From e1546321e9abdf72931c353e4a41b69bdea59e76 Mon Sep 17 00:00:00 2001
From: Alessandro Vullo <avullo@ebi.ac.uk>
Date: Tue, 28 May 2013 13:30:52 +0000
Subject: [PATCH] Added (private) method _make_stop_codon_features
---
modules/Bio/EnsEMBL/Utils/IO/GTFSerializer.pm | 81 ++++++++++++++++---
1 file changed, 69 insertions(+), 12 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Utils/IO/GTFSerializer.pm b/modules/Bio/EnsEMBL/Utils/IO/GTFSerializer.pm
index aa5373610f..a681467fb8 100644
--- a/modules/Bio/EnsEMBL/Utils/IO/GTFSerializer.pm
+++ b/modules/Bio/EnsEMBL/Utils/IO/GTFSerializer.pm
@@ -76,11 +76,10 @@ sub print_feature {
sub _make_start_codon_features {
my ($self, $trans) = @_;
+ defined $trans or
+ throw("Transcript object not defined");
-
- if (!$trans->translation) {
- return (());
- }
+ return (()) unless $trans->translation;
my @translateable = @{$trans->get_all_translateable_Exons};
@@ -106,14 +105,14 @@ sub _make_start_codon_features {
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);
+ 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) {
@@ -121,8 +120,66 @@ sub _make_start_codon_features {
} else {
@startc_feat = sort {$b->start <=> $a->start } @startc_feat;
}
+
return @startc_feat;
}
+=head2 _make_stop_codon_features
+
+ Arg [1] : Bio::EnsEMBL::Transcript
+ Example :
+ Description:
+ Returntype : Array
+
+=cut
+
+sub _make_stop_codon_features {
+ my ($self, $trans) = @_;
+
+ defined $trans or
+ throw("Transcript object not defined");
+
+ return (()) unless $trans->translation;
+
+ my @translateable = @{$trans->get_all_translateable_Exons};
+
+ my $cdna_endpos = $trans->cdna_coding_end;
+
+ my @pepgencoords = $trans->cdna2genomic($cdna_endpos-2,$cdna_endpos);
+
+ if(scalar(@pepgencoords) > 3) {
+ throw(sprintf "Pep end for transcript %s does not map cleanly", $trans->display_id);
+ }
+ unless($pepgencoords[0]->isa('Bio::EnsEMBL::Mapper::Coordinate')) {
+ throw(sprintf "Pep end for transcript %s maps to gap", $trans->display_id);
+ }
+ unless($pepgencoords[$#pepgencoords]->isa('Bio::EnsEMBL::Mapper::Coordinate')) {
+ throw(sprintf "Pep end (end of) for transcript %s maps to gap", $trans->display_id);
+ }
+
+ my @stopc_feat;
+ my $phase = 0;
+ foreach my $pepgencoord (@pepgencoords) {
+ push @stopc_feat,
+ new Bio::EnsEMBL::SeqFeature(-seqname => $trans->display_id,
+ -source_tag => 'endtrans',
+ -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) {
+ @stopc_feat = sort {$a->start <=> $b->start } @stopc_feat;
+ } else {
+ @stopc_feat = sort {$b->start <=> $a->start } @stopc_feat;
+ }
+
+ return @stopc_feat;
+
+}
+
1;
--
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