STARPS

A simulation tool for cultivation of bacterial populations according to a Wright-Fisher model of inheritance.

Usage

Compilation

To compile the C code, the Gnu Scientific Library is needed.

gcc -o WrightFisher_call WrightFisher_call.c -Wall -I/usr/include -lm -lgsl -lgslcblas

Running a simulation

The file WrightFisher_call.c is called within the R environment using WFwrapper_call.c:

source("/mnt/powervault/jonhall/Desktop/Forensics/STARPS/R/WFwrapper_call.R")
source("/mnt/powervault/jonhall/Desktop/Forensics/STARPS/R/draweff.R")
cat(sprintf('Generate fitness effects...\n'))
fitn.eff <- draweff(size = tsize)
cat(sprintf('Generate an initial population...\n'))
initPop<-matrix(0,2,4)

initPop[1:2,4]<-1
initPop[1,3]<-0.999
initPop[2,3]<-0.001
initPop[2,2]<-1
initPop[2,1]<-1
colnames(initPop)<-c("clone",157321,"frequency","fitness")

cat(sprintf('Start a cultivation...\n'))
init.pop <- WFwrapper(nGen=nGen, 
      popsize=popsize, 
      expfactor=expfactor, 
      mutrate=mutrate, 
      size=size, 
      verbosity=verbosity, 
      p1=p1, 
      p2=p2, 
      mu=mu, 
      initPop=initPop, 
      thresf=thresf, 
      marker=marker, 
      fitn.eff=fitn.eff, 
      simple=simple)

The input to WFwrapper_call.R is

nGen is number of generations per passage
popsize is the initial population size
expfact is the expansion factor for bacterial growth
mutrate is the mutation rate, per genome per cell division per base
size is the bacterial or viral genome size in base pairs
verbosity: should additional information be displayed on the screen: 0 for no additional info, 1 for additional info
p1 is the probability of a harmful mutation (on fitness)
p2 is the probability of a neutral mutation (on fitness)
mu is the average selective advantage (or disadvantage) of mutations (mean of exp dist)
thresn is a threshold used to avoid unneccesary extensive computational times to calculate the nucleotide diversity
thresf is a threshold used to avoid saving unneccesary large data (i.e skip low abundant genotypes and mutations) for computationally challenging runs, set saveadd to 0
marker is a flag for simulating biallelic (i.e. SNP or indels) data (marker = 1) or VNTR data (marker = 2)
flag is telling whether diversity calculations should be performed within the main loop
simple is a flag for allowing multiple mutations at the same bacteria in the same generation (i.e. at the same copy of a genotype). Default is simple = 0, i.e. allowing for multiple mutations. Warning! Might increase the required computational time substantially!

FOI-Bioinformatics/STARPS

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