From 32e03721e66e20c4af413126a9c07b490cd1ebe5 Mon Sep 17 00:00:00 2001
From: Kim Rutherford <kmr@aska.gen.nz>
Date: Thu, 13 Jan 2022 23:17:49 +1300
Subject: [PATCH] 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
---
 lib/PomBase/Chado/LoadFeat.pm         | 3 ++-
 lib/PomBase/Role/Embl/SystematicID.pm | 6 ++++--
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/lib/PomBase/Chado/LoadFeat.pm b/lib/PomBase/Chado/LoadFeat.pm
index 30ba3b1..2ecb3a8 100644
--- 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
index 0cb233b..221cb99 100644
--- 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";