aedes_aegypti.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::aedes_aegypti;
 
use  XrefMapper::BasicMapper;
 
use vars '@ISA';
 
@ISA = qw{ XrefMapper::BasicMapper };
 
 
 
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;
}
 
 
 
#Reverse order: last one has higher priority! <- This comment is wrong (mikkel 12/10/2012)
# index [0] has higher priority! 
sub gene_description_sources {
  return qw(
         VB_Community_Annotation
         Uniprot/SWISSPROT
         VB_External_Description
         );
}
#Old order VB_External_Description Uniprot/SWISSPROT VB_Community_Annotation
# only sources in this list are used when setting  display_xref_id
sub transcript_display_xref_sources {
  my @list = qw(
        VB_Community_Annotation
        Uniprot/SWISSPROT
        VB_External_Description
        );
#old VB_External_Description Uniprot/SWISSPROT VB_Community_Annotation
  my %ignore;
  #$ignore{"EntrezGene"}= 'FROM:RefSeq_[pd][en][pa].*_predicted';
 
  return [\@list,\%ignore];
 
}
 
 
1;