my ($self) = @_;
# wormbase_gene
# wormbase_transcript
# wormbase_locus
# wormpep_id
print "Building Transcript and Gene display_xrefs using WormBase direct xrefs\n" if ($self->verbose);
# strategy:
# - populate transcript display xref with wormbase_transcript
# - populate gene display xref with wormbase_locus
my (%external_dbs, %gene_display_xrefs, %tran_display_xrefs);
#
# Get external_db ids for the sources we are interested in
#
my $edb_sth = $self->core->dbc->prepare("SELECT external_db_id, db_name from external_db WHERE db_name like 'wormbase%'");
$edb_sth->execute;
while( my ($edb_id, $edb_name) = $edb_sth->fetchrow_array ) {
$external_dbs{$edb_name} = $edb_id;
}
$edb_sth->finish;
if (not exists $external_dbs{wormbase_transcript} or
not exists $external_dbs{wormbase_locus}) {
print "Could not find wormbase_transcript and wormbase_locus in external_db table, so doing nothing\n" if $self->verbose;
return;
}
my $query_gseq_sth = $self->core->dbc->prepare("SELECT ensembl_id, x.xref_id " .
"FROM object_xref ox, xref x ".
"WHERE ox.xref_id = x.xref_id AND external_db_id = " . $external_dbs{wormbase_gseqname});
$query_gseq_sth->execute();
while( my ($gid, $xid) = $query_gseq_sth->fetchrow_array) {
$gene_display_xrefs{$gid} = $xid;
}
$query_gseq_sth->finish;
#
# Some genes will have a locus name. Over-write display xrefs for those that do
#
my $query_gene_sth = $self->core->dbc->prepare("SELECT ensembl_id, x.xref_id " .
"FROM object_xref ox, xref x ".
"WHERE ox.xref_id = x.xref_id AND external_db_id = " . $external_dbs{wormbase_locus});
$query_gene_sth->execute();
while( my ($gid, $xid) = $query_gene_sth->fetchrow_array) {
$gene_display_xrefs{$gid} = $xid;
}
$query_gene_sth->finish;
#
# Get the wormbase_transcript xrefs for the genes
#
my $query_tran_sth = $self->core->dbc->prepare("SELECT ensembl_id, x.xref_id " .
"FROM object_xref ox, xref x " .
"WHERE ox.xref_id = x.xref_id and external_db_id = " . $external_dbs{wormbase_transcript});
$query_tran_sth->execute();
while( my ($gid, $xid) = $query_tran_sth->fetchrow_array) {
$tran_display_xrefs{$gid} = $xid;
}
$query_tran_sth->finish;
#
# finally, update
#
my $reset_sth = $self->core->dbc->prepare("UPDATE gene SET display_xref_id = null");
$reset_sth->execute();
$reset_sth->finish;
$reset_sth = $self->core->dbc->prepare("UPDATE transcript SET display_xref_id = null");
$reset_sth->execute();
$reset_sth->finish;
my $update_gene_sth = $self->core->dbc->prepare("UPDATE gene g SET g.display_xref_id= ? WHERE g.gene_id=?");
my $update_tran_sth = $self->core->dbc->prepare("UPDATE transcript t SET t.display_xref_id= ? WHERE t.transcript_id=?");
foreach my $gid (keys %gene_display_xrefs) {
$update_gene_sth->execute( $gene_display_xrefs{$gid}, $gid );
}
$update_gene_sth->finish;
foreach my $tid (keys %tran_display_xrefs) {
$update_tran_sth->execute( $tran_display_xrefs{$tid}, $tid );
}
$update_tran_sth->finish;
print "Updated display xrefs in core for genes and transcripts\n" if $self->verbose;
}
Code:
