Commit a9f80e01 authored by Alessandro Vullo's avatar Alessandro Vullo
Browse files

Correct substringing CDS string

parent 09b3a039
......@@ -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);
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment