Raw content of XrefMapper::mus_musculus
<![CDATA[package XrefMapper::mus_musculus;
use XrefMapper::BasicMapper;
use vars '@ISA';
@ISA = qw{ XrefMapper::BasicMapper };
use strict;
sub get_set_lists {
return [["ExonerateGappedBest1", ["mus_musculus","*"]]];
}
sub get_official_name{
return "MGI";
}
sub get_canonical_name{
return "MGI";
}
sub species_specific_pre_attributes_set{
my $self = shift;
$self->official_naming();
}
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;
}
sub gene_description_sources {
return ("miRBase",
"RFAM",
"IMGT/GENE_DB",
"MGI_curated_gene",
"MGI_curated_transcript",
"MGI",
"Uniprot/SWISSPROT",
"Uniprot/Varsplic",
"RefSeq_peptide",
"RefSeq_dna",
"Uniprot/SPTREMBL" );
}
sub special_filter {
return ('\(?[0-9A-Z]{10}RIK PROTEIN\)?[ \.]',
'RIKEN CDNA [0-9A-Z]{10} GENE',
'.*RIKEN FULL-LENGTH ENRICHED LIBRARY.*PRODUCT:',
'.*RIKEN FULL-LENGTH ENRICHED LIBRARY.*',
'\(*HYPOTHETICAL\s+.*',
'^UNKNOWN\s+.*',
'CDNA SEQUENCE\s?,? [A-Z]+\d+[ \.;]',
'CLONE MGC:\d+[ \.;]',
' MGC:\s*\d+[ \.;]',
'HYPOTHETICAL PROTEIN,',
'HYPOTHETICAL PROTEIN \S+[\.;]',
'DNA SEGMENT, CHR.*',
'PROTEIN \S+ HOMOLOG\.?',
'^SIMILAR TO GENE.*',
'SIMILAR TO PUTATIVE[ \.]',
'^SIMILAR TO HYPOTHETICAL.*',
'SIMILAR TO (KIAA|LOC|RIKEN).*',
'SIMILAR TO GENBANK ACCESSION NUMBER\s+\S+',
'SIMILAR TO\s+$',
'EXPRESSED SEQUENCE [A-Z]+\d+[ \.;]',
'EST [A-Z]+\d+[ \.;]',
'^\s*\(FRAGMENT\)\.?\s*$',
'^\s*\(?GENE\)?\.?;?\s*$',
'\s*\(?GENE\)?\.?;?',
'\s*\(?PRECURSOR\)?\.?;?',
'^\s*\(\s*\)\s*$',
'^\s*\(\d*\)\s*[ \.]$',
'^\s+\(?\s*$');
}
sub gene_description_filter_regexps {
return ('\(*HYPOTHETICAL\s+.*',
'^UNKNOWN\s+.*',
'CDNA SEQUENCE\s?,? [A-Z]+\d+[ \.;]',
'CLONE MGC:\d+[ \.;]',
' MGC:\s*\d+[ \.;]',
'HYPOTHETICAL PROTEIN,',
'HYPOTHETICAL PROTEIN \S+[\.;]',
'DNA SEGMENT, CHR.*',
'PROTEIN \S+ HOMOLOG\.?',
'^SIMILAR TO GENE.*',
'SIMILAR TO PUTATIVE[ \.]',
'^SIMILAR TO HYPOTHETICAL.*',
'SIMILAR TO (KIAA|LOC|RIKEN).*',
'SIMILAR TO GENBANK ACCESSION NUMBER\s+\S+',
'SIMILAR TO\s+$',
'EXPRESSED SEQUENCE [A-Z]+\d+[ \.;]',
'EST [A-Z]+\d+[ \.;]',
'^\s*\(FRAGMENT\)\.?\s*$',
'^\s*\(?GENE\)?\.?;?\s*$',
'\s*\(?GENE\)?\.?;?',
'\s*\(?PRECURSOR\)?\.?;?',
'^\s*\(\s*\)\s*$',
'^\s*\(\d*\)\s*[ \.]$',
'^\s+\(?\s*$');
}
#sub get_list_of_sources_for_one_max_per_transcript{
# my $self = shift;
# my @list = qw(MGI);
# return @list;
#}
1;
]]>