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revision 1.21, Sat Nov 12 03:42:48 2005 UTC revision 1.69, Wed Sep 27 12:34:46 2006 UTC
# Line 30  Line 30 
30      $stats->Accumulate($spl->LoadFeatureData());      $stats->Accumulate($spl->LoadFeatureData());
31      print $stats->Show();      print $stats->Show();
32    
 This module makes use of the internal Sprout property C<_erdb>.  
   
33  It is worth noting that the FIG object does not need to be a real one. Any object  It is worth noting that the FIG object does not need to be a real one. Any object
34  that implements the FIG methods for data retrieval could be used. So, for example,  that implements the FIG methods for data retrieval could be used. So, for example,
35  this object could be used to copy data from one Sprout database to another, or  this object could be used to copy data from one Sprout database to another, or
# Line 80  Line 78 
78  =item subsysFile  =item subsysFile
79    
80  Either the name of the file containing the list of trusted subsystems or a reference  Either the name of the file containing the list of trusted subsystems or a reference
81  to a list of subsystem names. If nothing is specified, all known subsystems will be  to a list of subsystem names. If nothing is specified, all NMPDR subsystems will be
82  considered trusted. Only subsystem data related to the trusted subsystems is loaded.  considered trusted. (A subsystem is considered NMPDR if it has a file named C<NMPDR>
83    in its data directory.) Only subsystem data related to the trusted subsystems is loaded.
84    
85  =item options  =item options
86    
# Line 94  Line 93 
93  sub new {  sub new {
94      # Get the parameters.      # Get the parameters.
95      my ($class, $sprout, $fig, $genomeFile, $subsysFile, $options) = @_;      my ($class, $sprout, $fig, $genomeFile, $subsysFile, $options) = @_;
96      # Load the list of genomes into a hash.      # Create the genome hash.
97      my %genomes;      my %genomes = ();
98        # We only need it if load-only is NOT specified.
99        if (! $options->{loadOnly}) {
100      if (! defined($genomeFile) || $genomeFile eq '') {      if (! defined($genomeFile) || $genomeFile eq '') {
101          # Here we want all the complete genomes and an access code of 1.          # Here we want all the complete genomes and an access code of 1.
102          my @genomeList = $fig->genomes(1);          my @genomeList = $fig->genomes(1);
# Line 119  Line 120 
120                  # an omitted access code can be defaulted to 1.                  # an omitted access code can be defaulted to 1.
121                  for my $genomeLine (@genomeList) {                  for my $genomeLine (@genomeList) {
122                      my ($genomeID, $accessCode) = split("\t", $genomeLine);                      my ($genomeID, $accessCode) = split("\t", $genomeLine);
123                      if (undef $accessCode) {                          if (! defined($accessCode)) {
124                          $accessCode = 1;                          $accessCode = 1;
125                      }                      }
126                      $genomes{$genomeID} = $accessCode;                      $genomes{$genomeID} = $accessCode;
# Line 129  Line 130 
130              Confess("Invalid genome parameter ($type) in SproutLoad constructor.");              Confess("Invalid genome parameter ($type) in SproutLoad constructor.");
131          }          }
132      }      }
133        }
134      # Load the list of trusted subsystems.      # Load the list of trusted subsystems.
135      my %subsystems = ();      my %subsystems = ();
136        # We only need it if load-only is NOT specified.
137        if (! $options->{loadOnly}) {
138      if (! defined $subsysFile || $subsysFile eq '') {      if (! defined $subsysFile || $subsysFile eq '') {
139          # Here we want all the subsystems.              # Here we want all the usable subsystems. First we get the whole list.
140          %subsystems = map { $_ => 1 } $fig->all_subsystems();              my @subs = $fig->all_subsystems();
141                # Loop through, checking for usability.
142                for my $sub (@subs) {
143                    if ($fig->usable_subsystem($sub)) {
144                        $subsystems{$sub} = 1;
145                    }
146                }
147      } else {      } else {
148          my $type = ref $subsysFile;          my $type = ref $subsysFile;
149          if ($type eq 'ARRAY') {          if ($type eq 'ARRAY') {
# Line 153  Line 163 
163              Confess("Invalid subsystem parameter in SproutLoad constructor.");              Confess("Invalid subsystem parameter in SproutLoad constructor.");
164          }          }
165      }      }
166        }
167      # Get the data directory from the Sprout object.      # Get the data directory from the Sprout object.
168      my ($directory) = $sprout->LoadInfo();      my ($directory) = $sprout->LoadInfo();
169      # Create the Sprout load object.      # Create the Sprout load object.
# Line 162  Line 173 
173                    subsystems => \%subsystems,                    subsystems => \%subsystems,
174                    sprout => $sprout,                    sprout => $sprout,
175                    loadDirectory => $directory,                    loadDirectory => $directory,
176                    erdb => $sprout->{_erdb},                    erdb => $sprout,
177                    loaders => [],                    loaders => [],
178                    options => $options                    options => $options
179                   };                   };
# Line 171  Line 182 
182      return $retVal;      return $retVal;
183  }  }
184    
185    =head3 LoadOnly
186    
187    C<< my $flag = $spl->LoadOnly; >>
188    
189    Return TRUE if we are in load-only mode, else FALSE.
190    
191    =cut
192    
193    sub LoadOnly {
194        my ($self) = @_;
195        return $self->{options}->{loadOnly};
196    }
197    
198    =head3 PrimaryOnly
199    
200    C<< my $flag = $spl->PrimaryOnly; >>
201    
202    Return TRUE if only the main entity is to be loaded, else FALSE.
203    
204    =cut
205    
206    sub PrimaryOnly {
207        my ($self) = @_;
208        return $self->{options}->{primaryOnly};
209    }
210    
211  =head3 LoadGenomeData  =head3 LoadGenomeData
212    
213  C<< my $stats = $spl->LoadGenomeData(); >>  C<< my $stats = $spl->LoadGenomeData(); >>
# Line 198  Line 235 
235    
236  =back  =back
237    
 B<TO DO>  
   
 Real quality vectors instead of C<unknown> for everything.  
   
 GenomeGroup relation. (The original script took group information from the C<NMPDR> file  
 in each genome's main directory, but no such file exists anywhere in my version of the  
 data store.)  
   
238  =cut  =cut
239  #: Return Type $%;  #: Return Type $%;
240  sub LoadGenomeData {  sub LoadGenomeData {
# Line 216  Line 245 
245      # Get the genome count.      # Get the genome count.
246      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
247      my $genomeCount = (keys %{$genomeHash});      my $genomeCount = (keys %{$genomeHash});
     Trace("Beginning genome data load.") if T(2);  
248      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
249      my $loadGenome = $self->_TableLoader('Genome', $genomeCount);      my $loadGenome = $self->_TableLoader('Genome');
250      my $loadHasContig = $self->_TableLoader('HasContig', $genomeCount * 300);      my $loadHasContig = $self->_TableLoader('HasContig', $self->PrimaryOnly);
251      my $loadContig = $self->_TableLoader('Contig', $genomeCount * 300);      my $loadContig = $self->_TableLoader('Contig', $self->PrimaryOnly);
252      my $loadIsMadeUpOf = $self->_TableLoader('IsMadeUpOf', $genomeCount * 60000);      my $loadIsMadeUpOf = $self->_TableLoader('IsMadeUpOf', $self->PrimaryOnly);
253      my $loadSequence = $self->_TableLoader('Sequence', $genomeCount * 60000);      my $loadSequence = $self->_TableLoader('Sequence', $self->PrimaryOnly);
254        if ($self->{options}->{loadOnly}) {
255            Trace("Loading from existing files.") if T(2);
256        } else {
257            Trace("Generating genome data.") if T(2);
258      # Now we loop through the genomes, generating the data for each one.      # Now we loop through the genomes, generating the data for each one.
