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revision 1.3, Tue Jun 30 19:53:01 2009 UTC revision 1.5, Wed Sep 9 16:30:22 2009 UTC
# Line 258  Line 258 
258          # Get the data for this group.          # Get the data for this group.
259          my ($taxID, $parent, $type, undef, undef,          my ($taxID, $parent, $type, undef, undef,
260              undef,  undef,   undef, undef, undef, $hidden) = GetTaxData($ih);              undef,  undef,   undef, undef, undef, $hidden) = GetTaxData($ih);
261          # Determine whether or not this is a domain group.          # Determine whether or not this is a domain group. A domain group is
262          my $domain = ($type eq 'superkingdom');          # terminal when doing taxonomy searches. The NCBI indicates a top-level
263            # node by making it a child of the root node 1. We also include
264            # super-kingdoms (archaea, eukaryota, bacteria), which are below cellular
265            # organisms but are still terminal in our book.
266            my $domain = ($type eq 'superkingdom') || ($parent == 1);
267          # Get the node's name.          # Get the node's name.
268          my $name = $primaryNames{$taxID};          my $name = $primaryNames{$taxID};
269          # It's an error if there's no name.          # It's an error if there's no name.
# Line 318  Line 322 
322      my $dna_size = $fig->genome_szdna($genomeID);      my $dna_size = $fig->genome_szdna($genomeID);
323      my $pegs = $fig->genome_pegs($genomeID);      my $pegs = $fig->genome_pegs($genomeID);
324      my $rnas = $fig->genome_rnas($genomeID);      my $rnas = $fig->genome_rnas($genomeID);
325        my $domain = $fig->genome_domain($genomeID);
326        my $prokaryotic = ($domain =~ /bacter|archae/i);
327      # We need to compute the number of contigs from the list of contig IDs.      # We need to compute the number of contigs from the list of contig IDs.
328      my @contigIDs = $fig->contigs_of($genomeID);      my @contigIDs = $fig->contigs_of($genomeID);
329      my $contigs = scalar(@contigIDs);      my $contigs = scalar(@contigIDs);
330      # Write the genome record.      # Write the genome record.
331      $self->PutE(Genome => $genomeID, complete => $complete, contigs => $contigs,      $self->PutE(Genome => $genomeID, complete => $complete, contigs => $contigs,
332                  dna_size => $dna_size, scientific_name => $scientific_name,                  dna_size => $dna_size, scientific_name => $scientific_name,
333                  pegs => $pegs, rnas => $rnas);                  pegs => $pegs, rnas => $rnas, prokaryotic => $prokaryotic,
334                    domain => $domain);
335      # Now we create the Contigs. Each one needs to be split into DNA sequences.      # Now we create the Contigs. Each one needs to be split into DNA sequences.
336      for my $contigID (@contigIDs) {      for my $contigID (@contigIDs) {
337          $self->Track(Contigs => $contigID, 100);          $self->Track(Contigs => $contigID, 100);

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