<commit_before>``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
<commit_msg>docs: Update README badges<commit_after>``crimson``
===========

|pypi| |sourcehut|

.. |pypi| image:: https://img.shields.io/pypi/v/crimson
    :target: https://pypi.org/project/crimson/

.. |sourcehut| image:: https://builds.sr.ht/~bow/crimson.svg
    target: https://builds.sr.ht/~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

{'fraction_non_alphanumeric': 0.17877269881026925, 'fraction_numerical': 0.008766437069505322, 'mean_word_length': 4.685053380782918, 'pattern_counts': {'":': 0, '<': 17, '<?xml version=': 0, '>': 17, 'https://': 20, 'lorem ipsum': 0, 'www.': 6, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '2293675', 'n_tokens_mistral': 1189, 'n_tokens_neox': 1116, 'n_words': 243}