Commit e049277d authored by Elia Stupka's avatar Elia Stupka
Browse files

Fixed feature bug

parent ef78b55c
......@@ -404,7 +404,7 @@ sub check_update_status {
my $tdb = $self->connect($self->tolocator);
if ($tdb->current_update) {
$self->throw("Update already running in recipient database. Can't start update");
$self->warn("Update already running in recipient database. Can't start update");
}
my @clones;
......
......@@ -564,6 +564,10 @@ sub get_all_PredictionFeatures {
$out = new Bio::EnsEMBL::SeqFeature;
$out->id($fset);
$out->analysis($analysis);
$out->seqname($id);
$out->score(0);
$out->primary_tag('gene');
$out->source_tag($name);
$seen = $fset;
push(@array,$out);
}
......@@ -575,7 +579,7 @@ sub get_all_PredictionFeatures {
$feature->end ($end);
$feature->strand ($strand);
$feature->source_tag($name);
$feature->primary_tag('similarity');
$feature->primary_tag('exon');
$feature->id ($fid);
if( defined $score ) {
......
......@@ -1249,7 +1249,6 @@ sub delete_Gene{
# delete exons, transcripts, gene rows
foreach my $exon ( keys %exon ) {
print STDERR "Got exon $exon in delete_Gene\n";
my $sth = $self->prepare("delete from exon where id = '$exon'");
$sth->execute;
......@@ -1640,7 +1639,6 @@ sub write_Feature {
if( ! $feature->isa('Bio::EnsEMBL::SeqFeatureI') ) {
$self->throw("Feature $feature is not a feature!");
}
eval {
$feature->validate();
};
......@@ -2298,8 +2296,7 @@ sub write_Contig {
# write sequence features. We write all of them together as it
# is more efficient
$self->write_Feature($contig,$contig->get_all_SeqFeatures);
$self->write_Feature($contig,$contig->get_all_SeqFeatures);
return 1;
}
......
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