Overview

This package is meant to be an improvement on the pytfmpval by Jared Andrews which is itself a wrapper for the incredibly useful TFM-Pvalue C++ program. 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 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.

Contribute

Any and all contributions are welcome. Bug reporting via the Issue Tracker is much appeciated. Here’s how to contribute:

  1. Fork this repo on github (see forking help).

  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).

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.