parasite.pm

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=head1 LICENSE
 
See the NOTICE file distributed with this work for additional information
regarding copyright ownership.
 
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
 
     http://www.apache.org/licenses/LICENSE-2.0
 
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
 
=cut
 
package XrefMapper::parasite;
 
use  XrefMapper::BasicMapper;
 
use vars qw(@ISA);
 
@ISA = qw(XrefMapper::BasicMapper);
 
 
# This module is activated by specifying "taxon=wormbase" in the mapping input file
# It contains some common config for worms maintained by WormBase (i.e. having genes
# with WBGene ids etc)
 
sub set_methods{
 
  my $default_method = 'ExonerateGappedBest1';
  my %override_method_for_source = (  
           ExonerateGappedBest5 => ['RefSeq_mRNA',
                                    'RefSeq_mRNA_predicted', 
                                    'RefSeq_ncRNA', 
                                    'RefSeq_ncRNA_predicted' ],
         );
 
  return $default_method, \%override_method_for_source;
}
 
 
sub transcript_names_from_gene {
  return;
}
 
 
sub gene_description_sources {
 
  return ("RFAM",
          "RNAMMER",
          "TRNASCAN_SE",
      "miRBase",
          "HGNC",
          "IMGT/GENE_DB",
      "Uniprot/SWISSPROT",
      "RefSeq_peptide",
          "Uniprot/SPTREMBL",
      );
 
}
 
 
sub gene_description_filter_regexps {
 
  return (
           '^Uncharacterized protein\s*',
           '^Putative uncharacterized protein\s*',
           '^Hypothetical protein\s*',
   );
 
}
 
1;