PristionchusPacificus.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
 
 
=head1 CONTACT
 
  Please email comments or questions to the public WormBase
  help list at <help@wormbase.org>.
 
=cut
 
package Bio::EnsEMBL::IdMapping::StableIdGenerator::PristionchusPacificus;
 
# Class to generate WormBase conform Pristionchus IDs to be injected into the mapper
 
use strict;
use warnings;
 
use base qw(Bio::EnsEMBL::IdMapping::StableIdGenerator::EnsemblGeneric);
 
# PPAxxxxx
# ups the id by one
sub increment_stable_id {
  my ( $self, $lastId ) = @_;
 
  throw("invalid stable ID: $lastId.") unless ($lastId=~/PPA/);
 
  $lastId =~ /^PPA(\d+)/;
 
  my $number = $1+1;
  my $stable_id = sprintf("PPA%05d",$number);
 
  return $stable_id;
}
 
# just in case it is actually used somewhere
sub is_valid {
  my ( $self, $stableId ) = @_;
 
  if ( defined($stableId) && $stableId =~ /^PPA\d+/)
     {return 1} else {return undef}
}
 
1;