Correct use of transcript attributes

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

@@ -389,11 +389,11 @@ sub _check_start_and_stop {
 
   # transcript could be annotated has having incomplete
   # CDS at either 5', 3' end or both
-  # my @attrib = @{$trans->get_all_Attributes('cds_start_NF')};
-  # $has_start = scalar @attrib == 1 and $attrib[0]->value() == 1?0:1;
-  # @attrib = @{$trans->get_all_Attributes('cds_end_NF')};
-  # $has_end = scalar @attrib == 1 and $attrib[0]->value() == 1?0:1;
-  # return (0, 0) unless $has_start and $has_end;
+  my @attrib = @{$trans->get_all_Attributes('cds_start_NF')};
+  $has_start = (scalar @attrib == 1 and $attrib[0]->value() == 1)?0:1;
+  @attrib = @{$trans->get_all_Attributes('cds_end_NF')};
+  $has_end = (scalar @attrib == 1 and $attrib[0]->value() == 1)?0:1;
+  return (0, 0) unless $has_start and $has_end;
 
   #
   # even if the transcript is not annotated with incomplete start/end 
@@ -402,19 +402,18 @@ sub _check_start_and_stop {
   # use translateable_seq (CDS) instead of spliced_seq (CDNA) which is
   # not padded for non-triplet issues
   #
-  # my $cds_seq = uc($trans->translateable_seq); 
-  # my $startseq = substr($cds_seq, 0, 3); 
-  # my $endseq = substr($cds_seq, -3); 
-
-  $has_start = $has_end = 1;
-  my $coding_start = $trans->cdna_coding_start;
-  my $coding_end = $trans->cdna_coding_end;
-  my $cdna_seq = uc($trans->spliced_seq);
-  my $startseq = substr($cdna_seq, $coding_start-1, 3);
-  my $endseq = substr($cdna_seq, $coding_end-3, 3);
+  # $has_start = $has_end = 1;
+  # my $coding_start = $trans->cdna_coding_start;
+  # my $coding_end = $trans->cdna_coding_end;
+  # my $cdna_seq = uc($trans->spliced_seq);
+  # my $startseq = substr($cdna_seq, $coding_start-1, 3);
+  # my $endseq = substr($cdna_seq, $coding_end-3, 3);
+  #
+  my $cds_seq = uc($trans->translateable_seq); 
+  my $startseq = substr($cds_seq, 0, 3); 
+  my $endseq = substr($cds_seq, -3); 
 
   # reimplemented since there are alternatively valid codon tables
-  # $has_start = $has_end = 1;
   # $has_start = 0  if ($startseq ne "ATG");
   # $has_end = 0 if ($endseq ne "TAG" && $endseq ne "TGA" && $endseq ne "TAA");