From 9d978970e5f58882e873a53c1320b079692b8134 Mon Sep 17 00:00:00 2001
From: Alessandro Vullo <avullo@ebi.ac.uk>
Date: Tue, 28 May 2013 13:21:35 +0000
Subject: [PATCH] Added (private) method _make_start_codon_features
---
modules/Bio/EnsEMBL/Utils/IO/GTFSerializer.pm | 61 +++++++++++++++++++
1 file changed, 61 insertions(+)
diff --git a/modules/Bio/EnsEMBL/Utils/IO/GTFSerializer.pm b/modules/Bio/EnsEMBL/Utils/IO/GTFSerializer.pm
index 1da9d38b9c..aa5373610f 100644
--- a/modules/Bio/EnsEMBL/Utils/IO/GTFSerializer.pm
+++ b/modules/Bio/EnsEMBL/Utils/IO/GTFSerializer.pm
@@ -32,6 +32,7 @@ package Bio::EnsEMBL::Utils::IO::GTFSerializer;
use strict;
use warnings;
+use Bio::EnsEMBL::SeqFeature;
use Bio::EnsEMBL::Utils::Exception;
use Bio::EnsEMBL::Utils::IO::FeatureSerializer;
use Bio::EnsEMBL::Utils::Scalar qw/check_ref/;
@@ -64,4 +65,64 @@ sub print_feature {
}
+=head2 _make_start_codon_features
+
+ Arg [1] : Bio::EnsEMBL::Transcript
+ Example :
+ Description:
+ Returntype : Array
+
+=cut
+
+sub _make_start_codon_features {
+ my ($self, $trans) = @_;
+
+
+ if (!$trans->translation) {
+ return (());
+ }
+
+ my @translateable = @{$trans->get_all_translateable_Exons};
+
+ my @pepgencoords = $trans->pep2genomic(1,1);
+
+ # cdna can come padded these days so allow gap at the start
+ if($pepgencoords[0]->isa('Bio::EnsEMBL::Mapper::Gap')){
+ shift @pepgencoords;
+ }
+
+ if(scalar(@pepgencoords) > 3) {
+ throw(sprintf "Pep start for transcript %s does not map cleanly", $trans->display_id);
+ }
+
+ unless($pepgencoords[0]->isa('Bio::EnsEMBL::Mapper::Coordinate')) {
+ throw(sprintf "Pep start for transcript %s maps to gap", $trans->display_id);
+ }
+ unless($pepgencoords[$#pepgencoords]->isa('Bio::EnsEMBL::Mapper::Coordinate')) {
+ throw(sprintf "Pep start (end of) for transcript %s maps to gap", $trans->display_id);
+ }
+
+ @translateable = @{$trans->get_all_translateable_Exons};
+ my @startc_feat;
+ my $phase = 0;
+ foreach my $pepgencoord (@pepgencoords) {
+ push @startc_feat, new Bio::EnsEMBL::SeqFeature(
+ -seqname => $trans->stable_id,
+ -source_tag => 'starttrans',
+ -primary_tag => 'similarity',
+ -start => $pepgencoord->start,
+ -end => $pepgencoord->end,
+ -phase => $phase,
+ -strand => $translateable[0]->strand);
+ $phase = 3 - ($pepgencoord->end - $pepgencoord->start + 1);
+ }
+ if ($translateable[0]->strand == 1) {
+ @startc_feat = sort {$a->start <=> $b->start } @startc_feat;
+ } else {
+ @startc_feat = sort {$b->start <=> $a->start } @startc_feat;
+ }
+ return @startc_feat;
+
+}
+
1;
--
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