pbeerli / simulations_for_topiccontml Goto Github PK

To simulate data for the topic modelling paper use these scripts:

python generator.py Theta divergence_time number_loci

to run the script you need the manyloci.py and a modified version of ms (see instructions
on https://github.com/pbeerli/divergencesupplement/tree/main/simulations)
to then generate the inputfiles for the topiccontml.py (see https://github.com/TaraKhodaei/TopicContml)
you will need to run migrate-modern-to-single-locus.py on each of the files generated with generator.py

An example:

mkdir sim_100_0.01_10
cp generator.py sim_100_0.01_10
cp ms sim_100_0.01_10
cp manyloci.py sim_100_0.01_10
cp migrate-modern-to-single-locus.py sim_100_0.01_10
cd sim_100_0.01_100
python generator.py 0.1 0.01 10
# this will generate 100 datafiles (infile...)
# each with 10 loci 
# for each datafile run
# python migrate-modern-to-single-locus.py infile_...
# for example:
python migrate-modern-to-single-locus.py infile_72_0.1_0.01_10
# this will create a directory siminfile_72_0.1_0.01_10
# that then can be used for run with topiccontml.py
# python topiccontml.py -f siminfile_72_0.1_0.01_10

We also added an additional_scripts folder containing coverter scripts for the biological datasets used in the manuscript.