# TYPICAL USAGE
# xy.pos.prolines("IGQPGAVGPAGIR")
#' count the prolines in the x and y position of a collagen peptide
#' @param seq the amino acid sequence
#' @param verbose default is False
#' @keywords isotopes mass sequence deamidation hyroxylation
#' @export
xy.ypos.prolines <- function(seq,verbose = F){
gcount <- vector(length = 3)
pcount <- vector(length = 3)
if(verbose)
message(sprintf("Sequence is %d long",length(seq)))
for(ii in 1:nchar(seq)){
pos <- (ii%%3)+1
if(substr(seq,ii,ii) == "G")
gcount[pos] = gcount[pos] + 1#str_count(seq[ii],"G")
if(substr(seq,ii,ii) == "P")
pcount[pos] = pcount[pos] + 1#str_count(seq[ii],"P")
#if(verbose){
# message(sprintf("ii = %d, pos %d, letter = %s, gcount = %d %d %d, pcount = %d %d %d",ii,pos,
# substr(seq,ii,ii),
# gcount[1],gcount[2],gcount[3],
# pcount[1],pcount[2],pcount[3]))
#}
}
gmax = which.max(gcount)
ypos = (gmax+1)%%3+1
if(verbose){
message(sprintf("sequence: %s",seq))
message(sprintf("G count positions: %d %d %d, max %d",gcount[1],gcount[2],gcount[3],gmax))
message(sprintf("P count positions: %d %d %d, yct %d",pcount[1],pcount[2],pcount[3],ypos))
}
return(pcount[ypos])
}
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