From 5ef39c6e844a608e61ca7c61213131311378dfca Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Thu, 27 Oct 2011 23:06:19 +0000
Subject: [PATCH] Enable internal ID disabiguation for exons too.
---
.../Bio/EnsEMBL/IdMapping/InternalIdMapper.pm | 7 +++--
.../InternalIdMapper/EnsemblExonGeneric.pm | 29 +++++++++++++++++++
2 files changed, 33 insertions(+), 3 deletions(-)
diff --git a/modules/Bio/EnsEMBL/IdMapping/InternalIdMapper.pm b/modules/Bio/EnsEMBL/IdMapping/InternalIdMapper.pm
index 1ff9a12aeb..11dfaa587f 100644
--- a/modules/Bio/EnsEMBL/IdMapping/InternalIdMapper.pm
+++ b/modules/Bio/EnsEMBL/IdMapping/InternalIdMapper.pm
@@ -98,9 +98,9 @@ sub map_genes {
# determine which plugin methods to run
my @default_plugins = (qw(
Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblGeneGeneric::init_basic
- Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblGeneGeneric::synteny
Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblGeneGeneric::best_transcript
Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblGeneGeneric::biotype
+ Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblGeneGeneric::synteny
Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblGeneGeneric::internal_id
));
@@ -198,10 +198,10 @@ sub map_transcripts {
my @default_plugins = (qw(
Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblTranscriptGeneric::init_basic
Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblTranscriptGeneric::non_exact_translation
- Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblTranscriptGeneric::mapped_gene
Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblTranscriptGeneric::biotype
- Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblTranscriptGeneric::internal_id
+ Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblTranscriptGeneric::mapped_gene
Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblTranscriptGeneric::single_gene
+ Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblTranscriptGeneric::internal_id
));
my @plugins = $self->conf->param('plugin_internal_id_mappers_transcript');
@@ -299,6 +299,7 @@ sub map_exons {
my @default_plugins = (qw(
Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblExonGeneric::init_basic
Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblExonGeneric::mapped_transcript
+ Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblExonGeneric::internal_id
));
my @plugins = $self->conf->param('plugin_internal_id_mappers_exon');
diff --git a/modules/Bio/EnsEMBL/IdMapping/InternalIdMapper/EnsemblExonGeneric.pm b/modules/Bio/EnsEMBL/IdMapping/InternalIdMapper/EnsemblExonGeneric.pm
index 81729deb0d..e4597e34d3 100644
--- a/modules/Bio/EnsEMBL/IdMapping/InternalIdMapper/EnsemblExonGeneric.pm
+++ b/modules/Bio/EnsEMBL/IdMapping/InternalIdMapper/EnsemblExonGeneric.pm
@@ -88,5 +88,34 @@ sub mapped_transcript {
}
+#
+# selectively rescore by penalising scores between exons with
+# different internalIDs
+#
+sub internal_id {
+ my $self = shift;
+ my $num = shift;
+ my $esb = shift;
+ my $mappings = shift;
+ my $exon_scores = shift;
+
+ $self->logger->info( "Retry with internalID disambiguation...\n",
+ 0, 'stamped' );
+
+ if ( !$exon_scores->loaded() ) {
+ $esb->internal_id_rescore($exon_scores);
+ $exon_scores->write_to_file();
+ }
+
+ $mappings = $self->basic_mapping( $exon_scores, "exon_mappings$num" );
+ $num++;
+ my $new_scores =
+ $esb->create_shrinked_matrix( $exon_scores, $mappings,
+ "exon_matrix$num" );
+
+ return ( $new_scores, $mappings );
+}
+
+
1;
--
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