From 2cc78138d5ff9c37a933b9635fa3efa7d8f1f25c Mon Sep 17 00:00:00 2001
From: Glenn Proctor <gp1@sanger.ac.uk>
Date: Wed, 20 Dec 2006 10:47:48 +0000
Subject: [PATCH] Add biotype to comparison.
---
misc-scripts/probe_mapping/compare_mappings.pl | 5 ++---
1 file changed, 2 insertions(+), 3 deletions(-)
diff --git a/misc-scripts/probe_mapping/compare_mappings.pl b/misc-scripts/probe_mapping/compare_mappings.pl
index 3acf66e043..556d60903a 100644
--- a/misc-scripts/probe_mapping/compare_mappings.pl
+++ b/misc-scripts/probe_mapping/compare_mappings.pl
@@ -117,12 +117,11 @@ sub cache_mappings {
my %mappings;
# TODO - fix SQL when external_db changes
- my $sth = $db->dbc()->prepare("SELECT tsi.stable_id, e.db_name, x.dbprimary_acc FROM xref x, external_db e, object_xref ox, transcript_stable_id tsi WHERE x.xref_id=ox.xref_id AND x.external_db_id=e.external_db_id AND ox.ensembl_object_type='Transcript' AND ox.ensembl_id=tsi.transcript_id AND $restrict_sql");
+ my $sth = $db->dbc()->prepare("SELECT tsi.stable_id, e.db_name, x.dbprimary_acc, t.biotype FROM xref x, external_db e, object_xref ox, transcript_stable_id tsi, transcript t WHERE x.xref_id=ox.xref_id AND x.external_db_id=e.external_db_id AND ox.ensembl_object_type='Transcript' AND ox.ensembl_id=t.transcript_id AND t.transcript_id=tsi.transcript_id AND $restrict_sql");
$sth->execute();
while (my @row = $sth->fetchrow_array()) {
- my $key = $row[0] . "\t" . $row[1]. "\t" . $row[2];
- #my $key = $row[0] . "\t" . $row[2];
+ my $key = $row[0] . "\t" . $row[3] . "\t". $row[1]. "\t" . $row[2];
$mappings{$key} = $key;
print "$key\n" if ($print);
--
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