simdna: simulated datasets of DNA

Installation

git clone https://github.com/kundajelab/simdna.git
cd simdna
python setup.py develop

Examples

Please see the scripts folder for example scripts generating simulations and the scripts_test folder for example arguments.

• densityMotifSimulation.py generates a simulated dataset where multiple instances of motifs are present per sequence, as determined by a poisson distribution which could optionally be subject to zero-inflation.
• motifGrammarSimulation.py illustates how to set up a simulation where two motifs have a fixed-spacing or variable-spacing grammar (set --generationSetting to twoMotifsFixedSpacing or twoMotifsVariableSpacing as desired).
• emptyBackground.py just generates a background sequence with no motifs embedded.