From a1af8c221a7f48428bd22b3b5b20c41bef964b19 Mon Sep 17 00:00:00 2001
From: Rhoda Kinsella <rhoda@ebi.ac.uk>
Date: Wed, 8 Dec 2010 11:16:10 +0000
Subject: [PATCH] Changed go_xref to ontology_xref and removed line to replace
"_" with space.
---
misc-scripts/xref_projection/project_display_xrefs.pl | 10 ++++++----
1 file changed, 6 insertions(+), 4 deletions(-)
diff --git a/misc-scripts/xref_projection/project_display_xrefs.pl b/misc-scripts/xref_projection/project_display_xrefs.pl
index 61746b7c35..b44e47a992 100644
--- a/misc-scripts/xref_projection/project_display_xrefs.pl
+++ b/misc-scripts/xref_projection/project_display_xrefs.pl
@@ -605,7 +605,7 @@ sub delete_go_terms {
print "Deleting projected GO terms\n";
- my $sth = $to_ga->dbc()->prepare("DELETE x, ox, gx FROM xref x, external_db e, object_xref ox, go_xref gx WHERE x.xref_id=ox.xref_id AND x.external_db_id=e.external_db_id AND ox.object_xref_id=gx.object_xref_id AND e.db_name='GO' AND x.info_type='PROJECTION'");
+ my $sth = $to_ga->dbc()->prepare("DELETE x, ox, gx FROM xref x, external_db e, object_xref ox, ontology_xref gx WHERE x.xref_id=ox.xref_id AND x.external_db_id=e.external_db_id AND ox.object_xref_id=gx.object_xref_id AND e.db_name='GO' AND x.info_type='PROJECTION'");
$sth->execute();
# note don't need to delete synonyms as GO terms don't have any
@@ -710,7 +710,7 @@ sub fetch_homologies {
print "Fetching Compara homologies\n";
my $from_species_alias = lc(Bio::EnsEMBL::Registry->get_alias($from_species));
- $from_species_alias =~ tr/_/ /;
+
my %homology_cache;
@@ -725,6 +725,7 @@ sub fetch_homologies {
# order of member-attributes is arbitrary, so need to find which one corresponds to the "from" species
my @to_stable_ids;
my $from_stable_id;
+
foreach my $ma (@mas) {
my ($member, $attribute) = @{$ma};
@@ -732,6 +733,7 @@ sub fetch_homologies {
if (lc($member->genome_db()->name()) eq $from_species_alias) {
$from_stable_id = $member->stable_id();
} else {
+ push @arse, $member->genome_db()->name();
push @to_stable_ids, $member->stable_id();
}
}
@@ -805,9 +807,9 @@ sub clean_up {
$to_dbc->do("DROP TABLE IF EXISTS tmp_gx");
- $to_dbc->do("CREATE TEMPORARY TABLE tmp_gx SELECT gx.object_xref_id FROM go_xref gx LEFT JOIN object_xref ox ON ox.object_xref_id=gx.object_xref_id WHERE ox.object_xref_id IS NULL");
+ $to_dbc->do("CREATE TEMPORARY TABLE tmp_gx SELECT gx.object_xref_id FROM ontology_xref gx LEFT JOIN object_xref ox ON ox.object_xref_id=gx.object_xref_id WHERE ox.object_xref_id IS NULL");
- $to_dbc->do("DELETE FROM go_xref WHERE object_xref_id IN (SELECT object_xref_id FROM tmp_gx)");
+ $to_dbc->do("DELETE FROM ontology_xref WHERE object_xref_id IN (SELECT object_xref_id FROM tmp_gx)");
$to_dbc->do("DROP TABLE tmp_gx");
--
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