From 66169ca09e359d0e54c587b03720a60124db40c0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Wed, 14 Nov 2007 11:39:53 +0000
Subject: [PATCH] Move some initializations closer to where they are actually
used.
From code review:
Get rid of "UCSC" in variable names (was actually dead code anyway).
Change scoring function.
---
.../XrefMapper/CoordinateMapper.pm | 44 ++++++++-----------
1 file changed, 19 insertions(+), 25 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/CoordinateMapper.pm b/misc-scripts/xref_mapping/XrefMapper/CoordinateMapper.pm
index bd4c84ca79..110cd86069 100644
--- a/misc-scripts/xref_mapping/XrefMapper/CoordinateMapper.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/CoordinateMapper.pm
@@ -50,18 +50,6 @@ sub run_coordinatemapping {
my $unmapped_object_filename =
catfile( $output_dir, 'unmapped_object_coord.txt' );
- my $core_db_adaptor =
- Bio::EnsEMBL::DBSQL::DBAdaptor->new(
- -host => $core_db->dbc()->host(),
- -port => $core_db->dbc()->port(),
- -user => $core_db->dbc()->username(),
- -pass => $core_db->dbc()->password(),
- -dbname => $core_db->dbc()->dbname(),
- );
-
- my $slice_adaptor = $core_db_adaptor->get_SliceAdaptor();
- my @chromosomes = @{ $slice_adaptor->fetch_all('Chromosome') };
-
my $xref_dbh = $xref_db->dbc()->db_handle();
my $core_dbh = $core_db->dbc()->db_handle();
@@ -179,6 +167,18 @@ sub run_coordinatemapping {
# Do coordinate matching. #
######################################################################
+ my $core_db_adaptor =
+ Bio::EnsEMBL::DBSQL::DBAdaptor->new(
+ -host => $core_db->dbc()->host(),
+ -port => $core_db->dbc()->port(),
+ -user => $core_db->dbc()->username(),
+ -pass => $core_db->dbc()->password(),
+ -dbname => $core_db->dbc()->dbname(),
+ );
+
+ my $slice_adaptor = $core_db_adaptor->get_SliceAdaptor();
+ my @chromosomes = @{ $slice_adaptor->fetch_all('Chromosome') };
+
my $sql = qq(
SELECT coord_xref_id, accession,
txStart, txEnd,
@@ -385,23 +385,17 @@ sub run_coordinatemapping {
}
} ## end foreach my $exon (@exons)
- my $ucsc_exon_hit = $exon_match/$exonCount;
- my $ucsc_coding_hit = $coding_match/( $coding_count || 1 );
- my $ens_exon_hit = $rexon_match/scalar(@exons);
- my $ens_coding_hit = $rcoding_match/( $rcoding_count || 1 );
-
#-------------------------------------------------------------
# Calculate the match score.
#-------------------------------------------------------------
- my $score = (
- ( $exon_match/$ens_weight + $ens_weight*$rexon_match )/
- $coding_weight + $coding_weight*(
- $coding_match/$ens_weight + $ens_weight*$rcoding_match
- )
- )/( ( $exonCount/$ens_weight + $ens_weight*scalar(@exons) )/
- $coding_weight + $coding_weight*(
- $coding_count/$ens_weight + $ens_weight*$rcoding_count
+ my $score = ( ( $exon_match + $ens_weight*$rexon_match ) +
+ $coding_weight*(
+ $coding_match + $ens_weight*$rcoding_match
+ )
+ )/( ( $exonCount + $ens_weight*scalar(@exons) ) +
+ $coding_weight*(
+ $coding_count + $ens_weight*$rcoding_count
) );
if ( !defined( $transcript_result{$coord_xref_id} )
--
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