bedProject

#!/usr/bin/gawk -f
# maximilian, 6/06

BEGIN { 
	if (ARGC==1 || ARGC>4) {
	  print;
	  print "Will change the seqname-fields of a bed file and"
	  print "and will add a given offset to both start- and end-pos"
	  print "fields of bed. Is used to project results from a program"
	  print "that returned coordinates from 0...x to a given chromosome"
	  print "If you specify a fasta-file as parameter, we will "
	  print "read seqname/offset from the seqname-line of the fasta-file"
	  print "It has to be in UCSC-style format, eg:"
	  print "  >seqname range=chr4:1012-1050"
	  print "In this case seqname would be 'chr4' and offset '1012'. "
          print "If you add -r at the end, coordinates will be SUBSTRACTED"
          print "offset instead of added!"
	  print ""
	  print "SYNTAX:"
	  print " bedproject <seqname> <offset>" 
	  print " bedproject <seqname> <offset> -r" 
	  print " bedproject <fasta-file>"
	  print " bedproject <fasta-file> -r"
	  print "EXAMPLE:"
	  print " cat bla.bed | bedproject chr4 1204"
	  print " cat bla.bed | bedproject bla.fa"
          exit 1
        }
	
        OFS="\t"
	if (ARGV[ARGC-1]=="-r") {
            rev=1;
            ARGC-=1;
        }

	if (ARGC==3) {
	 seqname = ARGV[1]
	 offset = ARGV[2]
	 revOffset = ARGV[2]
        }

	if (ARGC==2) {
	 FS = " "
	 getline < ARGV[1]
	 split($2, range, "=")
	 split(range[2], coords, ":")
	 seqname = coords[1]
	 split(coords[2], positions, "-")
	 offset = positions[1]
         revOffset = positions[2]
	}

	 ARGV[1]="-"
	 ARGC=2
      }

/track/ { print; next;}
/browser/ {print; next;}

/.*[a-z]+.*/	{ 
	 if ($2 < 0) {
	    print "bedproject Error: negative position found!"  > "/dev/stderr"
	    exit 1
         }
	if (rev==1) {
            if ($6=="+") {
                $6="-"
            }
            else if ($6=="-") {
                $6="+"
            }
            if (revOffset-$3 < 0) {
                dropped+=1;
                next
                }
            print seqname, revOffset-$3, revOffset-$2, $4, $5, $6, $7, $8, $9, $10, $11, $12, $13;
        }
        else { 
        if (offset+$2 < 0) {
            print "warning: dropping negative startpos feature" > "/dev/stderr"
            next
        }
	if (NF>7) 
	    print seqname, offset+$2, offset+$3, $4, $5, $6, offset+$7, offset+$8, $9, $10, $11, $12, $13;
	else
	    print seqname, offset+$2, offset+$3, $4, $5, $6;
    }
       	}

END { if (dropped!=0) { 
                print "warning: dropped "dropped" negative startpos features" > "/dev/stderr"
            }
        }