Metadata-Version: 2.1
Name: crimson
Version: 0.5.2
Summary: Bioinformatics tool outputs converter to JSON or YAML.
Home-page: http://bow.web.id
Author: Wibowo Arindrarto
Author-email: bow@bow.web.id
License: BSD
Description: ``crimson``
        ===========
        
        |pypi| |ci| |cov| |qual|
        
        .. |pypi| image:: https://img.shields.io/pypi/v/crimson?labelColor=4d4d4d&color=007c5b&style=flat
            :target: https://pypi.org/project/crimson/
        
        .. |ci| image:: https://img.shields.io/travis/bow/crimson?labelColor=4d4d4d&color=007c5b&style=flat
            :target: https://travis-ci.org/bow/crimson
        
        .. |cov| image:: https://img.shields.io/codeclimate/coverage/bow/crimson?labelColor=4d4d4d&color=007c5b&style=flat
            :target: https://codeclimate.com/github/bow/crimson
        
        .. |qual| image:: https://img.shields.io/codeclimate/maintainability/bow/crimson?labelColor=4d4d4d&color=007c5b&style=flat
            :target: https://codeclimate.com/github/bow/crimson
        
        
        ``crimson`` converts non-standard bioinformatics tool outputs to JSON or YAML.
        
        Currently it accepts outputs of the following programs:
        
        * `FastQC <http://www.bioinformatics.babraham.ac.uk/projects/fastqc/>`_ (``fastqc``)
        * `FusionCatcher <https://github.com/ndaniel/fusioncatcher>`_ (``fusioncatcher``)
        * `samtools <http://www.htslib.org/doc/samtools.html>`_ flagstat (``flagstat``)
        * `Picard <https://broadinstitute.github.io/picard/>`_ metrics tools (``picard``)
        * `STAR <https://github.com/alexdobin/STAR>`_ log file (``star``)
        * `STAR-Fusion <https://github.com/STAR-Fusion/STAR-Fusion>`_ hits table (``star-fusion``)
        * `Variant Effect Predictor <http://www.ensembl.org/info/docs/tools/vep/index.html>`_ plain text output (``vep``)
        
        From those, you can convert the respective output files into JSON (the default) or YAML. You can also use ``crimson``
        in your scripts by importing the parser functions themselves.
        
        Installation
        ------------
        
        ``crimson`` is available via the Python Package Index and you can install it via ``pip``:
        
        .. code-block:: bash
        
            $ pip install crimson
        
        It is tested on the following Python versions:
        
        * 3.8
        * 3.7
        * 3.6
        
        and against the following bioinformatics tools:
        
        * FastQC (version 0.10.1)
        * FusionCatcher (version 0.99.5a)
        * samtools (version 0.19.1, 1.1)
        * Picard (version 1.124)
        * STAR (version 2.3.0)
        * STAR-Fusion (version 0.6.0, 1.6.0)
        * VEP (version 77)
        
        Usage
        -----
        
        Command-line
        ~~~~~~~~~~~~
        
        The general command is ``crimson {program_name}`` and by default the output is written to ``stdout``. For example,
        to use the ``picard`` parser, you would execute:
        
        .. code-block:: bash
        
            $ crimson picard /path/to/a/picard.metrics
        
        You can also specify a file name directly to write to a file. The following command will write the output to a file
        named ``converted.json``:
        
        .. code-block:: bash
        
            $ crimson picard /path/to/a/picard.metrics converted.json
        
        Some parsers may also accept additional input format. The FastQC parser, for example, also works if you give it a
        path to the FastQC output directory:
        
        .. code-block:: bash
        
            $ crimson fastqc /path/to/a/fastqc/dir
        
        or path to a zipped result:
        
        .. code-block:: bash
        
            $ crimson fastqc /path/to/a/fastqc_result.zip
        
        When in doubt, use the ``--help`` flag:
        
        .. code-block:: bash
        
            $ crimson --help            # for the general help
            $ crimson fastqc --help     # for parser-specific (FastQC) help
        
        Python Module
        ~~~~~~~~~~~~~
        
        The function to import is located at ``crimson.{program_name}.parser``. So to use the ``picard`` parser in your script,
        you can do this:
        
        .. code-block:: python
        
            from crimson import picard
        
            # You can supply the file name as string ...
            parsed = picard.parse("/path/to/a/picard.metrics")
        
            # ... or a file handle directly
            with open("/path/to/a/picard.metrics") as src:
                parsed = picard.parse(src)
        
        Why?
        ----
        
        * Not enough tools use standard output formats.
        * Writing and re-writing the same parsers across different scripts is not a productive way to spend the day.
        