259      for my $genomeID (sort keys %{$genomeHash}) {      for my $genomeID (sort keys %{$genomeHash}) {
260          Trace("Loading data for genome $genomeID.") if T(3);              Trace("Generating data for genome $genomeID.") if T(3);
261          $loadGenome->Add("genomeIn");          $loadGenome->Add("genomeIn");
262          # The access code comes in via the genome hash.          # The access code comes in via the genome hash.
263          my $accessCode = $genomeHash->{$genomeID};          my $accessCode = $genomeHash->{$genomeID};
264          # Get the genus, species, and strain from the scientific name. Note that we append              # Get the genus, species, and strain from the scientific name.
         # the genome ID to the strain. In some cases this is the totality of the strain name.  
265          my ($genus, $species, @extraData) = split / /, $self->{fig}->genus_species($genomeID);          my ($genus, $species, @extraData) = split / /, $self->{fig}->genus_species($genomeID);
266          my $extra = join " ", @extraData, "[$genomeID]";              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 268  Line 310 
310              }              }
311          }          }
312      }      }
313        }
314      # Finish the loads.      # Finish the loads.
315      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
316      # Return the result.      # Return the result.
# Line 308  Line 351 
351      my $fig = $self->{fig};      my $fig = $self->{fig};
352      # Get the genome hash.      # Get the genome hash.
353      my $genomeFilter = $self->{genomes};      my $genomeFilter = $self->{genomes};
354      my $genomeCount = (keys %{$genomeFilter});      # Set up an ID counter for the PCHs.
355      my $featureCount = $genomeCount * 4000;      my $pchID = 0;
356      # Start the loads.      # Start the loads.
357      my $loadCoupling = $self->_TableLoader('Coupling', $featureCount * $genomeCount);      my $loadCoupling = $self->_TableLoader('Coupling');
358      my $loadIsEvidencedBy = $self->_TableLoader('IsEvidencedBy', $featureCount * 8000);      my $loadIsEvidencedBy = $self->_TableLoader('IsEvidencedBy', $self->PrimaryOnly);
359      my $loadPCH = $self->_TableLoader('PCH', $featureCount * 2000);      my $loadPCH = $self->_TableLoader('PCH', $self->PrimaryOnly);
360      my $loadParticipatesInCoupling = $self->_TableLoader('ParticipatesInCoupling', $featureCount * 2000);      my $loadParticipatesInCoupling = $self->_TableLoader('ParticipatesInCoupling', $self->PrimaryOnly);
361      my $loadUsesAsEvidence = $self->_TableLoader('UsesAsEvidence', $featureCount * 8000);      my $loadUsesAsEvidence = $self->_TableLoader('UsesAsEvidence', $self->PrimaryOnly);
362      Trace("Beginning coupling data load.") if T(2);      if ($self->{options}->{loadOnly}) {
363            Trace("Loading from existing files.") if T(2);
364        } else {
365            Trace("Generating coupling data.") if T(2);
366      # Loop through the genomes found.      # Loop through the genomes found.
367      for my $genome (sort keys %{$genomeFilter}) {      for my $genome (sort keys %{$genomeFilter}) {
368          Trace("Generating coupling data for $genome.") if T(3);          Trace("Generating coupling data for $genome.") if T(3);
# Line 340  Line 386 
386              for my $coupleData (@couplings) {              for my $coupleData (@couplings) {
387                  my ($peg2, $score) = @{$coupleData};                  my ($peg2, $score) = @{$coupleData};
388                  # Compute the coupling ID.                  # Compute the coupling ID.
389                  my $coupleID = Sprout::CouplingID($peg1, $peg2);                      my $coupleID = $self->{erdb}->CouplingID($peg1, $peg2);
390                  if (! exists $dupHash{$coupleID}) {                  if (! exists $dupHash{$coupleID}) {
391                      $loadCoupling->Add("couplingIn");                      $loadCoupling->Add("couplingIn");
392                      # Here we have a new coupling to store in the load files.                      # Here we have a new coupling to store in the load files.
# Line 376  Line 422 
422                          }                          }
423                      }                      }
424                      for my $evidenceID (keys %evidenceMap) {                      for my $evidenceID (keys %evidenceMap) {
425                                # Get the ID for this evidence.
426                                $pchID++;
427                          # Create the evidence record.                          # Create the evidence record.
428                          my ($peg3, $peg4, $usage) = @{$evidenceMap{$evidenceID}};                          my ($peg3, $peg4, $usage) = @{$evidenceMap{$evidenceID}};
429                          $loadPCH->Put($evidenceID, $usage);                              $loadPCH->Put($pchID, $usage);
430                          # Connect it to the coupling.                          # Connect it to the coupling.
431                          $loadIsEvidencedBy->Put($coupleID, $evidenceID);                              $loadIsEvidencedBy->Put($coupleID, $pchID);
432                          # Connect it to the features.                          # Connect it to the features.
433                          $loadUsesAsEvidence->Put($evidenceID, $peg3, 1);                              $loadUsesAsEvidence->Put($pchID, $peg3, 1);
434                          $loadUsesAsEvidence->Put($evidenceID, $peg4, 2);                              $loadUsesAsEvidence->Put($pchID, $peg4, 2);
435                            }
436                      }                      }
437                  }                  }
438              }              }
# Line 410  Line 459 
459      FeatureTranslation      FeatureTranslation
460      FeatureUpstream      FeatureUpstream
461      IsLocatedIn      IsLocatedIn
462        HasFeature
463        HasRoleInSubsystem
464    
465  =over 4  =over 4
466    
# Line 426  Line 477 
477      my ($self) = @_;      my ($self) = @_;
478      # Get the FIG object.      # Get the FIG object.
479      my $fig = $self->{fig};      my $fig = $self->{fig};
     # Find out if this is a limited run.  
     my $limited = $self->{options}->{limitedFeatures};  
480      # Get the table of genome IDs.      # Get the table of genome IDs.
