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simdna: simulated datasets of DNA

license

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.