Mercurial > repos > genouest > feelnc2asko

annotate feelnc2asko.pl @ 0:e323c49b8bcc draft

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planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
author genouest
date Thu, 12 Apr 2018 06:05:23 -0400
parents
children af75f883cab4
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e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
genouest
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diff changeset
1 use strict;
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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2 use warnings;
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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3 use Getopt::Long;
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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4 use Bio::Tools::GFF;
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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5
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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6 my ($anngff, $lncgff, $newgff);
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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7
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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8 GetOptions("ann=s" => \$anngff, "lnc=s" => \$lncgff, "new=s" => \$newgff);
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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9
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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10 my $gffout = Bio::Tools::GFF->new(-fh=> \*STDOUT, -gff_version => 3);
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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11
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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12 #1. the standard annotation
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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13 my $gffin = Bio::Tools::GFF->new(-file => $anngff, -gff_version => 3);
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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14
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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15
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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16 while (my $feature = $gffin->next_feature()) {
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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17 if ($feature-> primary_tag eq 'mRNA') {
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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18 my ($gene)=$feature->get_tag_values("gene");
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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19 $feature->remove_tag("Parent");
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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20 $feature->add_tag_value("Parent", $gene);
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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21 $feature->add_tag_value("feelnc_type", "standard");
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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22 $gffout->write_feature($feature);
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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23 }
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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24 if ($feature-> primary_tag eq 'gene') {
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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25 my ($name)=$feature->get_tag_values("Name");
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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26 $feature->remove_tag("ID");
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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27 $feature->add_tag_value("ID", $name);
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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28 $feature->add_tag_value("feelnc_type", "standard");
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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29 $gffout->write_feature($feature);
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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30 }
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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31 }
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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32 $gffin->close();
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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33
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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34
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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35 my %genes=();
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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36 my %transcripts=();
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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37
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38 #2. The lncRNA gtf
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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39 my $fncgtf = Bio::Tools::GFF->new( -file => $lncgff, -gff_version => '2' );
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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40
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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41 while (my $feat = $fncgtf->next_feature()) {
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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42 next if ($feat->primary_tag() ne 'exon');
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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43
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44 my $mrna= ($feat->get_tag_values('transcript_id'))[0];
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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45 my $gene= ($feat->get_tag_values('gene_id'))[0];
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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46 # print STDERR "str: ", $feat->strand(), "\n";
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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47 if (exists($genes{$gene})) {
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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48 if ($genes{$gene}->start() > $feat->start()) {
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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49 $genes{$gene}->start($feat->start());
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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50 }
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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51 if ($genes{$gene}->end() < $feat->end()) {
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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52 $genes{$gene}->end($feat->end());
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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53 }
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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54 }
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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55 else {
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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56 my $geneft = Bio::SeqFeature::Generic->new(
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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57 -start => $feat->start(),
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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58 -end => $feat->end(),
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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59 -strand => $feat->strand(),
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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60 -primary_tag => 'gene',
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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61 -source_tag => $feat->source_tag(),
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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62 -seq_id => $feat->seq_id());
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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63 # $geneft->add_tag_value("feelnc_type", "lncRNA");
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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64 $genes{$gene}=$geneft;
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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65 }
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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66
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67 if (exists($transcripts{$mrna})) {
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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68 if ($transcripts{$mrna}->start() > $feat->start()) {
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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69 $transcripts{$mrna}->start($feat->start());
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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70 }
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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71 if ($transcripts{$mrna}->end() < $feat->end()) {
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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72 $transcripts{$mrna}->end($feat->end());
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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73 }
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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74 }
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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75 else {
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76 my $tr = Bio::SeqFeature::Generic->new(
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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77 -start => $feat->start(),
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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78 -end => $feat->end(),
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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79 -strand => $feat->strand(),
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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80 -primary_tag => 'mRNA',
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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81 -source_tag => $feat->source_tag(),
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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82 -seq_id => $feat->seq_id());
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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83 $tr->add_tag_value("ID", $mrna);
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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84 $tr->add_tag_value("Parent",$gene);
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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85 $tr->add_tag_value("feelnc_type", "lncRNA");
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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86 $transcripts{$mrna}=$tr;
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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87 }
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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88 }
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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89
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90 #3. The new mRNA gtf
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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91 my $nmgtf = Bio::Tools::GFF->new( -file => $newgff, -gff_version => '2' );
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92
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93 while (my $feat = $nmgtf->next_feature()) {
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94 next if ($feat->primary_tag() ne 'exon');
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95
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96 my $mrna= ($feat->get_tag_values('transcript_id'))[0];
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97 my $gene= ($feat->get_tag_values('gene_id'))[0];
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98 # print STDERR "str: ", $feat->strand() , "\n";
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99 if (exists($genes{$gene})) {
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100 if ($genes{$gene}->start() > $feat->start()) {
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101 $genes{$gene}->start($feat->start());
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102 }
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103 if ($genes{$gene}->end() < $feat->end()) {
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104 $genes{$gene}->end($feat->end());
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105 }
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106 }
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107 else {
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108 my $geneft = Bio::SeqFeature::Generic->new(
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109 -start => $feat->start(),
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110 -end => $feat->end(),
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111 -strand => $feat->strand(),
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112 -primary_tag => 'gene',
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113 -source_tag => $feat->source_tag(),
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114 -seq_id => $feat->seq_id());
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115 $geneft->add_tag_value("ID", $gene);
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116 # $geneft->add_tag_value("feelnc_type", "new");
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117 $genes{$gene}=$geneft;
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118 }
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119
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120 if (exists($transcripts{$mrna})) {
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121 if ($transcripts{$mrna}->start() > $feat->start()) {
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122 $transcripts{$mrna}->start($feat->start());
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123 }
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124 if ($transcripts{$mrna}->end() < $feat->end()) {
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125 $transcripts{$mrna}->end($feat->end());
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126 }
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127 }
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128 else {
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129 my $tr = Bio::SeqFeature::Generic->new(
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130 -start => $feat->start(),
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131 -end => $feat->end(),
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132 -strand => $feat->strand(),
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133 -primary_tag => 'mRNA',
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134 -source_tag => $feat->source_tag(),
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135 -seq_id => $feat->seq_id());
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136 $tr->add_tag_value("ID", $mrna);
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137 $tr->add_tag_value("Parent",$gene);
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138 $tr->add_tag_value("feelnc_type", "new");
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139 $transcripts{$mrna}=$tr;
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140 }
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141 }
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142
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143 foreach my $mrna (keys %transcripts) {
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144 my ($parent)=$transcripts{$mrna}->get_tag_values("Parent");
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145 $gffout->write_feature($genes{$parent});
e323c49b8bcc planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 92849224db1963d090fbb25d410cc659a5449241
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146 $gffout->write_feature($transcripts{$mrna});
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147 }