481      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
     my $featureCount = $genomeCount * 4000;  
482      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
483      my $loadFeature = $self->_TableLoader('Feature', $featureCount);      my $loadFeature = $self->_TableLoader('Feature');
484      my $loadIsLocatedIn = $self->_TableLoader('IsLocatedIn', $featureCount);      my $loadIsLocatedIn = $self->_TableLoader('IsLocatedIn', $self->PrimaryOnly);
485      my $loadFeatureAlias = $self->_TableLoader('FeatureAlias', $featureCount * 6);      my $loadFeatureAlias = $self->_TableLoader('FeatureAlias');
486      my ($loadFeatureLink, $loadFeatureTranslation, $loadFeatureUpstream);      my $loadFeatureLink = $self->_TableLoader('FeatureLink');
487      if (! $limited) {      my $loadFeatureTranslation = $self->_TableLoader('FeatureTranslation');
488          $loadFeatureLink = $self->_TableLoader('FeatureLink', $featureCount * 10);      my $loadFeatureUpstream = $self->_TableLoader('FeatureUpstream');
489          $loadFeatureTranslation = $self->_TableLoader('FeatureTranslation', $featureCount);      my $loadHasFeature = $self->_TableLoader('HasFeature', $self->PrimaryOnly);
490          $loadFeatureUpstream = $self->_TableLoader('FeatureUpstream', $featureCount);      my $loadHasRoleInSubsystem = $self->_TableLoader('HasRoleInSubsystem', $self->PrimaryOnly);
     }  
491      # Get the maximum sequence size. We need this later for splitting up the      # Get the maximum sequence size. We need this later for splitting up the
492      # locations.      # locations.
493      my $chunkSize = $self->{sprout}->MaxSegment();      my $chunkSize = $self->{sprout}->MaxSegment();
494      Trace("Beginning feature data load.") if T(2);      if ($self->{options}->{loadOnly}) {
495            Trace("Loading from existing files.") if T(2);
496        } else {
497            Trace("Generating feature data.") if T(2);
498      # Now we loop through the genomes, generating the data for each one.      # Now we loop through the genomes, generating the data for each one.
499      for my $genomeID (sort keys %{$genomeHash}) {      for my $genomeID (sort keys %{$genomeHash}) {
500          Trace("Loading features for genome $genomeID.") if T(3);          Trace("Loading features for genome $genomeID.") if T(3);
501          $loadFeature->Add("genomeIn");          $loadFeature->Add("genomeIn");
502          # Get the feature list for this genome.          # Get the feature list for this genome.
503          my $features = $fig->all_features_detailed($genomeID);          my $features = $fig->all_features_detailed($genomeID);
504                # Sort and count the list.
505                my @featureTuples = sort { $a->[0] cmp $b->[0] } @{$features};
506                my $count = scalar @featureTuples;
507                Trace("$count features found for genome $genomeID.") if T(3);
508                # Set up for our duplicate-feature check.
509                my $oldFeatureID = "";
510          # Loop through the features.          # Loop through the features.
511          for my $featureData (@{$features}) {              for my $featureTuple (@featureTuples) {
             $loadFeature->Add("featureIn");  
512              # Split the tuple.              # Split the tuple.
513              my ($featureID, $locations, undef, $type) = @{$featureData};                  my ($featureID, $locations, undef, $type) = @{$featureTuple};
514                    # Check for duplicates.
515                    if ($featureID eq $oldFeatureID) {
516                        Trace("Duplicate feature $featureID found.") if T(1);
517                    } else {
518                        $oldFeatureID = $featureID;
519                        # Count this feature.
520                        $loadFeature->Add("featureIn");
521                        # Get the functional assignment.
522                        my $assignment = $fig->function_of($featureID);
523              # Create the feature record.              # Create the feature record.
524              $loadFeature->Put($featureID, 1, $type);                      $loadFeature->Put($featureID, 1, $type, $assignment);
525                        # Link it to the parent genome.
526                        $loadHasFeature->Put($genomeID, $featureID, $type);
527              # Create the aliases.              # Create the aliases.
528              for my $alias ($fig->feature_aliases($featureID)) {              for my $alias ($fig->feature_aliases($featureID)) {
529                  $loadFeatureAlias->Put($featureID, $alias);                  $loadFeatureAlias->Put($featureID, $alias);
530              }              }
             # The next stuff is for a full load only.  
             if (! $limited) {  
531                  # Get the links.                  # Get the links.
532                  my @links = $fig->fid_links($featureID);                  my @links = $fig->fid_links($featureID);
533                  for my $link (@links) {                  for my $link (@links) {
# Line 483  Line 546 
546                          $loadFeatureUpstream->Put($featureID, $upstream);                          $loadFeatureUpstream->Put($featureID, $upstream);
547                      }                      }
548                  }                  }
549                        # Now we need to find the subsystems this feature participates in.
550                        my @subsystems = $fig->peg_to_subsystems($featureID);
551                        for my $subsystem (@subsystems) {
552                            $loadHasRoleInSubsystem->Put($featureID, $subsystem);
553              }              }
554              # This part is the roughest. We need to relate the features to contig              # This part is the roughest. We need to relate the features to contig
555              # locations, and the locations must be split so that none of them exceed              # locations, and the locations must be split so that none of them exceed
# Line 512  Line 579 
579              }              }
580          }          }
581      }      }
582            }
583        }
584      # Finish the loads.      # Finish the loads.
585      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
586      return $retVal;      return $retVal;
# Line 548  Line 617 
617      my $fig = $self->{fig};      my $fig = $self->{fig};
618      # Get the table of genome IDs.      # Get the table of genome IDs.
619      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
     my $featureCount = $genomeCount * 4000;  
620      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
621      my $loadIsBidirectionalBestHitOf = $self->_TableLoader('IsBidirectionalBestHitOf',      my $loadIsBidirectionalBestHitOf = $self->_TableLoader('IsBidirectionalBestHitOf');
622                                                             $featureCount * $genomeCount);      if ($self->{options}->{loadOnly}) {
623      Trace("Beginning BBH load.") if T(2);          Trace("Loading from existing files.") if T(2);
624        } else {
625            Trace("Generating BBH data.") if T(2);
626      # Now we loop through the genomes, generating the data for each one.      # Now we loop through the genomes, generating the data for each one.
627      for my $genomeID (sort keys %{$genomeHash}) {      for my $genomeID (sort keys %{$genomeHash}) {
628          $loadIsBidirectionalBestHitOf->Add("genomeIn");          $loadIsBidirectionalBestHitOf->Add("genomeIn");
629          Trace("Processing features for genome $genomeID.") if T(3);          Trace("Processing features for genome $genomeID.") if T(3);
630          # Get the feature list for this genome.          # Get the feature list for this genome.
631          my $features = $fig->all_features_detailed($genomeID);          my $features = $fig->all_features_detailed($genomeID);
632                # Count the BBHs we find.
633                my $bbhCount = 0;
634          # Loop through the features.          # Loop through the features.
635          for my $featureData (@{$features}) {          for my $featureData (@{$features}) {
636              # Split the tuple.              # Split the tuple.
# Line 575  Line 646 
646                  if ($genomeHash->{$targetGenomeID}) {                  if ($genomeHash->{$targetGenomeID}) {
647                      $loadIsBidirectionalBestHitOf->Put($featureID, $targetID, $targetGenomeID,                      $loadIsBidirectionalBestHitOf->Put($featureID, $targetID, $targetGenomeID,
648                                                         $score);                                                         $score);
649                            $bbhCount++;
650                        }
651                  }                  }
652              }              }
653                Trace("$bbhCount BBHs found for $genomeID.") if T(3);
654          }          }
655      }      }
656      # Finish the loads.      # Finish the loads.
