From d797a232afb5566aafe696767d36c6ef86870fb9 Mon Sep 17 00:00:00 2001
From: Amonida Zadissa <amonida@users.noreply.github.com>
Date: Thu, 2 Jun 2016 14:53:13 +0100
Subject: [PATCH] Update TranscriptSelector.pm
---
modules/Bio/EnsEMBL/Utils/TranscriptSelector.pm | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/modules/Bio/EnsEMBL/Utils/TranscriptSelector.pm b/modules/Bio/EnsEMBL/Utils/TranscriptSelector.pm
index b1177f0bba..a0dd0de548 100644
--- a/modules/Bio/EnsEMBL/Utils/TranscriptSelector.pm
+++ b/modules/Bio/EnsEMBL/Utils/TranscriptSelector.pm
@@ -142,6 +142,7 @@ my %source_priority = ('ccds' => 1,
my %biotype_priority = ('protein_coding' => 1,
'nonsense_mediated_decay' => 2,
'non_stop_decay' => 2,
+ 'polymorphic_pseudogene' => 2,
'other' => 3,
);
@@ -184,7 +185,8 @@ sub encode_transcript {
my $biotype;
if ( $transcript->biotype() ne 'protein_coding'
&& $transcript->biotype() ne 'nonsense_mediated_decay'
- && $transcript->biotype() ne 'non_stop_decay') {
+ && $transcript->biotype() ne 'non_stop_decay'
+ && $transcript->biotype() ne 'polymorphic_pseudogene' ) {
$biotype = 'other';
} else { $biotype = $transcript->biotype(); }
--
GitLab