From ad027771cf62a75612cf96256642b5dcbbb3ef99 Mon Sep 17 00:00:00 2001
From: Glenn Proctor <gp1@sanger.ac.uk>
Date: Thu, 3 Feb 2005 12:24:51 +0000
Subject: [PATCH] Added add_direct_xref() - will be needed for future parsers
that create direct_xrefs (e.g. CCDSParser).
Made add_xref return xref_id of last-inserted xref so that it can be passed to add_direct_xref.
---
.../xref_mapping/XrefParser/BaseParser.pm | 24 ++++++++++++++++---
1 file changed, 21 insertions(+), 3 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefParser/BaseParser.pm b/misc-scripts/xref_mapping/XrefParser/BaseParser.pm
index c455c03ca0..940e61aeb3 100644
--- a/misc-scripts/xref_mapping/XrefParser/BaseParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/BaseParser.pm
@@ -12,6 +12,7 @@ use Getopt::Long;
my $base_dir = ".";
my $add_xref_sth = undef;
+my $add_direct_xref_sth = undef;
my $add_dependent_xref_sth = undef;
my $get_xref_sth = undef;
@@ -732,15 +733,18 @@ sub get_xref{
return undef;
}
-sub add_xref{
- my ($self,$acc,$version,$label,$description,$source_id,$species_id) = @_;
+sub add_xref {
+
+ my ($self,$acc,$version,$label,$description,$source_id,$species_id) = @_;
if(!defined($add_xref_sth)){
$add_xref_sth = dbi->prepare("INSERT INTO xref (accession,version,label,description,source_id,species_id) VALUES(?,?,?,?,?,?)");
}
$add_xref_sth->execute($acc,$version,$label,$description,$source_id,$species_id)
|| die "$acc\t$label\t\t$source_id\t$species_id\n";
-
+
+ return $add_xref_sth->{'mysql_insertid'};
+
}
@@ -762,6 +766,20 @@ sub add_to_xrefs{
}
+# --------------------------------------------------------------------------------
+# Add a single record to the direct_xref table.
+# Note that an xref must already have been added to the xref table (xref_id passed as 1st arg)
+
+sub add_direct_xref {
+
+ my ($self, $general_xref_id, $ensembl_stable_id, $ensembl_type, $linkage_xref) = @_;
+
+ $add_direct_xref_sth = dbi->prepare("INSERT INTO direct_xref VALUES(?,?,?,?)") if (!defined($add_direct_xref_sth));
+
+ $add_direct_xref_sth->execute($general_xref_id, $ensembl_stable_id, $ensembl_type, $linkage_xref);
+
+}
+
# --------------------------------------------------------------------------------
# Remove potentially problematic characters from string used for file/dir names
--
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