# Line 599  Line 673 
673  The following relations are loaded by this method.  The following relations are loaded by this method.
674    
675      Subsystem      Subsystem
676        SubsystemClass
677      Role      Role
678      RoleEC      RoleEC
679      SSCell      SSCell
# Line 639  Line 714 
714      # Get the subsystem hash. This lists the subsystems we'll process.      # Get the subsystem hash. This lists the subsystems we'll process.
715      my $subsysHash = $self->{subsystems};      my $subsysHash = $self->{subsystems};
716      my @subsysIDs = sort keys %{$subsysHash};      my @subsysIDs = sort keys %{$subsysHash};
     my $subsysCount = @subsysIDs;  
     my $genomeCount = (keys %{$genomeHash});  
     my $featureCount = $genomeCount * 4000;  
717      # Get the map list.      # Get the map list.
718      my @maps = $fig->all_maps;      my @maps = $fig->all_maps;
     my $mapCount = @maps;  
719      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
720      my $loadDiagram = $self->_TableLoader('Diagram', $mapCount);      my $loadDiagram = $self->_TableLoader('Diagram', $self->PrimaryOnly);
721      my $loadRoleOccursIn = $self->_TableLoader('RoleOccursIn', $featureCount * 6);      my $loadRoleOccursIn = $self->_TableLoader('RoleOccursIn', $self->PrimaryOnly);
722      my $loadSubsystem = $self->_TableLoader('Subsystem', $subsysCount);      my $loadSubsystem = $self->_TableLoader('Subsystem');
723      my $loadRole = $self->_TableLoader('Role', $featureCount * 6);      my $loadRole = $self->_TableLoader('Role', $self->PrimaryOnly);
724      my $loadRoleEC = $self->_TableLoader('RoleEC', $featureCount * 6);      my $loadRoleEC = $self->_TableLoader('RoleEC', $self->PrimaryOnly);
725      my $loadCatalyzes = $self->_TableLoader('Catalyzes', $genomeCount * $featureCount);      my $loadCatalyzes = $self->_TableLoader('Catalyzes', $self->PrimaryOnly);
726      my $loadSSCell = $self->_TableLoader('SSCell', $featureCount * $genomeCount);      my $loadSSCell = $self->_TableLoader('SSCell', $self->PrimaryOnly);
727      my $loadContainsFeature = $self->_TableLoader('ContainsFeature', $featureCount * $subsysCount);      my $loadContainsFeature = $self->_TableLoader('ContainsFeature', $self->PrimaryOnly);
728      my $loadIsGenomeOf = $self->_TableLoader('IsGenomeOf', $featureCount * $genomeCount);      my $loadIsGenomeOf = $self->_TableLoader('IsGenomeOf', $self->PrimaryOnly);
729      my $loadIsRoleOf = $self->_TableLoader('IsRoleOf', $featureCount * $genomeCount);      my $loadIsRoleOf = $self->_TableLoader('IsRoleOf', $self->PrimaryOnly);
730      my $loadOccursInSubsystem = $self->_TableLoader('OccursInSubsystem', $featureCount * 6);      my $loadOccursInSubsystem = $self->_TableLoader('OccursInSubsystem', $self->PrimaryOnly);
731      my $loadParticipatesIn = $self->_TableLoader('ParticipatesIn', $subsysCount * $genomeCount);      my $loadParticipatesIn = $self->_TableLoader('ParticipatesIn', $self->PrimaryOnly);
732      my $loadHasSSCell = $self->_TableLoader('HasSSCell', $featureCount * $genomeCount);      my $loadHasSSCell = $self->_TableLoader('HasSSCell', $self->PrimaryOnly);
733      my $loadRoleSubset = $self->_TableLoader('RoleSubset', $subsysCount * 50);      my $loadRoleSubset = $self->_TableLoader('RoleSubset', $self->PrimaryOnly);
734      my $loadGenomeSubset = $self->_TableLoader('GenomeSubset', $subsysCount * 50);      my $loadGenomeSubset = $self->_TableLoader('GenomeSubset', $self->PrimaryOnly);
735      my $loadConsistsOfRoles = $self->_TableLoader('ConsistsOfRoles', $featureCount * $genomeCount);      my $loadConsistsOfRoles = $self->_TableLoader('ConsistsOfRoles', $self->PrimaryOnly);
736      my $loadConsistsOfGenomes = $self->_TableLoader('ConsistsOfGenomes', $featureCount * $genomeCount);      my $loadConsistsOfGenomes = $self->_TableLoader('ConsistsOfGenomes', $self->PrimaryOnly);
737      my $loadHasRoleSubset = $self->_TableLoader('HasRoleSubset', $subsysCount * 50);      my $loadHasRoleSubset = $self->_TableLoader('HasRoleSubset', $self->PrimaryOnly);
738      my $loadHasGenomeSubset = $self->_TableLoader('HasGenomeSubset', $subsysCount * 50);      my $loadHasGenomeSubset = $self->_TableLoader('HasGenomeSubset', $self->PrimaryOnly);
739      # Create load objects for each of the tables we're loading.      my $loadSubsystemClass = $self->_TableLoader('SubsystemClass', $self->PrimaryOnly);
740      Trace("Beginning subsystem data load.") if T(2);      if ($self->{options}->{loadOnly}) {
741            Trace("Loading from existing files.") if T(2);
742        } else {
743            Trace("Generating subsystem data.") if T(2);
744      # This hash will contain the role for each EC. When we're done, this      # This hash will contain the role for each EC. When we're done, this
745      # information will be used to generate the Catalyzes table.      # information will be used to generate the Catalyzes table.
746      my %ecToRoles = ();      my %ecToRoles = ();
# Line 678  Line 752 
752      my ($genomeID, $roleID);      my ($genomeID, $roleID);
753      my %roleData = ();      my %roleData = ();
754      for my $subsysID (@subsysIDs) {      for my $subsysID (@subsysIDs) {
         Trace("Creating subsystem $subsysID.") if T(3);  
         $loadSubsystem->Add("subsystemIn");  
755          # Get the subsystem object.          # Get the subsystem object.
756          my $sub = $fig->get_subsystem($subsysID);          my $sub = $fig->get_subsystem($subsysID);
757                # Only proceed if the subsystem has a spreadsheet.
758                if (! $sub->{empty_ss}) {
759                    Trace("Creating subsystem $subsysID.") if T(3);
760                    $loadSubsystem->Add("subsystemIn");
761          # Create the subsystem record.          # Create the subsystem record.
762          my $curator = $sub->get_curator();          my $curator = $sub->get_curator();
763          my $notes = $sub->get_notes();          my $notes = $sub->get_notes();
764          $loadSubsystem->Put($subsysID, $curator, $notes);          $loadSubsystem->Put($subsysID, $curator, $notes);
765                    my $classList = $fig->subsystem_classification($subsysID);
766                    my @classes = @$classList;
767                    if (@classes) {
768                        for my $class (@classes) {
769                            $loadSubsystemClass->Put($subsysID, $class);
770                        }
771                    }
772          # Connect it to its roles. Each role is a column in the subsystem spreadsheet.          # Connect it to its roles. Each role is a column in the subsystem spreadsheet.
773          for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {          for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {
774              # Connect to this role.              # Connect to this role.
# Line 729  Line 812 
812                  # part of the spreadsheet cell ID.                  # part of the spreadsheet cell ID.
