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revision 1.24, Tue Jan 17 01:10:54 2006 UTC revision 1.68, Sun Sep 24 17:14:16 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 184  Line 195 
195      return $self->{options}->{loadOnly};      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 211  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 231  Line 247 
247      my $genomeCount = (keys %{$genomeHash});      my $genomeCount = (keys %{$genomeHash});
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');      my $loadGenome = $self->_TableLoader('Genome');
250      my $loadHasContig = $self->_TableLoader('HasContig');      my $loadHasContig = $self->_TableLoader('HasContig', $self->PrimaryOnly);
251      my $loadContig = $self->_TableLoader('Contig');      my $loadContig = $self->_TableLoader('Contig', $self->PrimaryOnly);
252      my $loadIsMadeUpOf = $self->_TableLoader('IsMadeUpOf');      my $loadIsMadeUpOf = $self->_TableLoader('IsMadeUpOf', $self->PrimaryOnly);
253      my $loadSequence = $self->_TableLoader('Sequence');      my $loadSequence = $self->_TableLoader('Sequence', $self->PrimaryOnly);
254      if ($self->{options}->{loadOnly}) {      if ($self->{options}->{loadOnly}) {
255          Trace("Loading from existing files.") if T(2);          Trace("Loading from existing files.") if T(2);
256      } else {      } else {
# Line 245  Line 261 
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 325  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');      my $loadCoupling = $self->_TableLoader('Coupling');
358      my $loadIsEvidencedBy = $self->_TableLoader('IsEvidencedBy');      my $loadIsEvidencedBy = $self->_TableLoader('IsEvidencedBy', $self->PrimaryOnly);
359      my $loadPCH = $self->_TableLoader('PCH');      my $loadPCH = $self->_TableLoader('PCH', $self->PrimaryOnly);
360      my $loadParticipatesInCoupling = $self->_TableLoader('ParticipatesInCoupling');      my $loadParticipatesInCoupling = $self->_TableLoader('ParticipatesInCoupling', $self->PrimaryOnly);
361      my $loadUsesAsEvidence = $self->_TableLoader('UsesAsEvidence');      my $loadUsesAsEvidence = $self->_TableLoader('UsesAsEvidence', $self->PrimaryOnly);
362      if ($self->{options}->{loadOnly}) {      if ($self->{options}->{loadOnly}) {
363          Trace("Loading from existing files.") if T(2);          Trace("Loading from existing files.") if T(2);
364      } else {      } else {
# Line 360  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 396  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                  }                  }
# Line 431  Line 459 
459      FeatureTranslation      FeatureTranslation
460      FeatureUpstream      FeatureUpstream
461      IsLocatedIn      IsLocatedIn
462        HasFeature
463    
464  =over 4  =over 4
465    
# Line 451  Line 480 
480      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
481      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
482      my $loadFeature = $self->_TableLoader('Feature');      my $loadFeature = $self->_TableLoader('Feature');
483      my $loadIsLocatedIn = $self->_TableLoader('IsLocatedIn');      my $loadIsLocatedIn = $self->_TableLoader('IsLocatedIn', $self->PrimaryOnly);
484      my $loadFeatureAlias = $self->_TableLoader('FeatureAlias');      my $loadFeatureAlias = $self->_TableLoader('FeatureAlias');
485      my $loadFeatureLink = $self->_TableLoader('FeatureLink');      my $loadFeatureLink = $self->_TableLoader('FeatureLink');
486      my $loadFeatureTranslation = $self->_TableLoader('FeatureTranslation');      my $loadFeatureTranslation = $self->_TableLoader('FeatureTranslation');
487      my $loadFeatureUpstream = $self->_TableLoader('FeatureUpstream');      my $loadFeatureUpstream = $self->_TableLoader('FeatureUpstream');
488        my $loadHasFeature = $self->_TableLoader('HasFeature');
489      # 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
490      # locations.      # locations.
491      my $chunkSize = $self->{sprout}->MaxSegment();      my $chunkSize = $self->{sprout}->MaxSegment();
# Line 469  Line 499 
499              $loadFeature->Add("genomeIn");              $loadFeature->Add("genomeIn");
500              # Get the feature list for this genome.              # Get the feature list for this genome.