        
        Contributing
        ============
        
        If you are interested, ``crimson`` accepts the following types contribution:
        
        * Documentation additions (if anything seems unclear, feel free to open an issue)
        * Bug reports
        * Support for tools' outputs which can be converted to JSON or YAML.
        
        For any of these, feel free to open an issue in the
        `issue tracker <https://github.com/bow/crimson/issues>`_ or submitt a pull request.
        
        Local Development
        -----------------
        
        Setting up a local development requires any of the supported Python version. It is ideal if you have support Python 2.x
        and 3.x versions installed, as that will allow you to run the full tests suite against all versions using ``tox``.
        
        In any case, the following steps can be your guide for setting up your local development environment:
        
        .. code-block:: bash
        
            # Clone the repository and cd into it
            $ git clone {repo-url}
            $ cd crimson
        
            # Create your virtualenv, using pyenv for example (recommended, https://github.com/pyenv/pyenv)
            $ pyenv virtualenv 3.7.0 crimson-dev
            # or using virtualenvwrapper (https://virtualenvwrapper.readthedocs.io/en/latest/)
            $ mkvirtualenv -p /usr/bin/python3.7 crimson-dev
        
            # From within the root directory and with an active virtualenv, install the dependencies and package itself
            $ pip install -e .[dev]
        
        
        License
        =======
        
        ``crimson`` is BSD-licensed. Refer to the ``LICENSE`` file for the full license.
        
        
        Changelog
        =========
        
        This format is based on
        `Keep a Changelog <https://keepachangelog.com/en/1.0.0/>`_ and this project
        adheres to `Semantic Versioning <https://semver.org/spec/v2.0.0.html>`_.
        
        
        Unreleased
        ----------
        
        
        [0.5.2] - 2020-06-30
        --------------------
        
        Fixed
        ~~~~~
        * FusionCatcher v1.20 output without any result rows is now parsed properly (see #11).
        * Sections in VEP files containing no data is now parsed properly (see #13).
        
        
        [0.5.1] - 2020-02-27
        --------------------
        
        Changed
        ~~~~~~~
        * Relaxed Click and YAML requirements. Now crimon requires only minimum
          versions of these dependencies instead of exact ones.
        
        
        [0.5.0] - 2020-02-04
        --------------------
        
        Added
        ~~~~~
        * Support for parsing output of STAR-Fusion v1.6.0 under the same
          ``star-fusion`` parser. Thank you @Redmar-van-den-Berg!
        
        Removed
        ~~~~~~~
        * Support for Python 2.7, 3.3, 3.4, and 3.5
        
        
        [0.4.0] - 2018-07-25
        --------------------
        
        Added
        ~~~~~
        * Support for parsing zipped FastQC result.
        
        Changed
        ~~~~~~~
        * Improved detection of zipped FastQC input.
        * Set configurable file-size limits for flagstat, Picard, and FastQC.
        
        
        [0.3.0] - 2016-05-19
        --------------------
        
        Added
        ~~~~~
        * Support for parsing FusionCatcher final fusion genes file.
        
        
        [0.2.0] - 2016-04-13
        --------------------
        
        Added
        ~~~~~
        * Support for parsing STAR-Fusion hits table output.
        * Support for parsing STAR alignment log output.
        * Support for parsing VEP plain text output.
        
        
        [0.1.1] - 2016-02-02
        --------------------
        
        Changed
        ~~~~~~~
        * Test and build dependencies.
        
        
        [0.1.0] - 2015-07-27
        --------------------
        
        Added
        ~~~~~
        * First release.
        * Support for parsing FastQC, samtools flagstat, and Picard.
Keywords: crimson bioinformatics json yaml samtools picard fastqc
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: POSIX
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Topic :: Utilities
Classifier: Topic :: Software Development :: Testing
Classifier: Topic :: Software Development :: Libraries
Description-Content-Type: text/x-rst
Provides-Extra: dev
