-
Notifications
You must be signed in to change notification settings - Fork 1
/
fix_relationshiptype_lc.diff
31 lines (29 loc) · 1.58 KB
/
fix_relationshiptype_lc.diff
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
diff --git a/bin/gmod_load_cvterms.pl b/bin/gmod_load_cvterms.pl
index 6414639..b423fa7 100644
--- a/bin/gmod_load_cvterms.pl
+++ b/bin/gmod_load_cvterms.pl
@@ -306,7 +306,7 @@ foreach my $new_ont(@onts) {
});
#maybe it's stored with another cv_id?
if ($p_term) {
- message("predicate term '" .$t->name() . "' already exists with cv_id " . $p_term->get_column('cv_id') . "\n", 1);
+ message("predicate term '" .lc($t->name()) . "' already exists with cv_id " . $p_term->get_column('cv_id') . "\n", 1);
}else { #the predicate term will be stored at the time of storing a term with that relationship, using the term's cv_id
#this stores the relationship types under 'relationship' cv namespace
@@ -314,7 +314,7 @@ foreach my $new_ont(@onts) {
#but with the current ontology cv namespace .
#To do this we need to add to the obo parser (Bio::OntologyIO::obo.pm)
#a 'get_typedefs' funciton
- my $accession = $t->identifier() || $t->name();
+ my $accession = $t->identifier() || lc($t->name());
message("Predicate term $accession will be stored later if used as a relationship in an ontology term\n",1);
}
}
@@ -694,7 +694,7 @@ foreach my $new_ont(@onts) {
}
############################################
push @novel_relationships, $r;
- my $predicate_term_name = $file_relationships{$r}->predicate_term()->name();
+ my $predicate_term_name = lc($file_relationships{$r}->predicate_term()->name());
my $predicate_term;
my ($rel_db)= $schema->resultset('General::Db')->search( { name => 'OBO_REL' } );