Created; create xrefs & direct_xrefs from stable IDs for WormBase-imported...

Created; create xrefs & direct_xrefs from stable IDs for WormBase-imported genomes (e.g. elegans). Subclass of DatabaseParser.pm

misc-scripts/xref_mapping/XrefParser/WormbaseDatabaseStableIDParser.pm

+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 XrefParser::DatabaseParser;
+
+use vars qw(@ISA);
+@ISA = qw(XrefParser::DatabaseParser);
+
+sub run {
+
+  my ($self, $dsn, $source_id, $species_id) = @_;
+
+  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";
+
+    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
+
+}
+
+sub new {
+
+  my $self = {};
+  bless $self, "XrefParser::WormbaseDatabaseStableIDParser";
+  return $self;
+
+}
+
+1;
+