Mercurial > repos > xuebing > sharplabtool
view tools/mytools/bowtie2bed.pl @ 3:33c067c3ae34
Deleted selected files
author | xuebing |
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date | Fri, 09 Mar 2012 19:47:53 -0500 |
parents | 9071e359b9a3 |
children |
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#!/usr/bin/perl # write bowtie output to bed file # perl bowtie2bed.pl s_5_trimmed.map outputfile 200 # input # inputfile # extension $inputfile = $ARGV[0]; $extension = $ARGV[2]; $outputfile = $ARGV[1];#$inputfile.".extended_$extension"."bp.bed"; print "input file: $inputfile\n"; print "output file: $outputfile\n"; print "track name: $outputfile\n"; open (IN,$inputfile) or die $!; open (OUT,">$outputfile") or die $!; print OUT "track name=$outputfile itemRgb=On\n"; while(<IN>) { @flds = split/\t/; $flds[0] =~ s/ /-/g;#substitute space to dash if ($flds[1] eq "+") { print OUT join("\t",$flds[2],$flds[3],$flds[3]+$extension+length($flds[4]),$flds[0],1,$flds[1],$flds[3],$flds[3]+length($flds[4]),"255,0,0","\n"); } else { print OUT join("\t",$flds[2],max(0,$flds[3]-$extension),$flds[3]+length($flds[4]),$flds[0],1,$flds[1],$flds[3],$flds[3]+length($flds[4]),"0,255,0","\n"); } } close(IN); close(OUT); sub max() { ($a,$b) = @_; return $a>$b?$a:$b; }