From c75f8546b4129da166b382ce99dc784cfd4a304b Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Thu, 2 May 2013 09:38:23 +0000
Subject: [PATCH] ENSCORESW-62: updated call to mapped_transcript was giving it
an exon mapping list where a transcript mapping list was required
---
modules/Bio/EnsEMBL/IdMapping/InternalIdMapper.pm | 3 ++-
.../EnsEMBL/IdMapping/InternalIdMapper/EnsemblExonGeneric.pm | 4 +++-
2 files changed, 5 insertions(+), 2 deletions(-)
diff --git a/modules/Bio/EnsEMBL/IdMapping/InternalIdMapper.pm b/modules/Bio/EnsEMBL/IdMapping/InternalIdMapper.pm
index 741a0f0bc9..8d59e5d960 100644
--- a/modules/Bio/EnsEMBL/IdMapping/InternalIdMapper.pm
+++ b/modules/Bio/EnsEMBL/IdMapping/InternalIdMapper.pm
@@ -317,7 +317,7 @@ sub map_exons {
#
foreach my $plugin (@plugins) {
($exon_scores, $new_mappings) = $self->delegate_to_plugin($plugin, $i++,
- $esb, $new_mappings, $exon_scores);
+ $esb, $new_mappings, $exon_scores, $transcript_mappings);
push(@mappings, $new_mappings);
}
@@ -642,6 +642,7 @@ sub write_ambiguous {
print $fh "\n " unless (($i++)%10);
print $fh $e->$other_db_type, ", ";
}
+ print $fh "\n";
}
print $fh "\n";
diff --git a/modules/Bio/EnsEMBL/IdMapping/InternalIdMapper/EnsemblExonGeneric.pm b/modules/Bio/EnsEMBL/IdMapping/InternalIdMapper/EnsemblExonGeneric.pm
index f4228072f1..8f820e497a 100644
--- a/modules/Bio/EnsEMBL/IdMapping/InternalIdMapper/EnsemblExonGeneric.pm
+++ b/modules/Bio/EnsEMBL/IdMapping/InternalIdMapper/EnsemblExonGeneric.pm
@@ -64,6 +64,7 @@ sub init_basic {
#
# reduce score for mappings of exons which do not belong to mapped
# transcripts
+# (ie where source exon transcript does not map target exon transcript)
#
sub mapped_transcript {
my $self = shift;
@@ -71,11 +72,12 @@ sub mapped_transcript {
my $esb = shift;
my $mappings = shift;
my $exon_scores = shift;
+ my $transcript_mappings = shift;
$self->logger->info("Exons in mapped transcript...\n", 0, 'stamped');
unless ($exon_scores->loaded) {
- $esb->non_mapped_transcript_rescore($exon_scores, $mappings);
+ $esb->non_mapped_transcript_rescore($exon_scores, $transcript_mappings);
$exon_scores->write_to_file;
}
--
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