culex_quinquefasciatus.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::culex_quinquefasciatus;
 
use  XrefMapper::BasicMapper;
use  XrefMapper::VBCoordinateMapper;
 
use vars '@ISA';
 
@ISA = qw{ XrefMapper::BasicMapper };
 
sub set_methods{
 
  my $default_method = 'ExonerateGappedBest1_55_perc_id';
  my %override_method_for_source = (  
       ExonerateGappedBest5_55_perc_id => ['RefSeq_mRNA','RefSeq_mRNA_predicted', 'RefSeq_ncRNA', 'RefSeq_ncRNA_predicted' ],
         );
 
  return $default_method, \%override_method_for_source;
}
 
 
# transcript, gene display_xrefs can use defaults
# since anopheles_symbol is "before" Uniprot
 
#Reverse order: the latest one is the list has higher precedence!
 
sub gene_description_sources {
 
  return qw(
        VB_Community_Annotation
        Uniprot/SWISSPROT
        VB_RNA_Description
        VB_External_Description
            );
}
 
sub transcript_display_xref_sources {
 
  my @list = qw(        
        VB_Community_Annotation
        Uniprot/SWISSPROT
        VB_RNA_Description
        VB_External_Description
        );
 
  my %ignore;
  return [\@list,\%ignore];
 
}
 
# regexps to match any descriptons we want to filter out
sub gene_description_filter_regexps {
 
  return ();
 
}
 
sub no_source_label_list{
  my $self = shift;
  my @list;
 
  print "Using no_source_label_list :-)\n";
  #foreach my $ex (qw("VB RNA Description" "VB External Description")){
  #  $list{$ex} = 1;
  #}    
 
  push @list,"VB_RNA_Description";
  push @list,"VB_External_Description";
 
  return \@list;
}
 
1;