FastaUtils.R.txt

#' @title read sequences from a fasta file
#'
#' @description
#'
#' @param infile input filename of a standard
#' fasta file
#' ...
#' @export
read.fasta <- function (filename,n=-1,id='')  {
        fasta=list()
        fin = file(filename,'r')
        i=0
        while(length((line=readLines(fin,n=1L)))>0)  {
          if (grepl('^>',line)) {
                  i=i+1
                if (n != - 1 & i > n) {
                        break
                }
                  cid = gsub('^>([^ ]+).+','\\1',line)
                  
                  if(id !='' & cid == id)
                  {
                         fasta[[cid]]=''
                  }
                  else if (id=='') {
                  
                         fasta[[cid]]='' 
                         }
                  else if (id != '' & cid != id & length(names(fasta)) > 0) {
					  break
				  }
                
          } else if (grepl ('^[A-Za-z]',line)) {
                  seq=gsub('[^A-Za-z]','',line)
                  fasta[[cid]]=paste(fasta[[cid]],seq,sep='')
                   
                }
                
        }
        
        close(fin)
        class(fasta)="FastaUtils"
        return(fasta)
}

print.FastaUtils <- function (x) {
        for (nm in names (x)) {
                cat(paste(nm,"\t",nchar(x[[nm]]),"\n",sep=''))
        }
}

#creating the data frames with elements ( coloumns id and length)
summary.FastaUtils <- function (x) {
        df=data.frame(id=names(x),length=rep(0,length(names(x))))
        #TODO: create a data frame with coloumns id and length and return it
          i=1
        for (n in names(x)) {
            df[i,'length']= nchar(x[n])
            i=i+1
            
            
        }
        return(df)
        
}
#fu=read.fasta(commandArgs(trailingOnly=TRUE)[1],n=5)
Main <- function () {
	args=commandArgs(trailingOnly=TRUE)
	if (length(args) == 1) {
		fu=read.fasta(args[1])
	} else if (length(args) == 2 & grepl('^[0-9]+$',args[2])) {
		fu=read.fasta(args[1],n=as.integer(args[2]))
	} else if (length(args) == 2) {
		fu=read.fasta(args[1],id=args[2])
	} else {
		print("Usage ...")
		q()
	}
	print(fu)
}
if (sys.nframe() == 0 & !interactive()) {
	Main()
}