--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/MUMmer/nucmer_coords2ACT_galaxy.pl	Tue Mar 31 14:19:49 2015 +0200
@@ -0,0 +1,42 @@
+#!/usr/bin/perl
+
+# converts the MUMmer-nucmer coords file in a file readable for Artemis Comparison Tool
+# Output format is like crunch of BLAST
+#
+# [nov 2010] Galaxy wrapped up version
+#
+# Alex.Bossers@wur.nl
+
+
+use warnings;
+use strict;
+
+#$filename=shift;
+   #$ARGV[0] =~ m/^([A-Z0-9_.-]+)$/ig;
+my $filename = $ARGV[0];
+   #$ARGV[1] =~ m/^([A-Z0-9_.-]+)$/ig;
+my $fileout = $ARGV[1];
+#my $filename	=	"Curated_vs_noncurated_8067_01.nucmer.coords";
+#my $fileout	=	"Curated_vs_noncurated_8067_01.nucmer.tab";
+
+open (COORDS,$filename) || die "error opening input coords file";
+open (OUT,">$fileout") || die "error opening tab output file";
+
+while (<COORDS>)
+         {
+    unless ($_ =~ /^(\s*)\d/){next}
+    $_ =~ s/\|//g;
+
+    my @f = split;
+          # create crude match score = ((length_of_match * %identity)-(length_of_match * (100 - %identity))) /20
+    my $crude_plus_score=($f[4]*$f[6]);
+    my $crude_minus_score=($f[4]*(100-$f[6]));
+    my $crude_score=  int(($crude_plus_score  - $crude_minus_score) / 20);
+          # reorganise columns and print crunch format to stdout
+          # score        %id   S1    E1    seq1  S2    E2    seq2  (description)
+    print OUT " $crude_score $f[6] $f[0] $f[1] $f[7] $f[2] $f[3] $f[8] nucmer comparison coordinates\n"
+         }
+
+close (COORDS);
+close (OUT);
+print "Done!\n\n";