Use 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 
@@ -407,7 +407,7 @@ sub _check_start_and_stop {
   my $endseq = substr($cds_seq, -3); 
 
   # reimplemented since there are alternatively valid codon tables
-  $has_start = $has_end = 1;
+  # $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");