Mercurial > repos > kuyt002 > mummer_toolsuite

comparison MUMmer/nucmer_coords2ACT_galaxy.pl @ 0:61f30d177448 default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
initial commit on Mummer toolsuite on toolshed
author eric
date Tue, 31 Mar 2015 14:19:49 +0200
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:61f30d177448
1 #!/usr/bin/perl
2
3 # converts the MUMmer-nucmer coords file in a file readable for Artemis Comparison Tool
4 # Output format is like crunch of BLAST
5 #
6 # [nov 2010] Galaxy wrapped up version
7 #
8 # Alex.Bossers@wur.nl
9
10
11 use warnings;
12 use strict;
13
14 #$filename=shift;
15 #$ARGV[0] =~ m/^([A-Z0-9_.-]+)$/ig;
16 my $filename = $ARGV[0];
17 #$ARGV[1] =~ m/^([A-Z0-9_.-]+)$/ig;
18 my $fileout = $ARGV[1];
19 #my $filename = "Curated_vs_noncurated_8067_01.nucmer.coords";
20 #my $fileout = "Curated_vs_noncurated_8067_01.nucmer.tab";
21
22 open (COORDS,$filename) || die "error opening input coords file";
23 open (OUT,">$fileout") || die "error opening tab output file";
24
25 while (<COORDS>)
26 {
27 unless ($_ =~ /^(\s*)\d/){next}
28 $_ =~ s/\|//g;
29
30 my @f = split;
31 # create crude match score = ((length_of_match * %identity)-(length_of_match * (100 - %identity))) /20
32 my $crude_plus_score=($f[4]*$f[6]);
33 my $crude_minus_score=($f[4]*(100-$f[6]));
34 my $crude_score= int(($crude_plus_score - $crude_minus_score) / 20);
35 # reorganise columns and print crunch format to stdout
36 # score %id S1 E1 seq1 S2 E2 seq2 (description)
37 print OUT " $crude_score $f[6] $f[0] $f[1] $f[7] $f[2] $f[3] $f[8] nucmer comparison coordinates\n"
38 }
39
40 close (COORDS);
41 close (OUT);
42 print "Done!\n\n";