From d9081608994507062ac1773f01a7b110214f9acb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Fri, 12 Mar 2010 09:58:35 +0000
Subject: [PATCH] Penalize genes jumping to new biotypes harder (0.8 --> 0.5).
---
modules/Bio/EnsEMBL/IdMapping/GeneScoreBuilder.pm | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/modules/Bio/EnsEMBL/IdMapping/GeneScoreBuilder.pm b/modules/Bio/EnsEMBL/IdMapping/GeneScoreBuilder.pm
index 3b84ad64d1..7484576ede 100644
--- a/modules/Bio/EnsEMBL/IdMapping/GeneScoreBuilder.pm
+++ b/modules/Bio/EnsEMBL/IdMapping/GeneScoreBuilder.pm
@@ -409,9 +409,10 @@ sub biotype_gene_rescore {
my $target_gene = $self->cache->get_by_key('genes_by_id', 'target',
$entry->target);
- if ($source_gene->biotype ne $target_gene->biotype) {
+ if ( $source_gene->biotype() ne $target_gene->biotype() ) {
#$self->logger->debug("biotype ".$entry->to_string."\n");
- $matrix->set_score($entry->source, $entry->target, ($entry->score * 0.8));
+ $matrix->set_score( $entry->source(), $entry->target(),
+ ( $entry->score()*0.5 ) );
$i++;
}
}
--
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