501              my $features = $fig->all_features_detailed($genomeID);              my $features = $fig->all_features_detailed($genomeID);
502                # Sort and count the list.
503                my @featureTuples = sort { $a->[0] cmp $b->[0] } @{$features};
504                my $count = scalar @featureTuples;
505                Trace("$count features found for genome $genomeID.") if T(3);
506                # Set up for our duplicate-feature check.
507                my $oldFeatureID = "";
508              # Loop through the features.              # Loop through the features.
509              for my $featureData (@{$features}) {              for my $featureTuple (@featureTuples) {
                 $loadFeature->Add("featureIn");  
510                  # Split the tuple.                  # Split the tuple.
511                  my ($featureID, $locations, undef, $type) = @{$featureData};                  my ($featureID, $locations, undef, $type) = @{$featureTuple};
512                    # Check for duplicates.
513                    if ($featureID eq $oldFeatureID) {
514                        Trace("Duplicate feature $featureID found.") if T(1);
515                    } else {
516                        $oldFeatureID = $featureID;
517                        # Count this feature.
518                        $loadFeature->Add("featureIn");
519                        # Get the functional assignment.
520                        my $assignment = $fig->function_of($featureID);
521                  # Create the feature record.                  # Create the feature record.
522                  $loadFeature->Put($featureID, 1, $type);                      $loadFeature->Put($featureID, 1, $type, $assignment);
523                        # Link it to the parent genome.
524                        $loadHasFeature->Put($genomeID, $featureID, $type);
525                  # Create the aliases.                  # Create the aliases.
526                  for my $alias ($fig->feature_aliases($featureID)) {                  for my $alias ($fig->feature_aliases($featureID)) {
527                      $loadFeatureAlias->Put($featureID, $alias);                      $loadFeatureAlias->Put($featureID, $alias);
# Line 527  Line 573 
573              }              }
574          }          }
575      }      }
576        }
577      # Finish the loads.      # Finish the loads.
578      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
579      return $retVal;      return $retVal;
# Line 575  Line 622 
622              Trace("Processing features for genome $genomeID.") if T(3);              Trace("Processing features for genome $genomeID.") if T(3);
623              # Get the feature list for this genome.              # Get the feature list for this genome.
624              my $features = $fig->all_features_detailed($genomeID);              my $features = $fig->all_features_detailed($genomeID);
625                # Count the BBHs we find.
626                my $bbhCount = 0;
627              # Loop through the features.              # Loop through the features.
628              for my $featureData (@{$features}) {              for my $featureData (@{$features}) {
629                  # Split the tuple.                  # Split the tuple.
# Line 590  Line 639 
639                      if ($genomeHash->{$targetGenomeID}) {                      if ($genomeHash->{$targetGenomeID}) {
640                          $loadIsBidirectionalBestHitOf->Put($featureID, $targetID, $targetGenomeID,                          $loadIsBidirectionalBestHitOf->Put($featureID, $targetID, $targetGenomeID,
641                                                             $score);                                                             $score);
642                            $bbhCount++;
643                      }                      }
644                  }                  }
645              }              }
646                Trace("$bbhCount BBHs found for $genomeID.") if T(3);
647          }          }
648      }      }
649      # Finish the loads.      # Finish the loads.
# Line 615  Line 666 
666  The following relations are loaded by this method.  The following relations are loaded by this method.
667    
668      Subsystem      Subsystem
669        SubsystemClass
670      Role      Role
671      RoleEC      RoleEC
672      SSCell      SSCell
# Line 658  Line 710 
710      # Get the map list.      # Get the map list.
