find_repeat.R

#Gives the start locations and numbers of consecutive repeats in seq of any instances of at least
#repmin consecutive repeats of ms.
#
#Args
#ms       A character string with a prospective microsatellite (A, T, G, Cs)
#seq      A character string (possibly quite long) with the sequence (A, T, G, Cs)
#repmin   Number of repeats, at least this many required for ms to register
#
#Output - a data frame (possibly empty) with these columns:
#microsat     The microsat, ms
#loc          The start position
#numrep       The number of repeats
#
find_repeat<-function(ms,seq,repmin)
{
  #call find_fixed
  locs<-find_fixed(ms,seq)
  
  #use the output of find_fixed to find the repeats
  ncms<-nchar(ms)
  res<-data.frame(microsat=character(),loc=integer(),numrep=integer(),stringsAsFactors = F)
  while (length(locs>0))
  {
    #gets the number of repeats
    numrep<-1
    while ((locs[1]+numrep*ncms) %in% locs)
    {
      numrep<-numrep+1
    }
    
    #store the info
    dr1<-dim(res)[1]
    res[dr1+1,1]<-ms
    res[dr1+1,2:3]<-c(locs[1],numrep)
    
    #throw away the part of locs you have been over
    locs<-locs[locs>=locs[1]+numrep*ncms]
  }
  
  res<-res[res$numrep>=repmin,]
  
  return(res)
}


#find_repeat("AG","TAGAGAGTAGCAGAGCTTTTACAGAT",2)
#find_fixed("AG","AGTAGCAGAGCTTTTACAGAT")


#alternatively,

my_find_repeat<-function(ms,seq,repmin){
  
  z<-my_find_fixed(ms,seq)
  ncms<-nchar(ms)
  
  if(z[1]!=-1){
    s<-split(z, cumsum(c(1, diff(z) != ncms)))
    loc<-c()
    numrep<-c()
    for(i in 1:length(s)){
      temploc<-s[[i]][1]
      tempnumrep<-length(s[[i]])
      loc<-c(loc,temploc)
      numrep<-c(numrep,tempnumrep)
    }
    res<-data.frame(ms=ms,loc=loc,numrep=numrep)
    res<-res[res$numrep>=repmin,]
    
  }else{
    res<-data.frame(ms=ms,loc=NA,numrep=NA)
  }
  
  return(res)
}

#my_find_repeat(ms="AG",seq="TAGAGAGTAGCAGAGCTTTTACAGAT",repmin=2)