From fe6ad44c4e7a17204820147586fa8e894c3cb23c Mon Sep 17 00:00:00 2001
From: Kieron Taylor <ktaylor@ebi.ac.uk>
Date: Mon, 27 Feb 2012 17:44:49 +0000
Subject: [PATCH] Biotype groupings now including all transcript biotypes.
Correctness of classification may leave something to be desired.
---
modules/Bio/EnsEMBL/Utils/BiotypeMapper.pm | 7 ++++---
1 file changed, 4 insertions(+), 3 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Utils/BiotypeMapper.pm b/modules/Bio/EnsEMBL/Utils/BiotypeMapper.pm
index 8e28f73fdb..212fbb9978 100644
--- a/modules/Bio/EnsEMBL/Utils/BiotypeMapper.pm
+++ b/modules/Bio/EnsEMBL/Utils/BiotypeMapper.pm
@@ -139,7 +139,8 @@ my %grouping_of_biotypes = (
IG_J_gene TR_J_gene IG_D_gene IG_C_gene TR_C_gene pseudogene
retrotransposed IG_V_pseudogene TR_V_pseudogene
IG_J_pseudogene IG_C_pseudogene processed_transcript
-
+ antisense ambiguous_orf transcribed_processed_pseudogene
+ disrupted_domain
)],
'peptide_producing' => [qw( protein_coding polymorphic_pseudogene IG_V_gene TR_V_gene
IG_J_gene TR_J_gene IG_D_gene IG_C_gene TR_C_gene
@@ -147,7 +148,7 @@ my %grouping_of_biotypes = (
'ncRNA' => [qw( ncRNA miRNA miRNA_pseudogene misc_RNA misc_RNA_pseudogene Mt_tRNA
Mt_tRNA_pseudogene Mt_rRNA rRNA rRNA_pseudogene scRNA_pseudogene
snoRNA snoRNA_pseudogene snRNA snRNA_pseudogene tRNA_pseudogene
- 3prime_overlapping_ncrna antisense lincRNA ncrna_host non_coding
+ 3prime_overlapping_ncrna lincRNA ncrna_host non_coding
sense_intronic sense_overlapping tRNA
)],
);
@@ -163,7 +164,7 @@ my %grouping_of_biotypes = (
sub new {
my $class = shift;
my $self = {
- ontology_adaptor => shift,
+ ontology_adaptor => shift,
};
bless $self, $class;
--
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