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MPG: Markov Process Generator of DNA sequences

Project description

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.

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Installation

pip install cython numpy nose
pip install -U -e 'git+https://github.com/kdmurray91/mpg#egg=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 probablities for a 5th-order Markov chain from the Arabidopsis genome and store them in a file (ath.yml):

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

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

mpg -l 1000 -r ath.yml

To do the above operations at once:

mpg -l 1000 -k 5 TAIR_10.fasta

Project details


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