# HG changeset patch
# User dsobral
# Date 1331826473 14400
# Node ID a0e05808610a1ced73cb1422f01714810129c57c
# Parent  633ca40ded01f15100277614c933438dbf971734
Uploaded

diff -r 633ca40ded01 -r a0e05808610a reorient_coordinates.pl
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/reorient_coordinates.pl	Thu Mar 15 11:47:53 2012 -0400
@@ -0,0 +1,19 @@
+open(FILE,"<", $ARGV[0]) or die "cannot open for reading ".$ARGV[0].": $!";
+open(FO,">", $ARGV[1]) or die "cannot open for writing ".$ARGV[1].": $!";
+while(<FILE>){
+        chomp;
+        my @cols = split(/\t/);
+        print FO $cols[0];
+        if($cols[1]>$cols[2]){
+                print FO "\t".$cols[2]."\t".$cols[1];
+        } else {
+                print FO "\t".$cols[1]."\t".$cols[2];
+        }
+        #Can only take coordinates
+        #for($i=3;$i<scalar(@cols);$i++){
+        #        print "\t".$cols[$i];
+        #}
+        print FO "\n";
+}
+close FILE;
+close FO;
\ No newline at end of file