711      my @maps = $fig->all_maps;      my @maps = $fig->all_maps;
712      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
713      my $loadDiagram = $self->_TableLoader('Diagram');      my $loadDiagram = $self->_TableLoader('Diagram', $self->PrimaryOnly);
714      my $loadRoleOccursIn = $self->_TableLoader('RoleOccursIn');      my $loadRoleOccursIn = $self->_TableLoader('RoleOccursIn', $self->PrimaryOnly);
715      my $loadSubsystem = $self->_TableLoader('Subsystem');      my $loadSubsystem = $self->_TableLoader('Subsystem');
716      my $loadRole = $self->_TableLoader('Role');      my $loadRole = $self->_TableLoader('Role', $self->PrimaryOnly);
717      my $loadRoleEC = $self->_TableLoader('RoleEC');      my $loadRoleEC = $self->_TableLoader('RoleEC', $self->PrimaryOnly);
718      my $loadCatalyzes = $self->_TableLoader('Catalyzes');      my $loadCatalyzes = $self->_TableLoader('Catalyzes', $self->PrimaryOnly);
719      my $loadSSCell = $self->_TableLoader('SSCell');      my $loadSSCell = $self->_TableLoader('SSCell', $self->PrimaryOnly);
720      my $loadContainsFeature = $self->_TableLoader('ContainsFeature');      my $loadContainsFeature = $self->_TableLoader('ContainsFeature', $self->PrimaryOnly);
721      my $loadIsGenomeOf = $self->_TableLoader('IsGenomeOf');      my $loadIsGenomeOf = $self->_TableLoader('IsGenomeOf', $self->PrimaryOnly);
722      my $loadIsRoleOf = $self->_TableLoader('IsRoleOf');      my $loadIsRoleOf = $self->_TableLoader('IsRoleOf', $self->PrimaryOnly);
723      my $loadOccursInSubsystem = $self->_TableLoader('OccursInSubsystem');      my $loadOccursInSubsystem = $self->_TableLoader('OccursInSubsystem', $self->PrimaryOnly);
724      my $loadParticipatesIn = $self->_TableLoader('ParticipatesIn');      my $loadParticipatesIn = $self->_TableLoader('ParticipatesIn', $self->PrimaryOnly);
725      my $loadHasSSCell = $self->_TableLoader('HasSSCell');      my $loadHasSSCell = $self->_TableLoader('HasSSCell', $self->PrimaryOnly);
726      my $loadRoleSubset = $self->_TableLoader('RoleSubset');      my $loadRoleSubset = $self->_TableLoader('RoleSubset', $self->PrimaryOnly);
727      my $loadGenomeSubset = $self->_TableLoader('GenomeSubset');      my $loadGenomeSubset = $self->_TableLoader('GenomeSubset', $self->PrimaryOnly);
728      my $loadConsistsOfRoles = $self->_TableLoader('ConsistsOfRoles');      my $loadConsistsOfRoles = $self->_TableLoader('ConsistsOfRoles', $self->PrimaryOnly);
729      my $loadConsistsOfGenomes = $self->_TableLoader('ConsistsOfGenomes');      my $loadConsistsOfGenomes = $self->_TableLoader('ConsistsOfGenomes', $self->PrimaryOnly);
730      my $loadHasRoleSubset = $self->_TableLoader('HasRoleSubset');      my $loadHasRoleSubset = $self->_TableLoader('HasRoleSubset', $self->PrimaryOnly);
731      my $loadHasGenomeSubset = $self->_TableLoader('HasGenomeSubset');      my $loadHasGenomeSubset = $self->_TableLoader('HasGenomeSubset', $self->PrimaryOnly);
732        my $loadSubsystemClass = $self->_TableLoader('SubsystemClass', $self->PrimaryOnly);
733      if ($self->{options}->{loadOnly}) {      if ($self->{options}->{loadOnly}) {
734          Trace("Loading from existing files.") if T(2);          Trace("Loading from existing files.") if T(2);
735      } else {      } else {
# Line 692  Line 745 
745          my ($genomeID, $roleID);          my ($genomeID, $roleID);
746          my %roleData = ();          my %roleData = ();
747          for my $subsysID (@subsysIDs) {          for my $subsysID (@subsysIDs) {
             Trace("Creating subsystem $subsysID.") if T(3);  
             $loadSubsystem->Add("subsystemIn");  
748              # Get the subsystem object.              # Get the subsystem object.
749              my $sub = $fig->get_subsystem($subsysID);              my $sub = $fig->get_subsystem($subsysID);
750                # Only proceed if the subsystem has a spreadsheet.
751                if (! $sub->{empty_ss}) {
752                    Trace("Creating subsystem $subsysID.") if T(3);
753                    $loadSubsystem->Add("subsystemIn");
754              # Create the subsystem record.              # Create the subsystem record.
755              my $curator = $sub->get_curator();              my $curator = $sub->get_curator();
756              my $notes = $sub->get_notes();              my $notes = $sub->get_notes();
757              $loadSubsystem->Put($subsysID, $curator, $notes);              $loadSubsystem->Put($subsysID, $curator, $notes);
758                    my $classList = $fig->subsystem_classification($subsysID);
759                    my @classes = @$classList;
760                    if (@classes) {
761                        for my $class (@classes) {
762                            $loadSubsystemClass->Put($subsysID, $class);
763                        }
764                    }
765              # 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.
766              for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {              for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {
767                  # Connect to this role.                  # Connect to this role.
# Line 743  Line 805 
805                      # part of the spreadsheet cell ID.                      # part of the spreadsheet cell ID.
806                      for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {                      for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {
807                          # Get the features in the spreadsheet cell for this genome and role.                          # Get the features in the spreadsheet cell for this genome and role.
808                          my @pegs = $sub->get_pegs_from_cell($row, $col);                              my @pegs = grep { !$fig->is_deleted_fid($_) } $sub->get_pegs_from_cell($row, $col);
809                          # Only proceed if features exist.                          # Only proceed if features exist.
810                          if (@pegs > 0) {                          if (@pegs > 0) {
811                              # Create the spreadsheet cell.                              # Create the spreadsheet cell.
# Line 764  Line 826 
826                      if ($pegCount > 0) {                      if ($pegCount > 0) {
827                          Trace("$pegCount PEGs in $cellCount cells for $genomeID.") if T(3);                          Trace("$pegCount PEGs in $cellCount cells for $genomeID.") if T(3);
828                          $loadParticipatesIn->Put($genomeID, $subsysID, $variantCode);                          $loadParticipatesIn->Put($genomeID, $subsysID, $variantCode);
                         # Partition the PEGs found into clusters.  
                         my @clusters = $fig->compute_clusters(\@pegsFound, $sub);  
829                          # Create a hash mapping PEG IDs to cluster numbers.                          # Create a hash mapping PEG IDs to cluster numbers.
830                          # We default to -1 for all of them.                          # We default to -1 for all of them.
831                          my %clusterOf = map { $_ => -1 } @pegsFound;                          my %clusterOf = map { $_ => -1 } @pegsFound;
832                                # Partition the PEGs found into clusters.
833                                my @clusters = $fig->compute_clusters([keys %clusterOf], $sub);
834                          for (my $i = 0; $i <= $#clusters; $i++) {                          for (my $i = 0; $i <= $#clusters; $i++) {
835                              my $subList = $clusters[$i];                              my $subList = $clusters[$i];
836                              for my $peg (@{$subList}) {                              for my $peg (@{$subList}) {
# Line 796  Line 858 
858                  # Connect the subset to the subsystem.                  # Connect the subset to the subsystem.
859                  $loadHasRoleSubset->Put($subsysID, $actualID);                  $loadHasRoleSubset->Put($subsysID, $actualID);
860                  # Connect the subset to its roles.                  # Connect the subset to its roles.
861                  my @roles = $sub->get_subset($subsetID);                      my @roles = $sub->get_subsetC_roles($subsetID);
862                  for my $roleID (@roles) {                  for my $roleID (@roles) {
863                      $loadConsistsOfRoles->Put($actualID, $roleID);                      $loadConsistsOfRoles->Put($actualID, $roleID);
864                  }                  }
# Line 816  Line 878 
878                  }                  }
879              }              }
880          }          }
881            }
882          # 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
883          # 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
884          # in subsystems (and therefore appear in the %ecToRoles hash) are          # in subsystems (and therefore appear in the %ecToRoles hash) are
# Line 892  Line 955 
955      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
956      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
957      my $loadProperty = $self->_TableLoader('Property');      my $loadProperty = $self->_TableLoader('Property');
958      my $loadHasProperty = $self->_TableLoader('HasProperty');      my $loadHasProperty = $self->_TableLoader('HasProperty', $self->PrimaryOnly);
959      if ($self->{options}->{loadOnly}) {      if ($self->{options}->{loadOnly}) {
960          Trace("Loading from existing files.") if T(2);          Trace("Loading from existing files.") if T(2);
961      } else {      } else {
# Line 901  Line 964 
964          my %propertyKeys = ();          my %propertyKeys = ();
965          my $nextID = 1;          my $nextID = 1;
966          # Loop through the genomes.          # Loop through the genomes.