813                  for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {                  for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {
814                      # Get the features in the spreadsheet cell for this genome and role.                      # Get the features in the spreadsheet cell for this genome and role.
815                      my @pegs = $sub->get_pegs_from_cell($row, $col);                              my @pegs = grep { !$fig->is_deleted_fid($_) } $sub->get_pegs_from_cell($row, $col);
816                      # Only proceed if features exist.                      # Only proceed if features exist.
817                      if (@pegs > 0) {                      if (@pegs > 0) {
818                          # Create the spreadsheet cell.                          # Create the spreadsheet cell.
# Line 750  Line 833 
833                  if ($pegCount > 0) {                  if ($pegCount > 0) {
834                      Trace("$pegCount PEGs in $cellCount cells for $genomeID.") if T(3);                      Trace("$pegCount PEGs in $cellCount cells for $genomeID.") if T(3);
835                      $loadParticipatesIn->Put($genomeID, $subsysID, $variantCode);                      $loadParticipatesIn->Put($genomeID, $subsysID, $variantCode);
                     # Partition the PEGs found into clusters.  
                     my @clusters = $fig->compute_clusters(\@pegsFound, $sub);  
836                      # Create a hash mapping PEG IDs to cluster numbers.                      # Create a hash mapping PEG IDs to cluster numbers.
837                      # We default to -1 for all of them.                      # We default to -1 for all of them.
838                      my %clusterOf = map { $_ => -1 } @pegsFound;                      my %clusterOf = map { $_ => -1 } @pegsFound;
839                                # Partition the PEGs found into clusters.
840                                my @clusters = $fig->compute_clusters([keys %clusterOf], $sub);
841                      for (my $i = 0; $i <= $#clusters; $i++) {                      for (my $i = 0; $i <= $#clusters; $i++) {
842                          my $subList = $clusters[$i];                          my $subList = $clusters[$i];
843                          for my $peg (@{$subList}) {                          for my $peg (@{$subList}) {
# Line 782  Line 865 
865              # Connect the subset to the subsystem.              # Connect the subset to the subsystem.
866              $loadHasRoleSubset->Put($subsysID, $actualID);              $loadHasRoleSubset->Put($subsysID, $actualID);
867              # Connect the subset to its roles.              # Connect the subset to its roles.
868              my @roles = $sub->get_subset($subsetID);                      my @roles = $sub->get_subsetC_roles($subsetID);
869              for my $roleID (@roles) {              for my $roleID (@roles) {
870                  $loadConsistsOfRoles->Put($actualID, $roleID);                  $loadConsistsOfRoles->Put($actualID, $roleID);
871              }              }
# Line 802  Line 885 
885              }              }
886          }          }
887      }      }
888            }
889      # Now we loop through the diagrams. We need to create the diagram records      # Now we loop through the diagrams. We need to create the diagram records
890      # and link each diagram to its roles. Note that only roles which occur      # and link each diagram to its roles. Note that only roles which occur
891      # in subsystems (and therefore appear in the %ecToRoles hash) are      # in subsystems (and therefore appear in the %ecToRoles hash) are
# Line 834  Line 918 
918              }              }
919          }          }
920      }      }
921        }
922      # Finish the load.      # Finish the load.
923      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
924      return $retVal;      return $retVal;
# Line 875  Line 960 
960      my $fig = $self->{fig};      my $fig = $self->{fig};
961      # Get the genome hash.      # Get the genome hash.
962      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
963      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
964      my $loadProperty = $self->_TableLoader('Property', $genomeCount * 1500);      my $loadProperty = $self->_TableLoader('Property');
965      my $loadHasProperty = $self->_TableLoader('HasProperty', $genomeCount * 1500);      my $loadHasProperty = $self->_TableLoader('HasProperty', $self->PrimaryOnly);
966      Trace("Beginning property data load.") if T(2);      if ($self->{options}->{loadOnly}) {
967            Trace("Loading from existing files.") if T(2);
968        } else {
969            Trace("Generating property data.") if T(2);
970      # Create a hash for storing property IDs.      # Create a hash for storing property IDs.
971      my %propertyKeys = ();      my %propertyKeys = ();
972      my $nextID = 1;      my $nextID = 1;
973      # Loop through the genomes.      # Loop through the genomes.
974      for my $genomeID (keys %{$genomeHash}) {          for my $genomeID (sort keys %{$genomeHash}) {
975          $loadProperty->Add("genomeIn");          $loadProperty->Add("genomeIn");
976                Trace("Generating properties for $genomeID.") if T(3);
977          # Get the genome's features. The feature ID is the first field in the          # Get the genome's features. The feature ID is the first field in the
978          # tuples returned by "all_features_detailed". We use "all_features_detailed"          # tuples returned by "all_features_detailed". We use "all_features_detailed"
979          # rather than "all_features" because we want all features regardless of type.          # rather than "all_features" because we want all features regardless of type.
980          my @features = map { $_->[0] } @{$fig->all_features_detailed($genomeID)};          my @features = map { $_->[0] } @{$fig->all_features_detailed($genomeID)};
981                my $featureCount = 0;
982                my $propertyCount = 0;
983          # Loop through the features, creating HasProperty records.          # Loop through the features, creating HasProperty records.
984          for my $fid (@features) {          for my $fid (@features) {
             $loadProperty->Add("featureIn");  
985              # Get all attributes for this feature. We do this one feature at a time              # Get all attributes for this feature. We do this one feature at a time
986              # to insure we do not get any genome attributes.              # to insure we do not get any genome attributes.
987              my @attributeList = $fig->get_attributes($fid, '', '', '');              my @attributeList = $fig->get_attributes($fid, '', '', '');
988                    if (scalar @attributeList) {
989                        $featureCount++;
990                    }
991              # Loop through the attributes.              # Loop through the attributes.
992              for my $tuple (@attributeList) {              for my $tuple (@attributeList) {
993                        $propertyCount++;
994                  # Get this attribute value's data. Note that we throw away the FID,                  # Get this attribute value's data. Note that we throw away the FID,
995                  # since it will always be the same as the value if "$fid".                  # since it will always be the same as the value if "$fid".
996                  my (undef, $key, $value, $url) = @{$tuple};                  my (undef, $key, $value, $url) = @{$tuple};
# Line 919  Line 1012 
1012                  $loadHasProperty->Put($fid, $propertyID, $url);                  $loadHasProperty->Put($fid, $propertyID, $url);
1013              }              }
1014          }          }
1015                # Update the statistics.
1016                Trace("$propertyCount attributes processed for $featureCount features.") if T(3);
1017                $loadHasProperty->Add("featuresIn", $featureCount);
1018                $loadHasProperty->Add("propertiesIn", $propertyCount);
1019            }
1020      }      }
1021      # Finish the load.      # Finish the load.
1022      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
# Line 959  Line 1057 
1057      my $fig = $self->{fig};      my $fig = $self->{fig};
1058      # Get the genome hash.      # Get the genome hash.
