Mercurial > repos > genouest > feelnc2asko

comparison feelnc2asko.pl @ 2:d30ecf96e4cd draft default tip

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planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit c0c2ee6f693fd83d002ed5b19ac52639790d2b6f
author genouest
date Fri, 20 Apr 2018 03:07:40 -0400
parents af75f883cab4
children
comparison
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1:af75f883cab4 2:d30ecf96e4cd
41 while (my $feat = $fncgtf->next_feature()) { 41 while (my $feat = $fncgtf->next_feature()) {
42 next if ($feat->primary_tag() ne 'exon'); 42 next if ($feat->primary_tag() ne 'exon');
43 43
44 my $mrna= ($feat->get_tag_values('transcript_id'))[0]; 44 my $mrna= ($feat->get_tag_values('transcript_id'))[0];
45 my $gene= ($feat->get_tag_values('gene_id'))[0]; 45 my $gene= ($feat->get_tag_values('gene_id'))[0];
46 if ($gene eq $mrna) {$mrna.=".mrna"}
46 # print STDERR "str: ", $feat->strand(), "\n"; 47 # print STDERR "str: ", $feat->strand(), "\n";
47 if (exists($genes{$gene})) { 48 if (exists($genes{$gene})) {
48 if ($genes{$gene}->start() > $feat->start()) { 49 if ($genes{$gene}->start() > $feat->start()) {
49 $genes{$gene}->start($feat->start()); 50 $genes{$gene}->start($feat->start());
50 } 51 }
94 while (my $feat = $nmgtf->next_feature()) { 95 while (my $feat = $nmgtf->next_feature()) {
95 next if ($feat->primary_tag() ne 'exon'); 96 next if ($feat->primary_tag() ne 'exon');
96 97
97 my $mrna= ($feat->get_tag_values('transcript_id'))[0]; 98 my $mrna= ($feat->get_tag_values('transcript_id'))[0];
98 my $gene= ($feat->get_tag_values('gene_id'))[0]; 99 my $gene= ($feat->get_tag_values('gene_id'))[0];
100 if ($gene eq $mrna) {$mrna.=".mrna"}
99 # print STDERR "str: ", $feat->strand() , "\n"; 101 # print STDERR "str: ", $feat->strand() , "\n";
100 if (exists($genes{$gene})) { 102 if (exists($genes{$gene})) {
101 if ($genes{$gene}->start() > $feat->start()) { 103 if ($genes{$gene}->start() > $feat->start()) {
102 $genes{$gene}->start($feat->start()); 104 $genes{$gene}->start($feat->start());
103 } 105 }