967          for my $genomeID (keys %{$genomeHash}) {          for my $genomeID (sort keys %{$genomeHash}) {
968              $loadProperty->Add("genomeIn");              $loadProperty->Add("genomeIn");
969              Trace("Generating properties for $genomeID.") if T(3);              Trace("Generating properties for $genomeID.") if T(3);
970              # 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
# Line 989  Line 1052 
1052      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
1053      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
1054      my $loadAnnotation = $self->_TableLoader('Annotation');      my $loadAnnotation = $self->_TableLoader('Annotation');
1055      my $loadIsTargetOfAnnotation = $self->_TableLoader('IsTargetOfAnnotation');      my $loadIsTargetOfAnnotation = $self->_TableLoader('IsTargetOfAnnotation', $self->PrimaryOnly);
1056      my $loadSproutUser = $self->_TableLoader('SproutUser');      my $loadSproutUser = $self->_TableLoader('SproutUser', $self->PrimaryOnly);
1057      my $loadUserAccess = $self->_TableLoader('UserAccess');      my $loadUserAccess = $self->_TableLoader('UserAccess', $self->PrimaryOnly);
1058      my $loadMadeAnnotation = $self->_TableLoader('MadeAnnotation');      my $loadMadeAnnotation = $self->_TableLoader('MadeAnnotation', $self->PrimaryOnly);
1059      if ($self->{options}->{loadOnly}) {      if ($self->{options}->{loadOnly}) {
1060          Trace("Loading from existing files.") if T(2);          Trace("Loading from existing files.") if T(2);
1061      } else {      } else {
# Line 1010  Line 1073 
1073          # Loop through the genomes.          # Loop through the genomes.
1074          for my $genomeID (sort keys %{$genomeHash}) {          for my $genomeID (sort keys %{$genomeHash}) {
1075              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);  
1076                  # 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
1077                  # from showing up for a single PEG's annotations.                  # from showing up for a single PEG's annotations.
1078                  my %seenTimestamps = ();                  my %seenTimestamps = ();
1079                  # Loop through the annotations.              # Get the genome's annotations.
1080                  for my $tuple ($fig->feature_annotations($peg, "raw")) {              my @annotations = $fig->read_all_annotations($genomeID);
1081                      my ($fid, $timestamp, $user, $text) = @{$tuple};              Trace("Processing annotations.") if T(2);
1082                for my $tuple (@annotations) {
1083                    # Get the annotation tuple.
1084                    my ($peg, $timestamp, $user, $text) = @{$tuple};
1085                      # Here we fix up the annotation text. "\r" is removed,                      # Here we fix up the annotation text. "\r" is removed,
1086                      # and "\t" and "\n" are escaped. Note we use the "s"                  # and "\t" and "\n" are escaped. Note we use the "gs"
1087                      # modifier so that new-lines inside the text do not                      # modifier so that new-lines inside the text do not
1088                      # stop the substitution search.                      # stop the substitution search.
1089                      $text =~ s/\r//gs;                      $text =~ s/\r//gs;
# Line 1034  Line 1096 
1096                          # 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
1097                          # the key is unique.                          # the key is unique.
1098                          my $keyStamp = $timestamp;                          my $keyStamp = $timestamp;
1099                          while ($seenTimestamps{$keyStamp}) {                      while ($seenTimestamps{"$peg:$keyStamp"}) {
1100                              $keyStamp++;                              $keyStamp++;
1101                          }                          }
                         $seenTimestamps{$keyStamp} = 1;  
1102                          my $annotationID = "$peg:$keyStamp";                          my $annotationID = "$peg:$keyStamp";
1103                        $seenTimestamps{$annotationID} = 1;
1104                          # Insure the user exists.                          # Insure the user exists.
1105                          if (! $users{$user}) {                          if (! $users{$user}) {
1106                              $loadSproutUser->Put($user, "SEED user");                              $loadSproutUser->Put($user, "SEED user");
# Line 1056  Line 1118 
1118                  }                  }
1119              }              }
1120          }          }
     }  
1121      # Finish the load.      # Finish the load.
