preliminary converter for honey bee

misc-scripts/surgery/SeqStoreConverter/ApisMellifera.pm

+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" , $ass_def, "default_version", 1     ],
+     ["contig",      undef   , "default_version,sequence_level", 2]);
+
+  my @assembly_mappings =  ("chromosome:$ass_def|chunk");
+
+  my %cs = (gene                  => 'scaffold',
+            transcript            => 'scaffold',
+            exon                  => 'scaffold',
+            dna_align_feature     => 'contig',
+            protein_align_feature => 'contig',
+            marker_feature        => 'contig',
+            simple_feature        => 'contig',
+            repeat_feature        => 'contig',
+            qtl_feature           => 'scaffold',
+            misc_feature          => 'scaffold',
+            prediction_transcript => 'contig',
+            prediction_exon       => 'contig',
+            karyotype             => 'scaffold');
+
+  $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("Building meta_coord table");
+  $sth = $dbh->prepare("INSERT INTO $target.meta_coord VALUES (?, ?)");
+  foreach my $val (keys %cs) {
+    $sth->execute($val, $coord_system_ids{$cs{$val}});
+  }
+  $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("DrosophilaMelanogaster Specific: loading assembly data");
+
+  $self->assembly_contig_chromosome();
+}
+
+
+1;