Raw content of XrefMapper::homo_sapiens
<![CDATA[package XrefMapper::homo_sapiens;
use XrefMapper::BasicMapper;
use XrefMapper::SubmitMapper;
use strict;
use vars '@ISA';
@ISA = qw{ XrefMapper::BasicMapper };
sub get_set_lists {
return [["ExonerateGappedBest1", ["homo_sapiens","*"]]];
}
sub gene_description_filter_regexps {
return ('^BA\S+\s+\(NOVEL PROTEIN\)\.?',
'^DJ\S+\s+\(NOVEL PROTEIN\)\.?',
'^LOC\d+\s*(PROTEIN)?\.?',
'^ORF.*',
'^PROTEIN C\d+ORF\d+\.*',
'\(CLONE \S+\)\s+',
'^BC\d+\_\d+\.?',
'^CGI\-\d+ PROTEIN\.?\;?',
'[0-9A-Z]{10}RIK PROTEIN[ \.]',
'R\d{5}_\d[ \.,].*',
'PROTEIN KIAA\d+[ \.].*',
'RIKEN CDNA [0-9A-Z]{10}[ \.]',
'^\(*HYPOTHETICAL\s+.*',
'^UNKNOWN\s+.*',
'^DKFZP[A-Z0-9]+\s+PROTEIN[\.;]?.*',
'^CHROMOSOME\s+\d+\s+OPEN\s+READING\s+FRAME\s+\d+\.?.*',
'^FKSG\d+\.?.*',
'^HSPC\d+\s+PROTEIN\.?.*',
'^KIAA\d+\s+PROTEIN\.?.*',
'^KIAA\d+\s+GENE\s+PRODUCT\.?.*',
'^HSPC\d+.*',
'^PRO\d+\s+PROTEIN\.?.*',
'^PRO\d+\.?.*',
'^FLJ\d+\s+PROTEIN.*',
'^PRED\d+\s+PROTEIN.*',
'^WUGSC:.*\s+PROTEIN\.?.*',
'^SIMILAR TO GENE.*',
'^SIMILAR TO PUTATIVE[ \.]',
'^SIMILAR TO HYPOTHETICAL.*',
'^SIMILAR TO (KIAA|LOC).*',
'^SIMILAR TO\s+$',
'^WUGSC:H_.*',
'^\s*\(?PROTEIN\)?\.?\s*$',
'^\s*\(?FRAGMENT\)?\.?\s*$',
'^\s*\(?GENE\)?\.?\s*$',
'^\s*\(\s*\)\s*$',
'^\s*\(\d*\)\s*[ \.]$');
}
sub get_official_name{
return "HGNC";
}
sub get_canonical_name{
return "HGNC";
}
sub species_specific_cleanup{
my $self = shift;
my $dbname = $self->get_canonical_name;
print "Removing all $dbname from object_xref not on a Gene\n";
my $remove_old_ones = (<<JSQL);
delete ox
from object_xref ox, xref x, external_db e
where e.db_name like "$dbname" and
ox.ensembl_object_type != "Gene" and
ox.xref_id = x.xref_id and
x.external_db_id = e.external_db_id;
JSQL
#
# First Delete all the hgnc object_xrefs not on a gene. (i.e these are copys).
#
my $sth = $self->core->dbc->prepare($remove_old_ones);
$sth->execute() || die "Could not execute: \n$remove_old_ones \n";
$sth->finish;
}
# For human we want to make a copy of the HGNC references on the genes and put them on
# the "canonical" transcripts
#sub species_specific_pre_attributes_set{
# my $self = shift;
# $self->official_naming();
#}
1;
]]>