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revision 1.67, Tue Sep 19 00:11:12 2006 UTC revision 1.68, Sun Sep 24 17:14:16 2006 UTC
# Line 266  Line 266 
266              my $extra = join " ", @extraData;              my $extra = join " ", @extraData;
267              # Get the full taxonomy.              # Get the full taxonomy.
268              my $taxonomy = $fig->taxonomy_of($genomeID);              my $taxonomy = $fig->taxonomy_of($genomeID);
269                # Open the NMPDR group file for this genome.
270                my $group;
271                if (open(TMP, "<$FIG_Config::organisms/$genomeID/NMPDR") &&
272                    defined($group = <TMP>)) {
273                    # Clean the line ending.
274                    chomp $group;
275                } else {
276                    # No group, so use the default.
277                    $group = $FIG_Config::otherGroup;
278                }
279                close TMP;
280              # Output the genome record.              # Output the genome record.
281              $loadGenome->Put($genomeID, $accessCode, $fig->is_complete($genomeID), $genus,              $loadGenome->Put($genomeID, $accessCode, $fig->is_complete($genomeID), $genus,
282                               $species, $extra, $taxonomy);                               $group, $species, $extra, $taxonomy);
283              # Now we loop through each of the genome's contigs.              # Now we loop through each of the genome's contigs.
284              my @contigs = $fig->all_contigs($genomeID);              my @contigs = $fig->all_contigs($genomeID);
285              for my $contigID (@contigs) {              for my $contigID (@contigs) {
# Line 1379  Line 1390 
1390    
1391      GenomeGroups      GenomeGroups
1392    
1393  There is no direct support for genome groups in FIG, so we access the SEED  Currently, we do not use groups. We used to use them for NMPDR groups,
1394    butThere is no direct support for genome groups in FIG, so we access the SEED
1395  files directly.  files directly.
1396    
1397  =over 4  =over 4
# Line 1405  Line 1417 
1417          Trace("Loading from existing files.") if T(2);          Trace("Loading from existing files.") if T(2);
1418      } else {      } else {
1419          Trace("Generating group data.") if T(2);          Trace("Generating group data.") if T(2);
1420          # Loop through the genomes.          # Currently there are no groups.
         my $line;  
         for my $genomeID (sort keys %{$genomeHash}) {  
             Trace("Processing $genomeID.") if T(3);  
             # Open the NMPDR group file for this genome.  
             if (open(TMP, "<$FIG_Config::organisms/$genomeID/NMPDR") &&  
                 defined($line = <TMP>)) {  
                 # Clean the line ending.  
                 chomp $line;  
                 # Add the group to the table. Note that there can only be one group  
                 # per genome.  
                 $loadGenomeGroups->Put($genomeID, $line);  
             }  
             close TMP;  
         }  
1421      }      }
1422      # Finish the load.      # Finish the load.
1423      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();

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