From 041ad233382f943815f70c51a363026ad7a0489e Mon Sep 17 00:00:00 2001
From: Alessandro Vullo <avullo@ebi.ac.uk>
Date: Mon, 5 Aug 2013 09:16:38 +0000
Subject: [PATCH] Do not temporarily use CDS
---
modules/Bio/EnsEMBL/Utils/IO/GTFSerializer.pm | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Utils/IO/GTFSerializer.pm b/modules/Bio/EnsEMBL/Utils/IO/GTFSerializer.pm
index 5a97b55437..1bddfe9f9b 100644
--- a/modules/Bio/EnsEMBL/Utils/IO/GTFSerializer.pm
+++ b/modules/Bio/EnsEMBL/Utils/IO/GTFSerializer.pm
@@ -389,11 +389,11 @@ sub _check_start_and_stop {
# transcript could be annotated has having incomplete
# CDS at either 5', 3' end or both
- my @attrib = @{$trans->get_all_Attributes('cds_start_NF')};
- $has_start = scalar @attrib == 1 and $attrib[0]->value() == 1?0:1;
- @attrib = @{$trans->get_all_Attributes('cds_end_NF')};
- $has_end = scalar @attrib == 1 and $attrib[0]->value() == 1?0:1;
- return (0, 0) unless $has_start and $has_end;
+ # my @attrib = @{$trans->get_all_Attributes('cds_start_NF')};
+ # $has_start = scalar @attrib == 1 and $attrib[0]->value() == 1?0:1;
+ # @attrib = @{$trans->get_all_Attributes('cds_end_NF')};
+ # $has_end = scalar @attrib == 1 and $attrib[0]->value() == 1?0:1;
+ # return (0, 0) unless $has_start and $has_end;
#
# even if the transcript is not annotated with incomplete start/end
@@ -407,7 +407,7 @@ sub _check_start_and_stop {
my $endseq = substr($cds_seq, -3);
# reimplemented since there are alternatively valid codon tables
- # $has_start = $has_end = 1;
+ $has_start = $has_end = 1;
# $has_start = 0 if ($startseq ne "ATG");
# $has_end = 0 if ($endseq ne "TAG" && $endseq ne "TGA" && $endseq ne "TAA");
--
GitLab