Correct substringing CDS string

modules/Bio/EnsEMBL/Utils/IO/GTFSerializer.pm

@@ -393,32 +393,29 @@ sub _check_start_and_stop {
   return (0,0) unless defined $trans->translation;
 
   my $tln = $trans->translation;
+  my $cds_seq     = uc($trans->translateable_seq); 
 
-  my $coding_start = $trans->cdna_coding_start;
-  my $coding_end   = $trans->cdna_coding_end;
-  my $cds_seq     = uc($trans->translateable_seq); # uc($trans->spliced_seq);
-
-  my $startseq     = substr($cds_seq,$coding_start-1,3);
-  my $endseq       = substr($cds_seq,$coding_end-3,3);
+  my $startseq = substr($cds_seq, 0, 3); 
+  my $endseq = substr($cds_seq, -3); 
 
   my $has_start = 1;
   my $has_end = 1;
 
   # reimplemented because verterbrate specific
-  # $has_start = 0  if ($startseq ne "ATG");
-  # $has_end = 0 if ($endseq ne "TAG" && $endseq ne "TGA" && $endseq ne "TAA");
+  $has_start = 0  if ($startseq ne "ATG");
+  $has_end = 0 if ($endseq ne "TAG" && $endseq ne "TGA" && $endseq ne "TAA");
 
-  my ($attrib) = @{ $trans->slice()->get_all_Attributes('codon_table') };
+  # my ($attrib) = @{ $trans->slice()->get_all_Attributes('codon_table') };
 
-  my $codon_table_id;
-  $codon_table_id = $attrib->value()
-    if defined $attrib;
-  $codon_table_id ||= 1; # default vertebrate codon table
+  # my $codon_table_id;
+  # $codon_table_id = $attrib->value()
+  #   if defined $attrib;
+  # $codon_table_id ||= 1; # default vertebrate codon table
 
-  my $codon_table = Bio::Tools::CodonTable->new( -id => $codon_table_id );
+  # my $codon_table = Bio::Tools::CodonTable->new( -id => $codon_table_id );
 
-  $has_start = 0 unless $codon_table->is_start_codon($startseq);
-  $has_end = 0 unless $codon_table->is_ter_codon($endseq);
+  # $has_start = 0 unless $codon_table->is_start_codon($startseq);
+  # $has_end = 0 unless $codon_table->is_ter_codon($endseq);
 
   return ($has_start, $has_end);