Raw content of SeqStoreConverter::ApisMellifera 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;