From bbb06d2f304cce5803b4b113e888b55de57368b9 Mon Sep 17 00:00:00 2001
From: Patrick Meidl <pm2@sanger.ac.uk>
Date: Mon, 27 Aug 2007 10:52:07 +0000
Subject: [PATCH] moved internal_id_rescore() here from GeneScoreBuilder (for
reuse by TranscriptScoreBuilder)
---
modules/Bio/EnsEMBL/IdMapping/ScoreBuilder.pm | 53 ++++++++++++++++++-
1 file changed, 52 insertions(+), 1 deletion(-)
diff --git a/modules/Bio/EnsEMBL/IdMapping/ScoreBuilder.pm b/modules/Bio/EnsEMBL/IdMapping/ScoreBuilder.pm
index bc84d5dbcf..c9c88e5015 100644
--- a/modules/Bio/EnsEMBL/IdMapping/ScoreBuilder.pm
+++ b/modules/Bio/EnsEMBL/IdMapping/ScoreBuilder.pm
@@ -37,8 +37,10 @@ use Bio::EnsEMBL::IdMapping::BaseObject;
our @ISA = qw(Bio::EnsEMBL::IdMapping::BaseObject);
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
+use Bio::EnsEMBL::Utils::ScriptUtils qw(path_append);
use Bio::EnsEMBL::IdMapping::ScoredMappingMatrix;
+
#
# create a shrinked matrix which doesn't contain entries which were already
# mapped
@@ -62,8 +64,10 @@ sub create_shrinked_matrix {
throw('Need a cache file name.') unless ($cache_file);
+ my $dump_path = path_append($self->conf->param('dumppath'), 'matrix');
+
my $shrinked_matrix = Bio::EnsEMBL::IdMapping::ScoredMappingMatrix->new(
- -DUMP_PATH => $self->conf->param('dumppath'),
+ -DUMP_PATH => $dump_path,
-CACHE_FILE => $cache_file,
);
@@ -95,6 +99,53 @@ sub create_shrinked_matrix {
}
+sub internal_id_rescore {
+ my $self = shift;
+ my $matrix = shift;
+
+ unless ($matrix and
+ $matrix->isa('Bio::EnsEMBL::IdMapping::ScoredMappingMatrix')) {
+ throw('Need a Bio::EnsEMBL::IdMapping::ScoredMappingMatrix.');
+ }
+
+ my $i = 0;
+
+ foreach my $source (@{ $matrix->get_all_sources }) {
+
+ my @entries = sort { $b <=> $a }
+ @{ $matrix->get_Entries_for_source($source) };
+
+ # nothing to do if we only have one mapping
+ next unless (scalar(@entries) > 1);
+
+ # only penalise if mappings are ambiguous
+ next unless ($entries[0]->score == $entries[1]->score);
+
+ # only penalise if one source id == target id where score == best score
+ my $ambiguous = 0;
+
+ foreach my $e (@entries) {
+ if ($e->target == $source and $e->score == $entries[0]) {
+ $ambiguous = 1;
+ }
+ }
+
+ next unless ($ambiguous);
+
+ # now penalise those where source id != target id and score == best score
+ foreach my $e (@entries) {
+ if ($e->target != $source and $e->score == $entries[0]) {
+ $matrix->set_score($source, $e->target, ($e->score * 0.8));
+ $i++;
+ }
+ }
+
+ }
+
+ $self->logger->debug("Scored entries with internal ID mismatch: $i\n", 1);
+}
+
+
sub log_matrix_stats {
my $self = shift;
my $matrix = shift;
--
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