<commit_before>mafreader Quickstart
=================

mafreader is a simple command line tool that reads a `MAF https://wiki.nci.nih.gov/display/TCGA/Mutation+Annotation+Format+%28MAF%29+Specification` file, calls `CIViC https://civic.genome.wustl.edu` for each line therein.

mafreader outputs a table in `markdown https://help.github.com/articles/github-flavored-markdown/#tables` format for easy inclusion into downstream reports

mafreader requires Python 3.*. To check your python version, run:

.. code:: console

    $ python -V
    Python 3.4.2


Usage:

.. code:: console

    $ python mafreader.py -h
    usage: civic [-h] [-i INPUT_FILE] [-o OUTPUT_FILE] [-c HOST]
                 [-col ENTREZ_ID_COLUMN]

    optional arguments:
      -h, --help            show this help message and exit
      -i INPUT_FILE, --input_file INPUT_FILE<commit_msg>first commit<commit_after>mafreader Quickstart
=================

mafreader is a simple command line tool that reads a `MAF https://wiki.nci.nih.gov/display/TCGA/Mutation+Annotation+Format+%28MAF%29+Specification`_ file, calls `CIViC https://civic.genome.wustl.edu`_ for each line therein.

mafreader outputs a table in `markdown https://help.github.com/articles/github-flavored-markdown/#tables`_ format for easy inclusion into downstream reports

mafreader requires Python 3.*. To check your python version, run:

.. code:: console

    $ python -V
    Python 3.4.2


Usage:

.. code:: console

    $ python mafreader.py -h
    usage: civic [-h] [-i INPUT_FILE] [-o OUTPUT_FILE] [-c HOST]
                 [-col ENTREZ_ID_COLUMN]

    optional arguments:
      -h, --help            show this help message and exit
      -i INPUT_FILE, --input_file INPUT_FILE
{'fraction_non_alphanumeric': 0.12325581395348838, 'fraction_numerical': 0.009302325581395349, 'mean_word_length': 3.2389162561576357, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 6, 'lorem ipsum': 0, 'www.': 0, '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': '5035343', 'n_tokens_mistral': 567, 'n_tokens_neox': 538, 'n_words': 166}