1122      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
1123      return $retVal;      return $retVal;
# Line 1098  Line 1159 
1159      # Get the genome hash.      # Get the genome hash.
1160      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
1161      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
1162      my $loadComesFrom = $self->_TableLoader('ComesFrom');      my $loadComesFrom = $self->_TableLoader('ComesFrom', $self->PrimaryOnly);
1163      my $loadSource = $self->_TableLoader('Source');      my $loadSource = $self->_TableLoader('Source');
1164      my $loadSourceURL = $self->_TableLoader('SourceURL');      my $loadSourceURL = $self->_TableLoader('SourceURL');
1165      if ($self->{options}->{loadOnly}) {      if ($self->{options}->{loadOnly}) {
# Line 1185  Line 1246 
1246      } else {      } else {
1247          Trace("Generating external data.") if T(2);          Trace("Generating external data.") if T(2);
1248          # We loop through the files one at a time. First, the organism file.          # We loop through the files one at a time. First, the organism file.
1249          Open(\*ORGS, "<$FIG_Config::global/ext_org.table");          Open(\*ORGS, "sort +0 -1 -u -t\"\t\" $FIG_Config::global/ext_org.table |");
1250          my $orgLine;          my $orgLine;
1251          while (defined($orgLine = <ORGS>)) {          while (defined($orgLine = <ORGS>)) {
1252              # Clean the input line.              # Clean the input line.
# Line 1197  Line 1258 
1258          close ORGS;          close ORGS;
1259          # Now the function file.          # Now the function file.
1260          my $funcLine;          my $funcLine;
1261          Open(\*FUNCS, "<$FIG_Config::global/ext_func.table");          Open(\*FUNCS, "sort +0 -1 -u -t\"\t\" $FIG_Config::global/ext_func.table |");
1262          while (defined($funcLine = <FUNCS>)) {          while (defined($funcLine = <FUNCS>)) {
1263              # Clean the line ending.              # Clean the line ending.
1264              chomp $funcLine;              chomp $funcLine;
# Line 1256  Line 1317 
1317      my $fig = $self->{fig};      my $fig = $self->{fig};
1318      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
1319      my $loadReaction = $self->_TableLoader('Reaction');      my $loadReaction = $self->_TableLoader('Reaction');
1320      my $loadReactionURL = $self->_TableLoader('ReactionURL');      my $loadReactionURL = $self->_TableLoader('ReactionURL', $self->PrimaryOnly);
1321      my $loadCompound = $self->_TableLoader('Compound');      my $loadCompound = $self->_TableLoader('Compound', $self->PrimaryOnly);
1322      my $loadCompoundName = $self->_TableLoader('CompoundName');      my $loadCompoundName = $self->_TableLoader('CompoundName', $self->PrimaryOnly);
1323      my $loadCompoundCAS = $self->_TableLoader('CompoundCAS');      my $loadCompoundCAS = $self->_TableLoader('CompoundCAS', $self->PrimaryOnly);
1324      my $loadIsAComponentOf = $self->_TableLoader('IsAComponentOf');      my $loadIsAComponentOf = $self->_TableLoader('IsAComponentOf', $self->PrimaryOnly);
1325      if ($self->{options}->{loadOnly}) {      if ($self->{options}->{loadOnly}) {
1326          Trace("Loading from existing files.") if T(2);          Trace("Loading from existing files.") if T(2);
1327      } else {      } else {
# Line 1329  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 1355  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            # Currently there are no groups.
1421        }
1422        # Finish the load.
1423        my $retVal = $self->_FinishAll();
1424        return $retVal;
1425    }
1426    
1427    =head3 LoadSynonymData
1428    
1429    C<< my $stats = $spl->LoadSynonymData(); >>
1430    
1431    Load the synonym groups into Sprout.
1432    
1433    The following relations are loaded by this method.
1434    
1435        SynonymGroup
1436        IsSynonymGroupFor
1437    
1438    The source information for these relations is taken from the C<maps_to_id> method
1439    of the B<FIG> object. Unfortunately, to make this work, we need to use direct
1440    SQL against the FIG database.
1441    
1442    =over 4
1443    
1444    =item RETURNS
1445    
1446    Returns a statistics object for the loads.
1447    
1448    =back
1449    
1450    =cut
1451    #: Return Type $%;
1452    sub LoadSynonymData {
1453        # Get this object instance.
