From 5b578ef5205363c3881b91fc262781ed8301c370 Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Mon, 15 Nov 2004 15:07:02 +0000
Subject: [PATCH] check refseq and both uniprot sourcs for valid accessions
---
.../xref_mapping/XrefParser/MIMParser.pm | 44 +++++++++++++------
1 file changed, 31 insertions(+), 13 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefParser/MIMParser.pm b/misc-scripts/xref_mapping/XrefParser/MIMParser.pm
index 4ab2f0668f..9f7d28ff5f 100644
--- a/misc-scripts/xref_mapping/XrefParser/MIMParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/MIMParser.pm
@@ -78,32 +78,50 @@ sub gene_name_2_xref_from_hugo{
my $source_id_for_hugo=0;
- my $sth2 = $dbi->prepare("select * from source where name like 'HUGO'");
- $sth2->execute() || die $dbi->errstr;
+ my $sth2 = $dbi->prepare("select * from source where name like ?");
+ $sth2->execute('HUGO') || die $dbi->errstr;
while(my @row = $sth2->fetchrow_array()) {
$source_id_for_hugo = $row[0];
}
- $sth2->finish;
-
if(! $source_id_for_hugo){
die "Could not find source id for HUGO.\n";
}
+
+ my @source_list=();
+
+ $sth2->execute('Refseq') || die $dbi->errstr;
+ while(my @row = $sth2->fetchrow_array()) {
+ push @source_list, $row[0];
+ }
+
+ $sth2->execute('Uniprot') || die $dbi->errstr;
+ while(my @row = $sth2->fetchrow_array()) {
+ push @source_list, $row[0];
+ }
+
+
+ $sth2->finish;
+
+
my $sql = "select y.label, x.xref_id ";
$sql .= " from dependent_xref d, xref x, xref y ";
$sql .= " where d.source_id = $source_id_for_hugo and ";
$sql .= " x.xref_id = d.master_xref_id and ";
$sql .= " y.xref_id = d.dependent_xref_id and ";
- $sql .= " x.source_id = 1";
-
-
+ $sql .= " x.source_id = ?";
+
+
my $sth = $dbi->prepare($sql);
- $sth->execute() || die $dbi->errstr;
- while(my @row = $sth->fetchrow_array()) {
- my $gene_name = $row[0];
- my $xref = $row[1];
- $gene_name2xref{$gene_name} = $xref;
- }
+
+ foreach my $id (@source_list){
+ $sth->execute($id) || die $dbi->errstr;
+ while(my @row = $sth->fetchrow_array()) {
+ my $gene_name = $row[0];
+ my $xref = $row[1];
+ $gene_name2xref{$gene_name} = $xref;
+ }
+ }
$sth->finish;
return %gene_name2xref;
}
--
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