From 1ed754dc15deb9ccc2eab68f80e4130e105c7fe7 Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Tue, 29 Sep 2009 12:56:18 +0000
Subject: [PATCH] Remember to load dependents for the GO terms
---
.../xref_mapping/XrefMapper/Interpro.pm | 29 +++++++++++++++++++
1 file changed, 29 insertions(+)
diff --git a/misc-scripts/xref_mapping/XrefMapper/Interpro.pm b/misc-scripts/xref_mapping/XrefMapper/Interpro.pm
index 68831350ee..6629427c53 100644
--- a/misc-scripts/xref_mapping/XrefMapper/Interpro.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/Interpro.pm
@@ -52,6 +52,8 @@ sub process{
$domain_to_translation{$domain} ||= [];
push @{$domain_to_translation{$domain}}, $translation;
}
+
+ my $dep_sth = $self->xref->dbc->prepare("select dependent_xref_id, linkage_annotation from dependent_xref where master_xref_id = ?");
# Get a list of interpro data, including dependent xrefs if avail
$sth = $self->xref->dbc->prepare("
@@ -87,6 +89,33 @@ sub process{
$add_go_xref_sth->execute($object_xref_id, $go_linkage );
$goxref_count ++;
}
+
+
+
+ #
+ # Also add dependents of the xref and its etc...!!!
+ #
+ my @master_xref_ids;
+ push @master_xref_ids, $dx_xref_id;
+ while (my $new_master_id = pop(@master_xref_ids)){
+ $dep_sth->execute($new_master_id);
+ my $dep_xref_id;
+ my $link;
+ $dep_sth->bind_columns(\$dep_xref_id, \$link);
+ while($dep_sth->fetch()){
+ $add_object_xref_sth->execute($object_xref_id, $ensembl_id, 'Translation', $dep_xref_id, 'DEPENDENT', $new_master_id);
+ if(!$add_object_xref_sth->err){
+ push @master_xref_ids, $dep_xref_id;
+ if($link){
+ $add_go_xref_sth->execute($object_xref_id, $link );
+ }
+ }
+ $object_xref_id++;
+ }
+ }
+
+
+
$object_xref_id++;
}
}
--
GitLab