R/clean.simphy.folder.R

In huatengh/Classiphy: Classify gene trees basing on the processes generating species-tree gene-tree discordance

#this is a function used to compile all the individual gt file generated by simphy in to on big file
#called by simphy.simu function
clean.simphy.folder<-function(repfolder,remove.individual.gtreefiles){
  gfiles<-dir(path = repfolder,pattern = "g_trees\\d+.trees")
  glist<-as.integer(sub("g_trees(\\d+).trees","\\1",gfiles))
  gfiles<-gfiles[order(glist)]
  gtrees<-c()
  for(gfile in gfiles){
    x<-scan(file = paste(repfolder,gfile,sep='/'),what='character',n=1,sep='\n',quiet=T)
    gtrees<-c(gtrees,x)

  }

  new.g.file=paste(repfolder,'g_trees.trees',sep='/')
  sink(new.g.file)
  cat(paste(gtrees,sep='',collapse = '\n'))
  sink()

  if(remove.individual.gtreefiles){
    for(gfile in gfiles){
      unlink(x = paste(repfolder,gfile,sep='/'))
    }
  }
}