Commit 17461aac authored by Glenn Proctor's avatar Glenn Proctor
Browse files

Removed conflict lines.

parent ec3c0781
......@@ -339,7 +339,7 @@ sub fetch_all_by_domain {
transcript tr,
translation tl
WHERE i.interpro_ac = ?
AND i.id = pf.hit_name
AND i.id = pf.hit_id
AND pf.translation_id = tl.translation_id
AND tr.transcript_id = tl.transcript_id
AND tr.is_current = 1
......@@ -1204,7 +1204,7 @@ sub get_Interpro_by_geneid {
AND t.is_current = 1
AND tl.transcript_id = t.transcript_id
AND tl.translation_id = pf.translation_id
AND i.id = pf.hit_name
AND i.id = pf.hit_id
AND i.interpro_ac = x.dbprimary_acc
);
......@@ -1305,7 +1305,6 @@ sub _objs_from_sth {
my $sa = $self->db()->get_SliceAdaptor();
my $aa = $self->db->get_AnalysisAdaptor();
my $ta = $self->db->get_TranscriptAdaptor();
my $dbEntryAdaptor = $self->db()->get_DBEntryAdaptor();
my @genes;
......@@ -1317,13 +1316,7 @@ sub _objs_from_sth {
my ( $gene_id, $seq_region_id, $seq_region_start, $seq_region_end,
$seq_region_strand, $analysis_id, $biotype, $display_xref_id,
$gene_description, $stable_id, $version, $created_date,
<<<<<<< GeneAdaptor.pm
$modified_date, $xref_display_id, $status, $source, $is_current,
$canonical_transcript_id, $canonical_annotation,
=======
$modified_date, $xref_display_id, $status, $source, $is_current,
$canonical_transcript_id, $canonical_annotation,
>>>>>>> 1.150
$xref_primary_acc, $xref_desc, $xref_version, $external_name,
$external_db, $external_status, $external_release, $external_db_name,
$info_type, $info_text);
......@@ -1332,7 +1325,6 @@ sub _objs_from_sth {
\$seq_region_end, \$seq_region_strand, \$analysis_id,
\$biotype, \$display_xref_id, \$gene_description,
\$status, \$source, \$is_current,
\$canonical_transcript_id, \$canonical_annotation,
\$stable_id, \$version,
\$created_date, \$modified_date,
\$xref_display_id, \$xref_primary_acc, \$xref_desc,
......@@ -1378,11 +1370,6 @@ sub _objs_from_sth {
my $analysis = $analysis_hash{$analysis_id} ||=
$aa->fetch_by_dbID($analysis_id);
#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) {
......@@ -1465,35 +1452,29 @@ sub _objs_from_sth {
$display_xref->status( $external_status );
}
# 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
} ) );
#finally, create the new gene
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
);
}
return \@genes;
......
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