1454        my ($self) = @_;
1455        # Get the FIG object.
1456        my $fig = $self->{fig};
1457        # Get the genome hash.
1458        my $genomeHash = $self->{genomes};
1459        # Create a load object for the table we're loading.
1460        my $loadSynonymGroup = $self->_TableLoader('SynonymGroup');
1461        my $loadIsSynonymGroupFor = $self->_TableLoader('IsSynonymGroupFor');
1462        if ($self->{options}->{loadOnly}) {
1463            Trace("Loading from existing files.") if T(2);
1464        } else {
1465            Trace("Generating synonym group data.") if T(2);
1466            # Get the database handle.
1467            my $dbh = $fig->db_handle();
1468            # Ask for the synonyms.
1469            my $sth = $dbh->prepare_command("SELECT maps_to, syn_id FROM peg_synonyms ORDER BY maps_to");
1470            my $result = $sth->execute();
1471            if (! defined($result)) {
1472                Confess("Database error in Synonym load: " . $sth->errstr());
1473            } else {
1474                # Remember the current synonym.
1475                my $current_syn = "";
1476                # Count the features.
1477                my $featureCount = 0;
1478                # Loop through the synonym/peg pairs.
1479                while (my @row = $sth->fetchrow()) {
1480                    # Get the synonym ID and feature ID.
1481                    my ($syn_id, $peg) = @row;
1482                    # Insure it's for one of our genomes.
1483                    my $genomeID = FIG::genome_of($peg);
1484                    if (exists $genomeHash->{$genomeID}) {
1485                        # Verify the synonym.
1486                        if ($syn_id ne $current_syn) {
1487                            # It's new, so put it in the group table.
1488                            $loadSynonymGroup->Put($syn_id);
1489                            $current_syn = $syn_id;
1490                        }
1491                        # Connect the synonym to the peg.
1492                        $loadIsSynonymGroupFor->Put($syn_id, $peg);
1493                        # Count this feature.
1494                        $featureCount++;
1495                        if ($featureCount % 1000 == 0) {
1496                            Trace("$featureCount features processed.") if T(3);
1497                        }
1498                    }
1499                }
1500            }
1501        }
1502        # Finish the load.
1503        my $retVal = $self->_FinishAll();
1504        return $retVal;
1505    }
1506    
1507    =head3 LoadFamilyData
1508    
1509    C<< my $stats = $spl->LoadFamilyData(); >>
1510    
1511    Load the protein families into Sprout.
1512    
1513    The following relations are loaded by this method.
1514    
1515        Family
1516        IsFamilyForFeature
1517    
1518    The source information for these relations is taken from the C<families_for_protein>,
1519    C<family_function>, and C<sz_family> methods of the B<FIG> object.
1520    
1521    =over 4
1522    
1523    =item RETURNS
1524    
1525    Returns a statistics object for the loads.
1526    
1527    =back
1528    
1529    =cut
1530    #: Return Type $%;
1531    sub LoadFamilyData {
1532        # Get this object instance.
1533        my ($self) = @_;
1534        # Get the FIG object.
1535        my $fig = $self->{fig};
1536        # Get the genome hash.
1537        my $genomeHash = $self->{genomes};
1538        # Create load objects for the tables we're loading.
1539        my $loadFamily = $self->_TableLoader('Family');
1540        my $loadIsFamilyForFeature = $self->_TableLoader('IsFamilyForFeature');
1541        if ($self->{options}->{loadOnly}) {
1542            Trace("Loading from existing files.") if T(2);
1543        } else {
1544            Trace("Generating family data.") if T(2);
1545            # Create a hash for the family IDs.
1546            my %familyHash = ();
1547          # Loop through the genomes.          # Loop through the genomes.