1059      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
1060      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
1061      my $loadAnnotation = $self->_TableLoader('Annotation', $genomeCount * 4000);      my $loadAnnotation = $self->_TableLoader('Annotation');
1062      my $loadIsTargetOfAnnotation = $self->_TableLoader('IsTargetOfAnnotation', $genomeCount * 4000);      my $loadIsTargetOfAnnotation = $self->_TableLoader('IsTargetOfAnnotation', $self->PrimaryOnly);
1063      my $loadSproutUser = $self->_TableLoader('SproutUser', 100);      my $loadSproutUser = $self->_TableLoader('SproutUser', $self->PrimaryOnly);
1064      my $loadUserAccess = $self->_TableLoader('UserAccess', 1000);      my $loadUserAccess = $self->_TableLoader('UserAccess', $self->PrimaryOnly);
1065      my $loadMadeAnnotation = $self->_TableLoader('MadeAnnotation', $genomeCount * 4000);      my $loadMadeAnnotation = $self->_TableLoader('MadeAnnotation', $self->PrimaryOnly);
1066      Trace("Beginning annotation data load.") if T(2);      if ($self->{options}->{loadOnly}) {
1067            Trace("Loading from existing files.") if T(2);
1068        } else {
1069            Trace("Generating annotation data.") if T(2);
1070      # Create a hash of user names. We'll use this to prevent us from generating duplicate      # Create a hash of user names. We'll use this to prevent us from generating duplicate
1071      # user records.      # user records.
1072      my %users = ( FIG => 1, master => 1 );      my %users = ( FIG => 1, master => 1 );
# Line 980  Line 1080 
1080      # Loop through the genomes.      # Loop through the genomes.
1081      for my $genomeID (sort keys %{$genomeHash}) {      for my $genomeID (sort keys %{$genomeHash}) {
1082          Trace("Processing $genomeID.") if T(3);          Trace("Processing $genomeID.") if T(3);
         # Get the genome's PEGs.  
         my @pegs = $fig->pegs_of($genomeID);  
         for my $peg (@pegs) {  
             Trace("Processing $peg.") if T(4);  
1083              # Create a hash of timestamps. We use this to prevent duplicate time stamps              # Create a hash of timestamps. We use this to prevent duplicate time stamps
1084              # from showing up for a single PEG's annotations.              # from showing up for a single PEG's annotations.
1085              my %seenTimestamps = ();              my %seenTimestamps = ();
1086              # Check for a functional assignment.              # Get the genome's annotations.
1087              my $func = $fig->function_of($peg);              my @annotations = $fig->read_all_annotations($genomeID);
1088              if ($func) {              Trace("Processing annotations.") if T(2);
1089                  # If this is NOT a hypothetical assignment, we create an              for my $tuple (@annotations) {
1090                  # assignment annotation for it.                  # Get the annotation tuple.
1091                  if (! FIG::hypo($peg)) {                  my ($peg, $timestamp, $user, $text) = @{$tuple};
                     # Note that we double the slashes so that what goes into the database is  
                     # a new-line escape sequence rather than an actual new-line.  
                     $loadAnnotation->Put("$peg:$time", $time, "FIG\\nSet function to\\n$func");  
                     $loadIsTargetOfAnnotation->Put($peg, "$peg:$time");  
                     $loadMadeAnnotation->Put("FIG", "$peg:$time");  
                     # Denote we've seen this timestamp.  
                     $seenTimestamps{$time} = 1;  
                 }  
             }  
             # Now loop through the real annotations.  
             for my $tuple ($fig->feature_annotations($peg, "raw")) {  
                 my ($fid, $timestamp, $user, $text) = @{$tuple};  
1092                  # Here we fix up the annotation text. "\r" is removed,                  # Here we fix up the annotation text. "\r" is removed,
1093                  # and "\t" and "\n" are escaped. Note we use the "s"                  # and "\t" and "\n" are escaped. Note we use the "gs"
1094                  # modifier so that new-lines inside the text do not                  # modifier so that new-lines inside the text do not
1095                  # stop the substitution search.                  # stop the substitution search.
1096                  $text =~ s/\r//gs;                  $text =~ s/\r//gs;
# Line 1019  Line 1103 
1103                      # Here it's a number. We need to insure the one we use to form                      # Here it's a number. We need to insure the one we use to form
1104                      # the key is unique.                      # the key is unique.
1105                      my $keyStamp = $timestamp;                      my $keyStamp = $timestamp;
1106                      while ($seenTimestamps{$keyStamp}) {                      while ($seenTimestamps{"$peg:$keyStamp"}) {
1107                          $keyStamp++;                          $keyStamp++;
1108                      }                      }
                     $seenTimestamps{$keyStamp} = 1;  
1109                      my $annotationID = "$peg:$keyStamp";                      my $annotationID = "$peg:$keyStamp";
1110                        $seenTimestamps{$annotationID} = 1;
1111                      # Insure the user exists.                      # Insure the user exists.
1112                      if (! $users{$user}) {                      if (! $users{$user}) {
1113                          $loadSproutUser->Put($user, "SEED user");                          $loadSproutUser->Put($user, "SEED user");
# Line 1081  Line 1165 
1165      my $fig = $self->{fig};      my $fig = $self->{fig};
1166      # Get the genome hash.      # Get the genome hash.
1167      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
1168      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
1169      my $loadComesFrom = $self->_TableLoader('ComesFrom', $genomeCount * 4);      my $loadComesFrom = $self->_TableLoader('ComesFrom', $self->PrimaryOnly);
1170      my $loadSource = $self->_TableLoader('Source', $genomeCount * 4);      my $loadSource = $self->_TableLoader('Source');
1171      my $loadSourceURL = $self->_TableLoader('SourceURL', $genomeCount * 8);      my $loadSourceURL = $self->_TableLoader('SourceURL');
1172      Trace("Beginning source data load.") if T(2);      if ($self->{options}->{loadOnly}) {
1173            Trace("Loading from existing files.") if T(2);
1174        } else {
1175            Trace("Generating annotation data.") if T(2);
1176      # Create hashes to collect the Source information.      # Create hashes to collect the Source information.
1177      my %sourceURL = ();      my %sourceURL = ();
1178      my %sourceDesc = ();      my %sourceDesc = ();
# Line 1116  Line 1202 
1202      for my $sourceID (keys %sourceDesc) {      for my $sourceID (keys %sourceDesc) {
1203          $loadSource->Put($sourceID, $sourceDesc{$sourceID});          $loadSource->Put($sourceID, $sourceDesc{$sourceID});
1204      }      }
1205        }
1206      # Finish the load.      # Finish the load.
1207      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
1208      return $retVal;      return $retVal;
# Line 1155  Line 1242 
1242      my $fig = $self->{fig};      my $fig = $self->{fig};
1243      # Get the genome hash.      # Get the genome hash.
1244      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
1245      # Convert the genome hash. We'll get the genus and species for each genome and make      # Convert the genome hash. We'll get the genus and species for each genome and make
1246      # it the key.      # it the key.
1247      my %speciesHash = map { $fig->genus_species($_) => $_ } (keys %{$genomeHash});      my %speciesHash = map { $fig->genus_species($_) => $_ } (keys %{$genomeHash});
1248      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
1249      my $loadExternalAliasFunc = $self->_TableLoader('ExternalAliasFunc', $genomeCount * 4000);      my $loadExternalAliasFunc = $self->_TableLoader('ExternalAliasFunc');
1250      my $loadExternalAliasOrg = $self->_TableLoader('ExternalAliasOrg', $genomeCount * 4000);      my $loadExternalAliasOrg = $self->_TableLoader('ExternalAliasOrg');
1251      Trace("Beginning external data load.") if T(2);      if ($self->{options}->{loadOnly}) {
1252            Trace("Loading from existing files.") if T(2);
1253        } else {
1254            Trace("Generating external data.") if T(2);
1255      # We loop through the files one at a time. First, the organism file.      # We loop through the files one at a time. First, the organism file.
