Commit 928fa908 authored by Alessandro Vullo's avatar Alessandro Vullo
Browse files

Correct use of transcript attributes

parent f108efe5
......@@ -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");
......
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