From 8cea343db2a820b618e0bb9a43d7f833eaca462b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Wed, 19 Oct 2011 16:27:34 +0000
Subject: [PATCH] Allow TinyTranscript to have biotype.
---
modules/Bio/EnsEMBL/IdMapping/Cache.pm | 3 ++-
modules/Bio/EnsEMBL/IdMapping/TinyTranscript.pm | 7 +++++++
2 files changed, 9 insertions(+), 1 deletion(-)
diff --git a/modules/Bio/EnsEMBL/IdMapping/Cache.pm b/modules/Bio/EnsEMBL/IdMapping/Cache.pm
index bdcb08f759..8a4ef78f96 100644
--- a/modules/Bio/EnsEMBL/IdMapping/Cache.pm
+++ b/modules/Bio/EnsEMBL/IdMapping/Cache.pm
@@ -320,8 +320,9 @@ sub build_cache_from_genes {
$tr->modified_date, $tr->start,
$tr->end, $tr->strand,
$tr->length, md5_hex( $tr->spliced_seq ),
- ( $tr->is_known ? 1 : 0 ), ] );
+ ( $tr->is_known ? 1 : 0 ) ] );
+ $ltr->biotype( $tr->biotype() );
$lgene->add_Transcript($ltr);
# build transcript caches
diff --git a/modules/Bio/EnsEMBL/IdMapping/TinyTranscript.pm b/modules/Bio/EnsEMBL/IdMapping/TinyTranscript.pm
index e78273b700..9c3c24691c 100644
--- a/modules/Bio/EnsEMBL/IdMapping/TinyTranscript.pm
+++ b/modules/Bio/EnsEMBL/IdMapping/TinyTranscript.pm
@@ -71,6 +71,7 @@ package Bio::EnsEMBL::IdMapping::TinyTranscript;
# 10 is_known
# 11 translation
# 12 [exons]
+# 13 biotype
use strict;
@@ -287,6 +288,12 @@ sub get_all_Exons {
return $_[0]->[12] || [];
}
+sub biotype {
+ my $self = shift;
+ $self->[13] = shift if (@_);
+ return $self->[13];
+}
+
1;
--
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