ApisMellifera.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
 
use strict;
use warnings;
 
use SeqStoreConverter::BasicConverter;
 
package SeqStoreConverter::ApisMellifera;
 
use vars qw(@ISA);
 
@ISA = qw(SeqStoreConverter::BasicConverter);
 
 
sub create_coord_systems {
  my $self = shift;
 
  $self->debug("ApisMellifera Specific: creating " .
               "contig and scaffold coord systems");
 
  my $target = $self->target();
  my $dbh    = $self->dbh();
 
  my $ass_def = $self->get_default_assembly();
 
  my @coords = 
    (["scaffold" , $ass_def, "default_version", 1     ],
     ["contig",      undef   , "default_version,sequence_level", 2]);
 
  my @assembly_mappings =  ("scaffold:$ass_def|contig");
 
 
  $self->debug("Building coord_system table");
 
  my $sth = $dbh->prepare("INSERT INTO $target.coord_system " .
                           "(name, version, attrib, rank) VALUES (?,?,?,?)");
 
  my %coord_system_ids;
 
  foreach my $cs (@coords) {
    $sth->execute(@$cs);
    $coord_system_ids{$cs->[0]} = $sth->{'mysql_insertid'};
  }
  $sth->finish();
 
  $self->debug("Adding assembly.mapping entries to meta table");
 
  $sth = $dbh->prepare("INSERT INTO $target.meta(meta_key, meta_value) " .
                       "VALUES ('assembly.mapping', ?)");
 
  foreach my $mapping (@assembly_mappings) {
    $sth->execute($mapping);
  }
  
  $sth->finish();
 
  return;
}
 
 
 
sub create_seq_regions {
  my $self = shift;
 
  $self->debug( "ApisMellifera Specific: creating contig and " .
               "scaffold seq_regions");
 
  $self->contig_to_seq_region('contig');
  $self->chromosome_to_seq_region("scaffold");
}
 
 
sub create_assembly {
  my $self = shift;
 
  $self->debug("ApisMellifera Specific: loading assembly data");
 
  $self->assembly_contig_chromosome();
}
 
 
1;