dependency\n\n0.2.9 (2016-05-31)\n------------------\n\n* Do not fail silently on MEME failing\n* Support --cores to support parallel threads\n\n0.2.8 (2016-05-30)\n------------------\n* Fixed MEME pipeline missing from mocacli\n\n0.2.7 (2016-05-30)\n------------------\n* Fixed bug where missing wig keys were not handled in mocacli\n\n0.2.4 (2016-05-29)\n------------------\n\n* Cleaned up unused scripts under scripts directory\n* Add configuration file example\n\n\n0.2.3 (2016-05-29)\n------------------\n* Include package_dir in setup.py\n* Include requirements.txt in MANIFEST\n\n0.2.0 (2016-05-29)\n------------------\n\n* First release on PyPI.",
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