BedProject

1. !/usr/bin/gawk -f
2. max 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, $
       }
       else { 
       if (offset+$2 < 0) {
           print "warning: dropping negative startpos feature" > "/dev/stderr"
           next
       }
       print seqname, offset+$2, offset+$3, $4, $5, $6, $7, $8, $9, $10, $11, $
   }
       }

END { if (dropped!=0) {

               print "warning: dropped "dropped" negative startpos features" > 
           }
       }