Raw content of SeqStoreConverter::PanTroglodytes
<![CDATA[use strict;
use warnings;
use SeqStoreConverter::BasicConverter;
package SeqStoreConverter::PanTroglodytes;
use vars qw(@ISA);
@ISA = qw(SeqStoreConverter::BasicConverter);
sub create_coord_systems {
my $self = shift;
$self->debug("PanTroglodytes Specific: loading assembly data");
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("PanTroglodytes Specific: creating contig, " .
"clone, chromosome and supercontig seq_regions");
$self->contig_to_seq_region();
$self->chromosome_to_seq_region('scaffold');
}
sub create_assembly {
my $self = shift;
$self->debug("PanTroglodytes Specific: loading assembly data");
$self->assembly_contig_chromosome();
}
1;
]]>