same_sequence_order checks for internal STOP codons in translated seq…

…uences
eead-csic-compbio · Nov 3, 2023 · 93e30f4 · 93e30f4
1 parent f52b00d
commit 93e30f4
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/lib/phyTools.pm b/lib/phyTools.pm
@@ -598,14 +598,14 @@ sub same_sequence_order
     if($translated =~ m/\*/) {
       print "# same_sequence_order : translation of $refCDSnt->[$seq][NAME] contains internal STOP codons (*): ".
         "$translated\n";
-        return 0;
+      return 0;
     }   
 
     if($parsed ne $translated && 
-      $parsed !~ /$translated/ && $translated !~ /$parsed/) {
+      $parsed !~ /\Q$translated\E/ && $translated !~ /\Q$parsed\E/) {
       print "# same_sequence_order : sequence #$seq does not match: ".
         "$refCDSnt->[$seq][SEQ]\n$translated\n$refCDSaa->[$seq][SEQ]\n";
-        return 0;
+      return 0;
     }
   }