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Commit 630c70e3 authored by Glenn Proctor's avatar Glenn Proctor
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Removed stray call to get_seq_region_id_internal that crept in when porting from HEAD

parent f572bf16
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Showing with 23 additions and 29 deletions
modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
View file @ 630c70e3
......@@ -1377,8 +1377,6 @@ sub _objs_from_sth {
#get the canonical_transcript object
my $canonical_transcript = $ta->fetch_by_dbID($canonical_transcript_id);
#need to get the internal_seq_region, if present
$seq_region_id = $self->get_seq_region_id_internal($seq_region_id);
my $slice = $slice_hash{"ID:".$seq_region_id};
if(!$slice) {
......@@ -1462,33 +1460,29 @@ sub _objs_from_sth {
}
# Finally, create the new Gene.
push( @genes,
$self->_create_feature(
'Bio::EnsEMBL::Gene', {
'-analysis' => $analysis,
'-biotype' => $biotype,
'-start' => $seq_region_start,
'-end' => $seq_region_end,
'-strand' => $seq_region_strand,
'-adaptor' => $self,
'-slice' => $slice,
'-dbID' => $gene_id,
'-stable_id' => $stable_id,
'-version' => $version,
'-created_date' => $created_date || undef,
'-modified_date' => $modified_date
|| undef,
'-description' => $gene_description,
'-external_name' => $external_name,
'-external_db' => $external_db,
'-external_status' => $external_status,
'-display_xref' => $display_xref,
'-status' => $status,
'-source' => $source,
'-is_current' => $is_current,
'-canonical_transcript' => $canonical_transcript,
'-canonical_annotation' => $canonical_annotation
} ) );
push @genes, Bio::EnsEMBL::Gene->new('-analysis' => $analysis,
'-biotype' => $biotype,
'-start' => $seq_region_start,
'-end' => $seq_region_end,
'-strand' => $seq_region_strand,
'-adaptor' => $self,
'-slice' => $slice,
'-dbID' => $gene_id,
'-stable_id' => $stable_id,
'-version' => $version,
'-created_date' => $created_date || undef,
'-modified_date' => $modified_date
|| undef,
'-description' => $gene_description,
'-external_name' => $external_name,
'-external_db' => $external_db,
'-external_status' => $external_status,
'-display_xref' => $display_xref,
'-status' => $status,
'-source' => $source,
'-is_current' => $is_current,
'-canonical_transcript' => $canonical_transcript,
'-canonical_annotation' => $canonical_annotation);
}
......
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