Overview
===========

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This package is meant to be an improvement on the `pytfmpval <https://github.com/j-andrews7/pytfmpval>`_ by `Jared Andrews <https://github.com/j-andrews7>`_ which is itself
a wrapper for the incredibly useful `TFM-Pvalue C++ program <http://bioinfo.lifl.fr/tfm-pvalue/tfm-pvalue.php>`_.
It allows users to determine score thresholds for a given transcription factor position frequency matrix
associated with a specific p-value. Naturally, it can also perform the reverse, quickly calculating an accurate
p-value from a score for a given motif matrix.

The `pytfmpval <https://github.com/j-andrews7/pytfmpval>`_ is archived and has several super annoying uncaught
excpetions that cause the whole program to crash every time there is any error so to start this package will focus
on:

1. making this package more robust at runtime
2. modernizing the interface a bit
    2.1. This primarily includes adding support for pandas and numpy arrays as opposed to purely white space delimited lists and the like

This should make everything better to use and make it feel like you are writing python code
instead or old school R or something.

``tfm_utls`` allows this functionality to be easily utilized within a Python script, module, or package.

See full documentation and use examples `here <https://mcclain-thiel.github.io/tfm-utils>`_.

.. toctree::
   :maxdepth: 2

   install
   examples
   docs


Contribute
---------------

Any and all contributions are welcome. Bug reporting via the `Issue Tracker <https://github.com/j-andrews7/pytfmpval/issues>`_ is much appeciated. Here's how to contribute:

1. Fork  `this repo <https://github.com/j-andrews7/pytfmpval>`_ on github (see `forking help <https://help.github.com/articles/fork-a-repo/>`_).

2. Make your changes/fixes/improvements locally.

3. Optional, but much-appreciated: write some tests for your changes. (Don't worry about integrating your tests into the test framework - writing some in your commit comments or providing a test script is fine. I will integrate them later.)

4. Send a pull request (see `pull request help <https://help.github.com/articles/about-pull-requests/>`_).


Reference
--------------

| Efficient and accurate P-value computation for Position Weight Matrices
| H. Touzet and J.S. Varré
| *Algorithms for Molecular Biology 2007, 2:15*

License
-----------

This project is licensed under the GPL3 license. You are free to use, modify, and distribute it as you see fit. The program is provided as is, with no guarantees.