Raw content of XrefMapper::caenorhabditis_elegans
<![CDATA[package XrefMapper::caenorhabditis_elegans;
use XrefMapper::BasicMapper;
use vars qw(@ISA);
@ISA = qw(XrefMapper::BasicMapper);
sub get_set_lists {
return [["ExonerateGappedBest1", ["caenorhabditis_elegans","*"]]];
}
# Elegans is imported from WormBase. The gene and transcript stable IDs
# are the WormBase identifiers. The display_xref_ids for genes and
# transcripts are calculated directly rather than via the more complex
# priority-based method in BasicMapper.pm
sub build_display_xrefs {
my ($self, $type, $external_db) = @_;
print "Setting $type display_xrefs from $type stable IDs\n";
my $dir = $self->core()->dir();
my $sql = "UPDATE $type t, ${type}_stable_id s, xref x, external_db e SET t.display_xref_id=x.xref_id WHERE t.${type}_id=s.${type}_id AND s.stable_id=x.dbprimary_acc AND e.external_db_id=x.external_db_id AND e.db_name=\'${external_db}\'\n";
open (SQL, ">$dir/${type}_display_xref.sql");
print SQL $sql;
close(SQL);
}
sub build_transcript_display_xrefs {
my ($self) = @_;
$self->build_display_xrefs("transcript", "wormbase_transcript");
}
sub build_gene_display_xrefs {
my ($self) = @_;
$self->build_display_xrefs("gene", "wormbase_gene");
}
sub gene_description_filter_regexps {
return ('[0-9A-Z]+\.\d*[A-Z]* PROTEIN[ \.]',
'\(\d[A-Z]\d+\)\.',
'\([0-9A-Z]+\.\d*[A-Z]* PROTEIN\)[ \.]',
'^\(*HYPOTHETICAL\s+.*',
'^\s*\(FRAGMENT\)\.?\s*$' );
}
1;
]]>