From 24d38fdb326435cef42bebe5d834bbb580a02d55 Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Mon, 15 Dec 2014 16:19:59 +0000
Subject: [PATCH] ENSCORESW-1127: TSL and gencode_basic tags added to gtf dumps
as per gencode specifications
---
modules/Bio/EnsEMBL/Utils/IO/GTFSerializer.pm | 12 ++++++++++--
1 file changed, 10 insertions(+), 2 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Utils/IO/GTFSerializer.pm b/modules/Bio/EnsEMBL/Utils/IO/GTFSerializer.pm
index ff91f892a7..0ba0816ac6 100644
--- a/modules/Bio/EnsEMBL/Utils/IO/GTFSerializer.pm
+++ b/modules/Bio/EnsEMBL/Utils/IO/GTFSerializer.pm
@@ -439,12 +439,20 @@ sub _print_attribs {
}
if($transcript && $transcript->isa('Bio::EnsEMBL::Transcript')) {
- foreach my $tag (qw/cds_end_NF cds_start_NF mRNA_end_NF mRNA_start_NF/) {
+ foreach my $tag (qw/cds_end_NF cds_start_NF mRNA_end_NF mRNA_start_NF gencode_basic/) {
my $attributes = $transcript->get_all_Attributes($tag);
if(@{$attributes}) {
- print $fh qq{ tag "${tag}";};
+ my $value = $tag;
+ $value = "basic" if $tag eq "gencode_basic";
+ print $fh qq{ tag "${value}";};
}
}
+ my $attributes = $transcript->get_all_Attributes("TSL");
+ if (@{$attributes}) {
+ my $value = $attributes->[0]->value;
+ $value =~ s/tsl//;
+ print $fh qq{ transcript_support_level "${value}";};
+ }
}
return;
--
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