Mercurial > repos > abossers > mummer_toolsuite

annotate MUMmer/nucmer_coords2ACT_galaxy.pl @ 0:6753195df9e0 default tip

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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author abossers
date Tue, 07 Jun 2011 17:49:58 -0400
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6753195df9e0 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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1 #!/usr/bin/perl
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2
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3 # converts the MUMmer-nucmer coords file in a file readable for Artemis Comparison Tool
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4 # Output format is like crunch of BLAST
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5 #
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6 # [nov 2010] Galaxy wrapped up version
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7 #
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8 # Alex.Bossers@wur.nl
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11 use warnings;
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12 use strict;
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14 #$filename=shift;
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15 #$ARGV[0] =~ m/^([A-Z0-9_.-]+)$/ig;
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16 my $filename = $ARGV[0];
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17 #$ARGV[1] =~ m/^([A-Z0-9_.-]+)$/ig;
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18 my $fileout = $ARGV[1];
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19 #my $filename = "Curated_vs_noncurated_8067_01.nucmer.coords";
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20 #my $fileout = "Curated_vs_noncurated_8067_01.nucmer.tab";
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21
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22 open (COORDS,$filename) || die "error opening input coords file";
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23 open (OUT,">$fileout") || die "error opening tab output file";
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24
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25 while (<COORDS>)
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26 {
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27 unless ($_ =~ /^(\s*)\d/){next}
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28 $_ =~ s/\|//g;
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29
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30 my @f = split;
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31 # create crude match score = ((length_of_match * %identity)-(length_of_match * (100 - %identity))) /20
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32 my $crude_plus_score=($f[4]*$f[6]);
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33 my $crude_minus_score=($f[4]*(100-$f[6]));
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34 my $crude_score= int(($crude_plus_score - $crude_minus_score) / 20);
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35 # reorganise columns and print crunch format to stdout
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36 # score %id S1 E1 seq1 S2 E2 seq2 (description)
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37 print OUT " $crude_score $f[6] $f[0] $f[1] $f[7] $f[2] $f[3] $f[8] nucmer comparison coordinates\n"
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38 }
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39
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40 close (COORDS);
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41 close (OUT);
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42 print "Done!\n\n";