From a9f80e01acd4f4c758366ddb31640c9c8b95db95 Mon Sep 17 00:00:00 2001
From: Alessandro Vullo <avullo@ebi.ac.uk>
Date: Mon, 29 Jul 2013 13:31:05 +0000
Subject: [PATCH] Correct substringing CDS string
---
modules/Bio/EnsEMBL/Utils/IO/GTFSerializer.pm | 29 +++++++++----------
1 file changed, 13 insertions(+), 16 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Utils/IO/GTFSerializer.pm b/modules/Bio/EnsEMBL/Utils/IO/GTFSerializer.pm
index fadb1e5158..a450ff773b 100644
--- a/modules/Bio/EnsEMBL/Utils/IO/GTFSerializer.pm
+++ b/modules/Bio/EnsEMBL/Utils/IO/GTFSerializer.pm
@@ -393,32 +393,29 @@ sub _check_start_and_stop {
return (0,0) unless defined $trans->translation;
my $tln = $trans->translation;
+ my $cds_seq = uc($trans->translateable_seq);
- my $coding_start = $trans->cdna_coding_start;
- my $coding_end = $trans->cdna_coding_end;
- my $cds_seq = uc($trans->translateable_seq); # uc($trans->spliced_seq);
-
- my $startseq = substr($cds_seq,$coding_start-1,3);
- my $endseq = substr($cds_seq,$coding_end-3,3);
+ my $startseq = substr($cds_seq, 0, 3);
+ my $endseq = substr($cds_seq, -3);
my $has_start = 1;
my $has_end = 1;
# reimplemented because verterbrate specific
- # $has_start = 0 if ($startseq ne "ATG");
- # $has_end = 0 if ($endseq ne "TAG" && $endseq ne "TGA" && $endseq ne "TAA");
+ $has_start = 0 if ($startseq ne "ATG");
+ $has_end = 0 if ($endseq ne "TAG" && $endseq ne "TGA" && $endseq ne "TAA");
- my ($attrib) = @{ $trans->slice()->get_all_Attributes('codon_table') };
+ # my ($attrib) = @{ $trans->slice()->get_all_Attributes('codon_table') };
- my $codon_table_id;
- $codon_table_id = $attrib->value()
- if defined $attrib;
- $codon_table_id ||= 1; # default vertebrate codon table
+ # my $codon_table_id;
+ # $codon_table_id = $attrib->value()
+ # if defined $attrib;
+ # $codon_table_id ||= 1; # default vertebrate codon table
- my $codon_table = Bio::Tools::CodonTable->new( -id => $codon_table_id );
+ # my $codon_table = Bio::Tools::CodonTable->new( -id => $codon_table_id );
- $has_start = 0 unless $codon_table->is_start_codon($startseq);
- $has_end = 0 unless $codon_table->is_ter_codon($endseq);
+ # $has_start = 0 unless $codon_table->is_start_codon($startseq);
+ # $has_end = 0 unless $codon_table->is_ter_codon($endseq);
return ($has_start, $has_end);
--
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