Raw content of XrefParser::WormbaseDatabaseStableIDParser
<![CDATA[package XrefParser::WormbaseDatabaseStableIDParser;
# Read gene and transcript stable IDs from a WormBase-imported database and create
# xrefs and direct xrefs for them.
# Note the only things that are actually WormBase specific here are the source names
# for the wormbase_gene and wormbase_transcript sources.
use strict;
use base qw( XrefParser::DatabaseParser );
sub run {
my ($self, $dsn, $source_id, $species_id, $verbose) = @_;
my $db = $self->connect($dsn); # source db (probably core)
my $xref_db = $self->dbi();
my $xref_sth = $xref_db->prepare( "INSERT INTO xref (accession,label,source_id,species_id) VALUES (?,?,?,?)" );
my $direct_xref_sth = $xref_db->prepare( "INSERT INTO direct_xref (general_xref_id,ensembl_stable_id,type,linkage_xref) VALUES (?,?,?,?)" );
# read stable IDs
foreach my $type ('gene', 'transcript') {
print "Building xrefs from $type stable IDs\n" if($verbose);
my $wb_source_id = $self->get_source_id_for_source_name("wormbase_$type");
my $sth = $db->prepare( "SELECT stable_id FROM ${type}_stable_id" );
$sth->execute();
while(my @row = $sth->fetchrow_array()) {
my $id = $row[0];
# add an xref & a direct xref
$xref_sth->execute($id, $id, $wb_source_id, $species_id);
my $xref_id = $xref_sth->{'mysql_insertid'};
$direct_xref_sth->execute($xref_id, $id, $type, "Stable ID direct xref");
} # while fetch stable ID
} # foreach type
return 0;
}
1;
]]>