mpg

MPG: Markov Process Generator of DNA sequences


Keywords
bioinformatics
License
MIT
Install
pip install mpg==0.2.1

Documentation

Markovian Sequence Generator

Generates DNA sequences using a Markov Chain, learned from some reference sequence(s).

Many thanks to Ben Kaehler for a proof of concept and mathematical assistance.

Disclaimer: This is unstable software at the moment. Use with caution.

https://travis-ci.org/kdmurray91/mpg.svg?branch=master

Installation

pip3 install mpg

Usage

The script mpg should have been installed. This learns the transition probablitlies from sequences (in Fasta format) and generates random sequences from this Markov chain.

To learn transition probabilities for a 5th-order Markov chain from the Arabidopsis genome and store them in a file (ath.h5):

mpg -k 5 -d ath.h5 TAIR_10.fasta

To use these transition probablitlies to generate a sequence of 1000bp:

mpg -l 1000 -r ath.h5

To do the above operations at once:

mpg -l 1000 -k 5 TAIR_10.fasta