--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bowtie_to_bed.pl	Sat Mar 31 22:57:16 2012 -0400
@@ -0,0 +1,45 @@
+#!/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;
+}