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revision 1.91, Thu Feb 14 19:15:18 2008 UTC revision 1.92, Sun Mar 23 16:33:15 2008 UTC
# Line 255  Line 255 
255          Trace("Loading from existing files.") if T(2);          Trace("Loading from existing files.") if T(2);
256      } else {      } else {
257          Trace("Generating genome data.") if T(2);          Trace("Generating genome data.") if T(2);
258            # Get the full info for the FIG genomes.
259            my %genomeInfo = map { $_->[0] => { gname => $_->[1], szdna => $_->[2], maindomain => $_->[3],
260                                                pegs => $_->[4], rnas => $_->[5], complete => $_->[6] } } @{$fig->genome_info()};
261          # Now we loop through the genomes, generating the data for each one.          # Now we loop through the genomes, generating the data for each one.
262          for my $genomeID (sort keys %{$genomeHash}) {          for my $genomeID (sort keys %{$genomeHash}) {
263              Trace("Generating data for genome $genomeID.") if T(3);              Trace("Generating data for genome $genomeID.") if T(3);
# Line 284  Line 287 
287                  $group = $FIG_Config::otherGroup;                  $group = $FIG_Config::otherGroup;
288              }              }
289              close TMP;              close TMP;
290                # Get the contigs.
291                my @contigs = $fig->all_contigs($genomeID);
292                # Get this genome's info array.
293                my $info = $genomeInfo{$genomeID};
294              # Output the genome record.              # Output the genome record.
295              $loadGenome->Put($genomeID, $accessCode, $fig->is_complete($genomeID),              $loadGenome->Put($genomeID, $accessCode, $info->{complete}, scalar(@contigs),
296                               $dnaSize, $genus, $group, $species, $extra, $version, $taxonomy);                               $dnaSize, $genus, $info->{pegs}, $group, $info->{rnas}, $species, $extra, $version, $taxonomy);
297              # Now we loop through each of the genome's contigs.              # Now we loop through each of the genome's contigs.
             my @contigs = $fig->all_contigs($genomeID);  
298              for my $contigID (@contigs) {              for my $contigID (@contigs) {
299                  Trace("Processing contig $contigID for $genomeID.") if T(4);                  Trace("Processing contig $contigID for $genomeID.") if T(4);
300                  $loadContig->Add("contigIn");                  $loadContig->Add("contigIn");
# Line 451  Line 457 
457                              $alias{$alias} = 1;                              $alias{$alias} = 1;
458                          }                          }
459                      }                      }
460                        # Add the corresponding IDs. Note we have to remove the FIG ID from the
461                        # return list. It's already among the keywords.
462                        my @corresponders = grep { $_ !~ /^fig/} $fig->get_corresponding_ids($featureID);
463                        push @keywords, @corresponders;
464                      Trace("Assignment for $featureID is: $assignment") if T(4);                      Trace("Assignment for $featureID is: $assignment") if T(4);
465                      # Break the assignment into words and shove it onto the                      # Break the assignment into words and shove it onto the
466                      # keyword list.                      # keyword list.
# Line 739  Line 749 
749                  # Create the subsystem record.                  # Create the subsystem record.
750                  my $curator = $sub->get_curator();                  my $curator = $sub->get_curator();
751                  my $notes = $sub->get_notes();                  my $notes = $sub->get_notes();
752                  $loadSubsystem->Put($subsysID, $curator, $notes);                  my $description = $sub->get_description();
753                    $loadSubsystem->Put($subsysID, $curator, $description, $notes);
754                  # Now for the classification string. This comes back as a list                  # Now for the classification string. This comes back as a list
755                  # reference and we convert it to a space-delimited string.                  # reference and we convert it to a space-delimited string.
756                  my $classList = $fig->subsystem_classification($subsysID);                  my $classList = $fig->subsystem_classification($subsysID);

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