1548          my $line;          for my $genomeID (sort keys %{$genomeHash}) {
1549          for my $genomeID (keys %{$genomeHash}) {              Trace("Processing features for $genomeID.") if T(2);
1550              Trace("Processing $genomeID.") if T(3);              # Loop through this genome's PEGs.
1551              # Open the NMPDR group file for this genome.              for my $fid ($fig->all_features($genomeID, "peg")) {
1552              if (open(TMP, "<$FIG_Config::organisms/$genomeID/NMPDR") &&                  $loadIsFamilyForFeature->Add("features", 1);
1553                  defined($line = <TMP>)) {                  # Get this feature's families.
1554                  # Clean the line ending.                  my @families = $fig->families_for_protein($fid);
1555                  chomp $line;                  # Loop through the families, connecting them to the feature.
1556                  # Add the group to the table. Note that there can only be one group                  for my $family (@families) {
1557                  # per genome.                      $loadIsFamilyForFeature->Put($family, $fid);
1558                  $loadGenomeGroups->Put($genomeID, $line);                      # If this is a new family, create a record for it.
1559                        if (! exists $familyHash{$family}) {
1560                            $familyHash{$family} = 1;
1561                            $loadFamily->Add("families", 1);
1562                            my $size = $fig->sz_family($family);
1563                            my $func = $fig->family_function($family);
1564                            $loadFamily->Put($family, $size, $func);
1565                        }
1566                    }
1567              }              }
             close TMP;  
1568          }          }
1569      }      }
1570      # Finish the load.      # Finish the load.
# Line 1392  Line 1588 
1588    
1589  Name of the table (relation) being loaded.  Name of the table (relation) being loaded.
1590    
1591    =item ignore
1592    
1593    TRUE if the table should be ignored entirely, else FALSE.
1594    
1595  =item RETURN  =item RETURN
1596    
1597  Returns an ERDBLoad object for loading the specified table.  Returns an ERDBLoad object for loading the specified table.
# Line 1402  Line 1602 
1602    
1603  sub _TableLoader {  sub _TableLoader {
1604      # Get the parameters.      # Get the parameters.
1605      my ($self, $tableName, $loadOnly) = @_;      my ($self, $tableName, $ignore) = @_;
1606      # Create the load object.      # Create the load object.
1607      my $retVal = ERDBLoad->new($self->{erdb}, $tableName, $self->{loadDirectory}, $self->LoadOnly);      my $retVal = ERDBLoad->new($self->{erdb}, $tableName, $self->{loadDirectory}, $self->LoadOnly,
1608                                   $ignore);
1609      # Cache it in the loader list.      # Cache it in the loader list.
1610      push @{$self->{loaders}}, $retVal;      push @{$self->{loaders}}, $retVal;
1611      # Return it to the caller.      # Return it to the caller.
# Line 1438  Line 1639 
1639      my $retVal = Stats->new();      my $retVal = Stats->new();
1640      # Get the loader list.      # Get the loader list.
1641      my $loadList = $self->{loaders};      my $loadList = $self->{loaders};
1642        # Create a hash to hold the statistics objects, keyed on relation name.
1643        my %loaderHash = ();
1644      # 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
1645      # 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.
1646      while (my $loader = pop @{$loadList}) {      while (my $loader = pop @{$loadList}) {
1647          # Trace the fact that we're cleaning up.          # Get the relation name.
1648          my $relName = $loader->RelName;          my $relName = $loader->RelName;
1649            # Check the ignore flag.
1650            if ($loader->Ignore) {
1651                Trace("Relation $relName not loaded.") if T(2);
1652            } else {
1653                # Here we really need to finish.
1654          Trace("Finishing $relName.") if T(2);          Trace("Finishing $relName.") if T(2);
1655          my $stats = $loader->Finish();          my $stats = $loader->Finish();
1656                $loaderHash{$relName} = $stats;
1657            }
1658        }
1659        # Now we loop through again, actually loading the tables. We want to finish before
1660        # loading so that if something goes wrong at this point, all the load files are usable
1661        # and we don't have to redo all that work.
1662        for my $relName (sort keys %loaderHash) {
1663            # Get the statistics for this relation.
1664            my $stats = $loaderHash{$relName};
1665            # Check for a database load.
1666          if ($self->{options}->{dbLoad}) {          if ($self->{options}->{dbLoad}) {
1667              # 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.
1668              Trace("Loading relation $relName.") if T(2);              Trace("Loading relation $relName.") if T(2);

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