HomoSapiens.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;
 
package SeqStoreConverter::HomoSapiens;
 
use SeqStoreConverter::BasicConverter;
 
use vars qw(@ISA);
 
@ISA = qw(SeqStoreConverter::BasicConverter);
 
 
sub create_attribs {
  my $self = shift;
 
  #
  # Human clones need their htg phase information copied
  #
 
  my $source = $self->source();
  my $target = $self->target();
  my $dbh    = $self->dbh();
 
  $self->SUPER::create_attribs();
  
  $self->debug("HomoSapiens specific: Creating HTG Phase seq_region attribs");
 
  $dbh->do
    ("INSERT INTO $target.attrib_type( code, name, description ) " .
     "VALUES ('htg_phase', 'HTG Phase', 'High Throughput Genome Phase')");
 
 
  $dbh->do
    ("INSERT INTO $target.seq_region_attrib( seq_region_id, attrib_type_id, " .
                                            "value) " .
     "SELECT tmp_cln.new_id, attrib_type.attrib_type_id, cln.htg_phase " .
     "FROM   $target.tmp_cln_map tmp_cln, $target.attrib_type attrib_type, " .
     "       $source.clone cln " .
     "WHERE  cln.clone_id = tmp_cln.old_id " .
     "AND    attrib_type.code = 'htg_phase'");
 
  return;
}
 
 
1;