From 5967f6708a3ffa0f09eac14e19e6d34f841b6b03 Mon Sep 17 00:00:00 2001
From: Kieron Taylor <ktaylor@ebi.ac.uk>
Date: Fri, 24 Feb 2012 16:21:39 +0000
Subject: [PATCH] Added more groupings for use in FASTA dumping.
---
modules/Bio/EnsEMBL/Utils/BiotypeMapper.pm | 31 +++++++++++++++++++++-
1 file changed, 30 insertions(+), 1 deletion(-)
diff --git a/modules/Bio/EnsEMBL/Utils/BiotypeMapper.pm b/modules/Bio/EnsEMBL/Utils/BiotypeMapper.pm
index 0333e1dc80..a91c1b234b 100644
--- a/modules/Bio/EnsEMBL/Utils/BiotypeMapper.pm
+++ b/modules/Bio/EnsEMBL/Utils/BiotypeMapper.pm
@@ -118,8 +118,37 @@ my %feature_so_mapping = (
'Bio::EnsEMBL::Funcgen::RegulatoryFeature' => 'SO:0001679', # transcription_regulatory_region
);
+my %grouping_of_biotypes = (
+ # Genebuilder/Havana categorisation
+ 'protein_coding' => [qw( protein_coding polymorphic_pseudogene )],
+ 'pseudogene' => [qw( pseudogene retrotransposed )],
+ '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
+ )],
+ # practical Ensembl core categories for fasta dumping
+ 'cDNA' => [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 pseudogene
+ retrotransposed IG_V_pseudogene TR_V_pseudogene
+ IG_J_pseudogene IG_C_pseudogene
+
+ )],
+ '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
+ )],
+ '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
+ processed_transcript sense_intronic sense_overlapping tRNA
+ )],
+);
+
my %biotype_grouping = (
- 'protein-coding' => 'protein_coding',
+ 'protein_coding' => 'protein_coding',
'polymorphic_pseudogene' => 'protein_coding',
'pseudogene' => 'pseudogene',
'retrotransposed' => 'pseudogene',
--
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