1256      Open(\*ORGS, "<$FIG_Config::global/ext_org.table");          Open(\*ORGS, "sort +0 -1 -u -t\"\t\" $FIG_Config::global/ext_org.table |");
1257      my $orgLine;      my $orgLine;
1258      while (defined($orgLine = <ORGS>)) {      while (defined($orgLine = <ORGS>)) {
1259          # Clean the input line.          # Clean the input line.
# Line 1176  Line 1265 
1265      close ORGS;      close ORGS;
1266      # Now the function file.      # Now the function file.
1267      my $funcLine;      my $funcLine;
1268      Open(\*FUNCS, "<$FIG_Config::global/ext_func.table");          Open(\*FUNCS, "sort +0 -1 -u -t\"\t\" $FIG_Config::global/ext_func.table |");
1269      while (defined($funcLine = <FUNCS>)) {      while (defined($funcLine = <FUNCS>)) {
1270          # Clean the line ending.          # Clean the line ending.
1271          chomp $funcLine;          chomp $funcLine;
# Line 1192  Line 1281 
1281              $loadExternalAliasFunc->Put(@funcFields[0,1]);              $loadExternalAliasFunc->Put(@funcFields[0,1]);
1282          }          }
1283      }      }
1284        }
1285      # Finish the load.      # Finish the load.
1286      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
1287      return $retVal;      return $retVal;
# Line 1232  Line 1322 
1322      my ($self) = @_;      my ($self) = @_;
1323      # Get the FIG object.      # Get the FIG object.
1324      my $fig = $self->{fig};      my $fig = $self->{fig};
     # Get the genome hash.  
     my $genomeHash = $self->{genomes};  
     my $genomeCount = (keys %{$genomeHash});  
1325      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
1326      my $loadReaction = $self->_TableLoader('Reaction', $genomeCount * 4000);      my $loadReaction = $self->_TableLoader('Reaction');
1327      my $loadReactionURL = $self->_TableLoader('ReactionURL', $genomeCount * 4000);      my $loadReactionURL = $self->_TableLoader('ReactionURL', $self->PrimaryOnly);
1328      my $loadCompound = $self->_TableLoader('Compound', $genomeCount * 4000);      my $loadCompound = $self->_TableLoader('Compound', $self->PrimaryOnly);
1329      my $loadCompoundName = $self->_TableLoader('CompoundName', $genomeCount * 8000);      my $loadCompoundName = $self->_TableLoader('CompoundName', $self->PrimaryOnly);
1330      my $loadCompoundCAS = $self->_TableLoader('CompoundCAS', $genomeCount * 4000);      my $loadCompoundCAS = $self->_TableLoader('CompoundCAS', $self->PrimaryOnly);
1331      my $loadIsAComponentOf = $self->_TableLoader('IsAComponentOf', $genomeCount * 12000);      my $loadIsAComponentOf = $self->_TableLoader('IsAComponentOf', $self->PrimaryOnly);
1332      Trace("Beginning reaction/compound data load.") if T(2);      if ($self->{options}->{loadOnly}) {
1333            Trace("Loading from existing files.") if T(2);
1334        } else {
1335            Trace("Generating annotation data.") if T(2);
1336      # First we create the compounds.      # First we create the compounds.
1337      my @compounds = $fig->all_compounds();      my @compounds = $fig->all_compounds();
1338      for my $cid (@compounds) {      for my $cid (@compounds) {
# Line 1291  Line 1381 
1381              }              }
1382          }          }
1383      }      }
1384        }
1385      # Finish the load.      # Finish the load.
1386      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
1387      return $retVal;      return $retVal;
# Line 1306  Line 1397 
1397    
1398      GenomeGroups      GenomeGroups
1399    
1400  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,
1401    butThere is no direct support for genome groups in FIG, so we access the SEED
1402  files directly.  files directly.
1403    
1404  =over 4  =over 4
# Line 1326  Line 1418 
1418      my $fig = $self->{fig};      my $fig = $self->{fig};
1419      # Get the genome hash.      # Get the genome hash.
1420      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
1421      # Create a load object for the table we're loading.      # Create a load object for the table we're loading.
1422      my $loadGenomeGroups = $self->_TableLoader('GenomeGroups', $genomeCount * 4);      my $loadGenomeGroups = $self->_TableLoader('GenomeGroups');
1423      Trace("Beginning group data load.") if T(2);      if ($self->{options}->{loadOnly}) {
1424            Trace("Loading from existing files.") if T(2);
1425        } else {
1426            Trace("Generating group data.") if T(2);
1427            # Currently there are no groups.
1428        }
1429        # Finish the load.
1430        my $retVal = $self->_FinishAll();
1431        return $retVal;
1432    }
1433    
1434    =head3 LoadSynonymData
1435    
1436    C<< my $stats = $spl->LoadSynonymData(); >>
1437    
1438    Load the synonym groups into Sprout.
1439    
1440    The following relations are loaded by this method.
1441    
1442        SynonymGroup
1443        IsSynonymGroupFor
1444    
1445    The source information for these relations is taken from the C<maps_to_id> method
1446    of the B<FIG> object. Unfortunately, to make this work, we need to use direct
1447    SQL against the FIG database.
1448    
1449    =over 4
1450    
1451    =item RETURNS
1452    
1453    Returns a statistics object for the loads.
1454    
1455    =back
1456    
1457    =cut
1458    #: Return Type $%;
1459    sub LoadSynonymData {
1460        # Get this object instance.
1461        my ($self) = @_;
1462        # Get the FIG object.
1463        my $fig = $self->{fig};
1464        # Get the genome hash.
1465        my $genomeHash = $self->{genomes};
1466        # Create a load object for the table we're loading.
1467        my $loadSynonymGroup = $self->_TableLoader('SynonymGroup');
1468        my $loadIsSynonymGroupFor = $self->_TableLoader('IsSynonymGroupFor');
1469        if ($self->{options}->{loadOnly}) {
1470            Trace("Loading from existing files.") if T(2);
1471        } else {
1472            Trace("Generating synonym group data.") if T(2);
1473            # Get the database handle.
1474            my $dbh = $fig->db_handle();
1475            # Ask for the synonyms.
1476            my $sth = $dbh->prepare_command("SELECT maps_to, syn_id FROM peg_synonyms ORDER BY maps_to");
1477            my $result = $sth->execute();
1478            if (! defined($result)) {
1479                Confess("Database error in Synonym load: " . $sth->errstr());
1480            } else {
1481                # Remember the current synonym.
1482                my $current_syn = "";
1483                # Count the features.
1484                my $featureCount = 0;
1485                # Loop through the synonym/peg pairs.
1486                while (my @row = $sth->fetchrow()) {
1487                    # Get the synonym ID and feature ID.
1488                    my ($syn_id, $peg) = @row;
1489                    # Insure it's for one of our genomes.
