From 7edb69edf0b7cfa53bbbc1e721119619564d7648 Mon Sep 17 00:00:00 2001
From: Kieron Taylor <ktaylor@ebi.ac.uk>
Date: Thu, 29 Mar 2012 09:39:14 +0000
Subject: [PATCH] Reclassified pseudogenes into 'pseudogene' category instead
of 'short non-coding'
---
modules/Bio/EnsEMBL/Utils/BiotypeMapper.pm | 10 ++++++----
1 file changed, 6 insertions(+), 4 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Utils/BiotypeMapper.pm b/modules/Bio/EnsEMBL/Utils/BiotypeMapper.pm
index b3d99279b3..c9b6e7a022 100644
--- a/modules/Bio/EnsEMBL/Utils/BiotypeMapper.pm
+++ b/modules/Bio/EnsEMBL/Utils/BiotypeMapper.pm
@@ -126,13 +126,15 @@ my %feature_so_mapping = (
my %grouping_of_biotypes = (
# Genebuilder/Havana categorisation
'protein_coding' => [qw( protein_coding polymorphic_pseudogene )],
- 'pseudogene' => [qw( pseudogene retrotransposed )],
+ 'pseudogene' => [qw( pseudogene retrotransposed snRNA_pseudogene tRNA_pseudogene
+ miRNA_pseudogene Mt_tRNA_pseudogene rRNA_pseudogene
+ scRNA_pseudogene misc_RNA_pseudogene snoRNA_pseudogene
+ )],
'long_noncoding' => [qw( 3prime_overlapping_ncrna antisense lincRNA ncrna_host non_coding
processed_transcript sense_intronic sense_overlapping
)],
- 'short_noncoding'=> [qw( miRNA miRNA_pseudogene misc_RNA misc_RNA_pseudogene Mt_tRNA
- Mt_tRNA_pseudogene rRNA rRNA_pseudogene scRNA_pseudogene snoRNA
- snoRNA_pseudogene snRNA snRNA_pseudogene tRNA_pseudogene
+ 'short_noncoding'=> [qw( miRNA misc_RNA Mt_tRNA
+ rRNA snoRNA snRNA
)],
# practical Ensembl core categories for fasta dumping
'cDNA' => [qw( protein_coding polymorphic_pseudogene IG_V_gene TR_V_gene
--
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