Commit 1433dfbd authored by Alessandro Vullo's avatar Alessandro Vullo
Browse files

Use transcript attributes

parent 041ad233
...@@ -389,11 +389,11 @@ sub _check_start_and_stop { ...@@ -389,11 +389,11 @@ sub _check_start_and_stop {
# transcript could be annotated has having incomplete # transcript could be annotated has having incomplete
# CDS at either 5', 3' end or both # CDS at either 5', 3' end or both
# my @attrib = @{$trans->get_all_Attributes('cds_start_NF')}; my @attrib = @{$trans->get_all_Attributes('cds_start_NF')};
# $has_start = scalar @attrib == 1 and $attrib[0]->value() == 1?0:1; $has_start = scalar @attrib == 1 and $attrib[0]->value() == 1?0:1;
# @attrib = @{$trans->get_all_Attributes('cds_end_NF')}; @attrib = @{$trans->get_all_Attributes('cds_end_NF')};
# $has_end = scalar @attrib == 1 and $attrib[0]->value() == 1?0:1; $has_end = scalar @attrib == 1 and $attrib[0]->value() == 1?0:1;
# return (0, 0) unless $has_start and $has_end; return (0, 0) unless $has_start and $has_end;
# #
# even if the transcript is not annotated with incomplete start/end # even if the transcript is not annotated with incomplete start/end
...@@ -407,7 +407,7 @@ sub _check_start_and_stop { ...@@ -407,7 +407,7 @@ sub _check_start_and_stop {
my $endseq = substr($cds_seq, -3); my $endseq = substr($cds_seq, -3);
# reimplemented since there are alternatively valid codon tables # 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"); # $has_start = 0 if ($startseq ne "ATG");
# $has_end = 0 if ($endseq ne "TAG" && $endseq ne "TGA" && $endseq ne "TAA"); # $has_end = 0 if ($endseq ne "TAG" && $endseq ne "TGA" && $endseq ne "TAA");
......
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