1490                    my $genomeID = FIG::genome_of($peg);
1491                    if (exists $genomeHash->{$genomeID}) {
1492                        # Verify the synonym.
1493                        if ($syn_id ne $current_syn) {
1494                            # It's new, so put it in the group table.
1495                            $loadSynonymGroup->Put($syn_id);
1496                            $current_syn = $syn_id;
1497                        }
1498                        # Connect the synonym to the peg.
1499                        $loadIsSynonymGroupFor->Put($syn_id, $peg);
1500                        # Count this feature.
1501                        $featureCount++;
1502                        if ($featureCount % 1000 == 0) {
1503                            Trace("$featureCount features processed.") if T(3);
1504                        }
1505                    }
1506                }
1507            }
1508        }
1509        # Finish the load.
1510        my $retVal = $self->_FinishAll();
1511        return $retVal;
1512    }
1513    
1514    =head3 LoadFamilyData
1515    
1516    C<< my $stats = $spl->LoadFamilyData(); >>
1517    
1518    Load the protein families into Sprout.
1519    
1520    The following relations are loaded by this method.
1521    
1522        Family
1523        IsFamilyForFeature
1524    
1525    The source information for these relations is taken from the C<families_for_protein>,
1526    C<family_function>, and C<sz_family> methods of the B<FIG> object.
1527    
1528    =over 4
1529    
1530    =item RETURNS
1531    
1532    Returns a statistics object for the loads.
1533    
1534    =back
1535    
1536    =cut
1537    #: Return Type $%;
1538    sub LoadFamilyData {
1539        # Get this object instance.
1540        my ($self) = @_;
1541        # Get the FIG object.
1542        my $fig = $self->{fig};
1543        # Get the genome hash.
1544        my $genomeHash = $self->{genomes};
1545        # Create load objects for the tables we're loading.
1546        my $loadFamily = $self->_TableLoader('Family');
1547        my $loadIsFamilyForFeature = $self->_TableLoader('IsFamilyForFeature');
1548        if ($self->{options}->{loadOnly}) {
1549            Trace("Loading from existing files.") if T(2);
1550        } else {
1551            Trace("Generating family data.") if T(2);
1552            # Create a hash for the family IDs.
1553            my %familyHash = ();
1554      # Loop through the genomes.      # Loop through the genomes.
1555      my $line;          for my $genomeID (sort keys %{$genomeHash}) {
1556      for my $genomeID (keys %{$genomeHash}) {              Trace("Processing features for $genomeID.") if T(2);
1557          Trace("Processing $genomeID.") if T(3);              # Loop through this genome's PEGs.
1558          # Open the NMPDR group file for this genome.              for my $fid ($fig->all_features($genomeID, "peg")) {
1559          if (open(TMP, "<$FIG_Config::organisms/$genomeID/NMPDR") &&                  $loadIsFamilyForFeature->Add("features", 1);
1560              defined($line = <TMP>)) {                  # Get this feature's families.
1561              # Clean the line ending.                  my @families = $fig->families_for_protein($fid);
1562              chomp $line;                  # Loop through the families, connecting them to the feature.
1563              # Add the group to the table. Note that there can only be one group                  for my $family (@families) {
1564              # per genome.                      $loadIsFamilyForFeature->Put($family, $fid);
1565              $loadGenomeGroups->Put($genomeID, $line);                      # If this is a new family, create a record for it.
1566                        if (! exists $familyHash{$family}) {
1567                            $familyHash{$family} = 1;
1568                            $loadFamily->Add("families", 1);
1569                            my $size = $fig->sz_family($family);
1570                            my $func = $fig->family_function($family);
1571                            $loadFamily->Put($family, $size, $func);
1572                        }
1573                    }
1574                }
1575          }          }
         close TMP;  
1576      }      }
1577      # Finish the load.      # Finish the load.
1578      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
1579      return $retVal;      return $retVal;
1580  }  }
1581    
1582    
1583    
1584  =head2 Internal Utility Methods  =head2 Internal Utility Methods
1585    
1586  =head3 TableLoader  =head3 TableLoader
# Line 1366  Line 1597 
1597    
1598  Name of the table (relation) being loaded.  Name of the table (relation) being loaded.
1599    
1600  =item rowCount (optional)  =item ignore
1601    
1602  Estimated maximum number of rows in the table.  TRUE if the table should be ignored entirely, else FALSE.
1603    
1604  =item RETURN  =item RETURN
1605    
# Line 1380  Line 1611 
1611    
1612  sub _TableLoader {  sub _TableLoader {
1613      # Get the parameters.      # Get the parameters.
1614      my ($self, $tableName, $rowCount) = @_;      my ($self, $tableName, $ignore) = @_;
1615      # Create the load object.      # Create the load object.
1616      my $retVal = ERDBLoad->new($self->{erdb}, $tableName, $self->{loadDirectory}, $rowCount);      my $retVal = ERDBLoad->new($self->{erdb}, $tableName, $self->{loadDirectory}, $self->LoadOnly,
1617                                   $ignore);
1618      # Cache it in the loader list.      # Cache it in the loader list.
1619      push @{$self->{loaders}}, $retVal;      push @{$self->{loaders}}, $retVal;
1620      # Return it to the caller.      # Return it to the caller.
# Line 1416  Line 1648 
1648      my $retVal = Stats->new();      my $retVal = Stats->new();
1649      # Get the loader list.      # Get the loader list.
1650      my $loadList = $self->{loaders};      my $loadList = $self->{loaders};
1651        # Create a hash to hold the statistics objects, keyed on relation name.
1652        my %loaderHash = ();
1653      # Loop through the list, finishing the loads. Note that if the finish fails, we die      # Loop through the list, finishing the loads. Note that if the finish fails, we die
1654      # ignominiously. At some future point, we want to make the loads restartable.      # ignominiously. At some future point, we want to make the loads more restartable.
1655      while (my $loader = pop @{$loadList}) {      while (my $loader = pop @{$loadList}) {
1656          # Trace the fact that we're cleaning up.          # Get the relation name.
1657          my $relName = $loader->RelName;          my $relName = $loader->RelName;
1658          Trace("Finishing load for $relName.") if T(2);          # Check the ignore flag.
1659            if ($loader->Ignore) {
1660                Trace("Relation $relName not loaded.") if T(2);
1661            } else {
1662                # Here we really need to finish.
1663                Trace("Finishing $relName.") if T(2);
1664          my $stats = $loader->Finish();          my $stats = $loader->Finish();
1665                $loaderHash{$relName} = $stats;
1666            }
1667        }
1668        # Now we loop through again, actually loading the tables. We want to finish before
1669        # loading so that if something goes wrong at this point, all the load files are usable
1670        # and we don't have to redo all that work.
1671        for my $relName (sort keys %loaderHash) {
1672            # Get the statistics for this relation.
1673            my $stats = $loaderHash{$relName};
1674            # Check for a database load.
1675          if ($self->{options}->{dbLoad}) {          if ($self->{options}->{dbLoad}) {
1676              # Here we want to use the load file just created to load the database.              # Here we want to use the load file just created to load the database.
1677              Trace("Loading relation $relName.") if T(2);              Trace("Loading relation $relName.") if T(2);

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