From 1c4eec77d2c9bd8b2cc0877a8662fe8d05c6b831 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Thu, 24 Jan 2008 11:34:56 +0000
Subject: [PATCH] Similar changes as for rev. 1.24 of CoordinateMapper.pm:
Remove hard-coded external_db_id 11000.
Change xref.info_type from 'MISC' to 'COORDINATE_OVERLAP'.
---
.../XrefMapper/VBCoordinateMapper.pm | 35 +++++++++----------
1 file changed, 16 insertions(+), 19 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/VBCoordinateMapper.pm b/misc-scripts/xref_mapping/XrefMapper/VBCoordinateMapper.pm
index 4876cb9e57..7b56851ed6 100644
--- a/misc-scripts/xref_mapping/XrefMapper/VBCoordinateMapper.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/VBCoordinateMapper.pm
@@ -174,14 +174,13 @@ sub run_coordinatemapping {
while ( my $xref = $xref_sth->fetchrow_hashref() ) {
$unmapped{ $xref->{'coord_xref_id'} } = {
- 'external_db_id' =>
- $XrefMapper::BasicMapper::source_to_external_db_id{ $xref->{
- 'source_id'} }
- || 11000, # FIXME ('external_db' needs to be updated)
- 'accession' => $xref->{'accession'},
- 'reason' => 'No overlap',
- 'reason_full' =>
- 'No coordinate overlap with any Ensembl transcript' };
+ 'external_db_id' =>
+ $XrefMapper::BasicMapper::source_to_external_db_id{ $xref->{
+ 'source_id'} },
+ 'accession' => $xref->{'accession'},
+ 'reason' => 'No overlap',
+ 'reason_full' =>
+ 'No coordinate overlap with any Ensembl transcript' };
}
$xref_sth->finish();
@@ -573,17 +572,15 @@ sub dump_xref {
my ($version) = ( $accession =~ /\.(\d+)$/ );
$version ||= 0;
- $fh->printf(
- "%d\t%d\t%s\t%s\t%d\t%s\t%s\t%s\n",
- $xref->{'xref_id'},
- $xref->{'external_db_id'},
- $accession,
- $accession,
- $version,
- '\N',
- 'MISC', # FIXME (add new 'info_type' enum 'COORDINATEOVERLAP'
- # in release v49)
- '\N' # FIXME (possibly)
+ $fh->printf("%d\t%d\t%s\t%s\t%d\t%s\t%s\t%s\n",
+ $xref->{'xref_id'},
+ $xref->{'external_db_id'},
+ $accession,
+ $accession,
+ $version,
+ '\N',
+ 'COORDINATE_OVERLAP',
+ '\N' # FIXME (possibly)
);
}
$fh->close();
--
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