WormbaseCElegansUniProtParser.pm

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=head1 LICENSE
 
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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
 
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WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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=cut
use strict;
use warnings;
package XrefParser::WormbaseCElegansUniProtParser;
 
# UniProt xrefs are sometimes - really - dependent xrefs of
# INSDC entries which we get from somewhere else
# Attempt to find the parent (has to already be present in the xref table)
# INSDC and UniProt entries have the same protein sequence, and
# UniProt lists INSDC as a parent. We get INSDC entries from somewhere else,
# so make UniProt entries dependent on INSDC entries.
# Note:
# INSDC entries have coordinates, and UniProt entries don't.
# So for perfect homologs, there can be many INSDC entries per UniProt.
 
use parent qw/XrefParser::WormbaseCElegansBase XrefParser::UniProtParser/;
 
sub upload_xref_object_graphs {
  my ($self, $xrefs, $dbi) = @_;
  my $source_id = $self->get_source_id_for_source_name('protein_id'); 
  my $source_id_skip = $self->get_source_id_for_source_name('EMBL'); 
  my @adapted_xrefs;
  for my $xref ( @$xrefs) {
    push @adapted_xrefs, $self->swap_dependency($source_id, $dbi, $xref, $source_id_skip);
  }  
  return $self->SUPER::upload_xref_object_graphs(\@adapted_xrefs, $dbi);
}
1;