Fix load of RNA ID that looks like a transcript ID

"SPNCRNA.5" was confusing the code because it looks like the 5th transcript of gene "SPNCRNA". Fixed by adding special cases in the code. Refs pombase/pombase-chado#904
pombase · Jan 13, 2022 · 32e0372 · 32e0372
1 parent 5d94f69
commit 32e0372
Show file tree

Hide file tree

Showing 2 changed files with 6 additions and 3 deletions.
diff --git a/lib/PomBase/Chado/LoadFeat.pm b/lib/PomBase/Chado/LoadFeat.pm
@@ -682,7 +682,8 @@ sub store_transcript_parts {
   my $introns = shift;
 
   my $uniquename = ($bioperl_cds->get_tag_values('systematic_id'))[0];
-  if ($uniquename !~ /\.\d$/) {
+
+  if ($uniquename !~ /\.\d$/ || $uniquename =~ /^SPNCRNA\.\d+$/) {
     $uniquename .= '.1';
   }
 

diff --git a/lib/PomBase/Role/Embl/SystematicID.pm b/lib/PomBase/Role/Embl/SystematicID.pm
@@ -101,8 +101,10 @@ sub get_uniquename {
 
 #  warn "BEFORE $so_type - systematic_id: $systematic_id\n";
 
-  if ($is_transcript && $systematic_id !~ /\.\d$/) {
-    $systematic_id .= '.1';
+  if ($is_transcript) {
+    if ($systematic_id =~ /^SPNCRNA\.\d+$/ || $systematic_id !~ /\.\d$/) {
+      $systematic_id .= '.1';
+    }
   }
 
 #  warn "AFTER $so_type - systematic_id: $systematic_id\n";