Raw content of XrefMapper::rattus_norvegicus
<![CDATA[package XrefMapper::rattus_norvegicus;
use XrefMapper::BasicMapper;
use vars '@ISA';
@ISA = qw{ XrefMapper::BasicMapper };
sub get_set_lists {
return [["ExonerateGappedBest1", ["rattus_norvegicus","*"]]];
}
sub transcript_display_xref_sources {
my @list = qw(RFAM
miRBase
HUGO
RGD
MGI
flybase_symbol
Anopheles_symbol
Genoscope_annotated_gene
Uniprot/SWISSPROT
Uniprot/Varsplic
RefSeq_peptide
RefSeq_dna
Uniprot/SPTREMBL
EntrezGene);
my %ignore;
$ignore{"EntrezGene"}= 'FROM:RefSeq_[pd][en][pa].*_predicted';
return [\@list,\%ignore];
}
sub gene_description_filter_regexps {
return ('^\(CLONE REM\d+\) ORF \(FRAGMENT\)\.*',
'^ORF\s*\d+\s+PROTEIN\.*',
'\(?[0-9A-Z]{10}RIK PROTEIN\)?[ \.]',
'RIKEN CDNA [0-9A-Z]{10}[ \.;]',
'.*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*$');
}
1;
]]>