Mercurial > repos > earlhaminst > blast_parser

annotate blast_parser.pl @ 0:87eda806422d draft

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
author earlhaminst
date Mon, 12 Dec 2016 07:13:57 -0500
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87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
1 #!/usr/bin/perl
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
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2 use strict;
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
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3 use warnings;
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
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4 use List::Util qw(min max);
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
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87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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6 # A simple Perl parser to convert a BLAST 12-column or 24-column output into a
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
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7 # 3-column input for hcluster_hg (id1, id2, weight):
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
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8 # parse_blast.pl <file>
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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10 use constant LOG_E_10 => log(10);
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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11
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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12 my $file1 = $ARGV[0];
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
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13 open my $fh1, '<', $file1;
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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15 while (my $line = <$fh1>) {
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
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16 my @row = split(/\t/, $line);
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
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18 if ($row[0] eq $row[1]) {
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
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19 # ignore self matching hits
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
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20 } else {
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
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21 # Convert evalue to an integer weight with max 100
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
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22 my $weight = 100;
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
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24 #if the evalue is 0, leave weight at 100
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
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25 if ($row[10] != 0 && $row[10] != 0.0) {
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
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26 $weight = min(100, positive_round(-1 * log10($row[10])));
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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27 }
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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28 print"$row[0]\t$row[1]\t$weight\n";
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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29 }
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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30 }
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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31 close $fh1;
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
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33 # Calculate logarithm to base 10 of a number
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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34 sub log10 {
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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35 my $n = shift;
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
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36 return log($n) / LOG_E_10;
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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37 }
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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38
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
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39 # Round a positive float to the nearest integer
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
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40 sub positive_round{
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
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41 my $n = shift;
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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42 return int($n + 0.5);
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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43 }