{
    "info": {
        "author": "Wibowo Arindrarto",
        "author_email": "bow@bow.web.id",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 3 - Alpha",
            "Environment :: Console",
            "Intended Audience :: Developers",
            "License :: OSI Approved :: BSD License",
            "Operating System :: POSIX",
            "Programming Language :: Python :: 2.7",
            "Programming Language :: Python :: 3.3",
            "Programming Language :: Python :: 3.4",
            "Programming Language :: Python :: 3.5",
            "Programming Language :: Python :: 3.6",
            "Programming Language :: Python :: 3.7",
            "Topic :: Software Development :: Libraries",
            "Topic :: Software Development :: Testing",
            "Topic :: Utilities"
        ],
        "description": "Crimson\n=======\n\n|ci| |coverage| |pypi|\n\n.. |ci| image:: https://travis-ci.org/bow/crimson.svg?branch=master\n    :target: https://travis-ci.org/bow/crimson\n\n.. |coverage| image:: https://codecov.io/gh/bow/crimson/branch/master/graph/badge.svg\n    :target: https://codecov.io/gh/bow/crimson\n\n.. |pypi| image:: https://badge.fury.io/py/Crimson.svg\n    :target: http://badge.fury.io/py/crimson\n\nCrimson converts non-standard bioinformatics tool outputs to JSON or YAML.\n\nCurrently it accepts outputs of the following programs:\n\n* `FastQC <http://www.bioinformatics.babraham.ac.uk/projects/fastqc/>`_ (``fastqc``)\n* `FusionCatcher <https://github.com/ndaniel/fusioncatcher>`_ (``fusioncatcher``)\n* `samtools <http://www.htslib.org/doc/samtools.html>`_ flagstat (``flagstat``)\n* `Picard <https://broadinstitute.github.io/picard/>`_ metrics tools (``picard``)\n* `STAR <https://github.com/alexdobin/STAR>`_ log file (``star``)\n* `STAR-Fusion <https://github.com/STAR-Fusion/STAR-Fusion>`_ hits table (``star-fusion``)\n* `Variant Effect Predictor <http://www.ensembl.org/info/docs/tools/vep/index.html>`_ plain text output (``vep``)\n\nFrom those, you can convert the respective output files into JSON (the default) or YAML. You can also use ``crimson``\nin your scripts by importing the parser functions themselves.\n\nInstallation\n------------\n\nCrimson is available via the Python Package Index and you can install it via ``pip``:\n\n.. code-block:: bash\n\n    $ pip install crimson\n\nIt is tested on Python 2.7, Python 3.3, and Python 3.4, Python 3.5, Python 3.6, Python 3.7, and against the following\nbioinformatics tools:\n\n* FastQC (version 0.10.1)\n* FusionCatcher (version 0.99.5a)\n* samtools (version 0.19.1, 1.1)\n* Picard (version 1.124)\n* STAR (version 2.3.0)\n* STAR-Fusion (version 0.6.0)\n* VEP (version 77)\n\nUsage\n-----\n\nCommand-line\n^^^^^^^^^^^^\n\nThe general command is ``crimson {program_name}`` and by default the output is written to ``stdout``. For example,\nto use the ``picard`` parser, you would execute:\n\n.. code-block:: bash\n\n    $ crimson picard /path/to/a/picard.metrics\n\nYou can also specify a file name directly to write to a file. The following command will write the output to a file\nnamed ``converted.json``:\n\n.. code-block:: bash\n\n    $ crimson picard /path/to/a/picard.metrics converted.json\n\nSome parsers may also accept additional input format. The FastQC parser, for example, also works if you give it a\npath to the FastQC output directory:\n\n.. code-block:: bash\n\n    $ crimson fastqc /path/to/a/fastqc/dir\n\nor path to a zipped result:\n\n.. code-block:: bash\n\n    $ crimson fastqc /path/to/a/fastqc_result.zip\n\nWhen in doubt, use the ``--help`` flag:\n\n.. code-block:: bash\n\n    $ crimson --help            # for the general help\n    $ crimson fastqc --help     # for parser-specific (FastQC) help\n\nPython Module\n^^^^^^^^^^^^^\n\nThe function to import is located at ``crimson.{program_name}.parser``. So to use the ``picard`` parser in your script,\nyou can do this:\n\n.. code-block:: python\n\n    from crimson import picard\n\n    # You can supply the file name as string ...\n    parsed = picard.parse(\"/path/to/a/picard.metrics\")\n\n    # ... or a file handle directly\n    with open(\"/path/to/a/picard.metrics\") as src:\n        parsed = picard.parse(src)\n\nWhy?\n----\n\n* Not enough tools use standard output formats.\n* Writing and re-writing the same parsers across different scripts is not a productive way to spend the day.\n\n\nContributing\n============\n\nIf you are interested, Crimson accepts the following types contribution:\n\n* Documentation additions (if anything seems unclear, feel free to open an issue)\n* Bug reports\n* Support for tools' outputs which can be converted to JSON or YAML.\n\nFor any of these, feel free to open an issue in the\n`issue tracker <https://github.com/bow/crimson/issues>`_ or submitt a pull request.\n\nLocal Development\n-----------------\n\nSetting up a local development requires any of the supported Python version. It is ideal if you have support Python 2.x\nand 3.x versions installed, as that will allow you to run the full tests suite against all versions using ``tox``.\n\nIn any case, the following steps can be your guide for setting up your local development environment:\n\n.. code-block:: bash\n\n    # Clone the repository and cd into it\n    $ git clone {repo-url}\n    $ cd crimson\n\n    # Create your virtualenv, using pyenv for example (recommended, https://github.com/pyenv/pyenv)\n    $ pyenv virtualenv 3.7.0 crimson-dev\n    # or using virtualenvwrapper (https://virtualenvwrapper.readthedocs.io/en/latest/)\n    $ mkvirtualenv -p /usr/bin/python3.7 crimson-dev\n\n    # From within the root directory and with an active virtualenv, install the dependencies and package itself\n    $ pip install -e .[dev]\n\n\nLicense\n=======\n\nCrimson is BSD-licensed. Refer to the ``LICENSE`` file for the full license.\n\n\nChangelog\n=========\n\nVersion 0.4\n-----------\n\nRelease 0.4.0\n^^^^^^^^^^^^^\n\n`release date: 25 July 2018`\n\n* Adds support for parsing zipped FastQC result.\n* Improves detection of zipped FastQC input.\n* Sets configurable file-size limits for flagstat, Picard, and FastQC.\n\n\nVersion 0.3\n-----------\n\nRelease 0.3.0\n^^^^^^^^^^^^^\n\n`release date: 19 May 2016`\n\n* Adds support for parsing FusionCatcher final fusion genes file.\n\n\nVersion 0.2\n-----------\n\nRelease 0.2.0\n^^^^^^^^^^^^^\n\n`release date: 13 April 2016`\n\n* Adds support for parsing STAR-Fusion hits table output.\n* Adds support for parsing STAR alignment log output.\n* Adds support for parsing VEP plain text output.\n\n\nVersions 0.1\n------------\n\nRelease 0.1.1\n^^^^^^^^^^^^^\n\n`release date: 2 February 2016`\n\n* Minor release that loosens the wheel dependency version, updates some\n  development dependencies, and fixes some typos.\n\nRelease 0.1.0\n^^^^^^^^^^^^^\n\n`release date: 27 July 2015`\n\n* First release.\n* Support for parsing FastQC, samtools flagstat, and Picard.\n\n",
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