Changes for new Annotation_relation using RO

WormBase · Aug 15, 2018 · df4063b · df4063b
1 parent b7248af
commit df4063b
Showing 1 changed file with 16 additions and 6 deletions.
diff --git a/scripts/ONTOLOGY/make_GO_GAF.pl b/scripts/ONTOLOGY/make_GO_GAF.pl
@@ -147,16 +147,26 @@
     $gaf_line->{taxon} = \@taxids;
 
     # qualifier (Annotation_relation)
-    my $annot_rel = "";
+    my @annot_rel;
+    if ($obj->Annotation_relation_not) {
+      push @annot_rel, "NOT";
+      my $al = $obj->Annotation_relation_not->Name;
+      $al =~ s/\s+/_/; 
+      if ($al eq 'colocalizes_with' or
+          $al eq 'contributes_to') {
+        push @annot_rel, $al;
+      }
+    }
     if ($obj->Annotation_relation) {
-      my $al = $obj->Annotation_relation->name;
+      my $al = $obj->Annotation_relation->Name;
+      $al =~ s/\s+/_/; 
       if ($al eq 'colocalizes_with' or
-          $al eq 'contributes_to' or
-          $al eq 'NOT') {
-        $annot_rel = $al;
+          $al eq 'contributes_to') {
+        push @annot_rel, $al;
       }
     }
-    $gaf_line->{qualifier} = $annot_rel;
+
+    $gaf_line->{qualifier} = join("|", @annot_rel);
 
     # Reference
     my @reference;