From 3723688400cff8ed204a30df756c68495da79653 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Wed, 19 Oct 2011 16:41:34 +0000
Subject: [PATCH] Implement biotype() based on the method with the same name in
EnsemblGeneGeneric.pm
---
.../EnsemblTranscriptGeneric.pm | 27 +++++++++++++++++++
1 file changed, 27 insertions(+)
diff --git a/modules/Bio/EnsEMBL/IdMapping/InternalIdMapper/EnsemblTranscriptGeneric.pm b/modules/Bio/EnsEMBL/IdMapping/InternalIdMapper/EnsemblTranscriptGeneric.pm
index 32bbc14f5a..cdfa0af9a1 100644
--- a/modules/Bio/EnsEMBL/IdMapping/InternalIdMapper/EnsemblTranscriptGeneric.pm
+++ b/modules/Bio/EnsEMBL/IdMapping/InternalIdMapper/EnsemblTranscriptGeneric.pm
@@ -119,6 +119,33 @@ sub mapped_gene {
return ($new_scores, $mappings);
}
+#
+# rescore by penalising scores between transcripts with different biotypes
+#
+sub biotype {
+ my $self = shift;
+ my $num = shift;
+ my $tsb = shift;
+ my $mappings = shift;
+ my $transcript_scores = shift;
+
+ $self->logger->info( "Retry with biotype disambiguation...\n",
+ 0, 'stamped' );
+
+ unless ( $transcript_scores->loaded() ) {
+ $tsb->biotype_transcript_rescore($transcript_scores);
+ $transcript_scores->write_to_file();
+ }
+
+ my $new_mappings = $self->basic_mapping( $transcript_scores,
+ "transcript_mappings$num" );
+ $num++;
+ my $new_scores =
+ $tsb->create_shrinked_matrix( $transcript_scores, $new_mappings,
+ "transcript_matrix$num" );
+
+ return ( $new_scores, $new_mappings );
+}
#
# selectively rescore by penalising scores between transcripts with
--
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