[Bio] / Sprout / GenomeSaplingLoader.pm Repository:
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revision 1.10, Wed Apr 28 14:04:49 2010 UTC revision 1.12, Thu Oct 14 17:27:37 2010 UTC
# Line 217  Line 217 
217      # Get the Sapling object.      # Get the Sapling object.
218      my $sapling = $self->db();      my $sapling = $self->db();
219      # Get the name of the taxonomy dump directory.      # Get the name of the taxonomy dump directory.
220      my $taxDir = $FIG_Config::taxData || "$FIG_Config::global/Taxonomy";      my $taxDir = "/vol/biodb/ncbi/taxonomy";
221      # The first step is to read in all the names. We will build a hash that maps      # The first step is to read in all the names. We will build a hash that maps
222      # each taxonomy ID to a list of its names. The first scientific name encountered      # each taxonomy ID to a list of its names. The first scientific name encountered
223      # will be saved as the primary name. Only scientific names, synonoyms, and      # will be saved as the primary name. Only scientific names, synonoyms, and
# Line 294  Line 294 
294              if ($merges{$taxID}) {              if ($merges{$taxID}) {
295                  $taxID = $merges{$taxID};                  $taxID = $merges{$taxID};
296                  $self->Add('merged-names' => 1);                  $self->Add('merged-names' => 1);
297                    Trace("$genomeID has alternate taxonomy ID $taxID.") if T(ERDBLoadGroup => 2);
298              } else {              } else {
299                  $taxID = undef;                  $taxID = undef;
300                  $self->Add('missing-groups' => 1);                  $self->Add('missing-groups' => 1);
301                    Trace("$genomeID has no taxonomy group.") if T(ERDBLoadGroup => 1);
302              }              }
303          }          }
304          # Connect the genome and the group if the group is real.          # Connect the genome and the group if the group is real.

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