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revision 1.26, Mon Jan 30 21:57:02 2006 UTC revision 1.74, Sat Oct 21 06:44:17 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            # Go through the subsys hash again, creating the keyword list for each subsystem.
167            for my $subsystem (keys %subsystems) {
168                my $name = $subsystem;
169                $name =~ s/_/ /g;
170                my $classes = $fig->subsystem_classification($subsystem);
171                my @classList = map { " $_" } @{$classes};
172                $name .= join("", @classList);
173                $subsystems{$subsystem} = $name;
174            }
175        }
176      # Get the data directory from the Sprout object.      # Get the data directory from the Sprout object.
177      my ($directory) = $sprout->LoadInfo();      my ($directory) = $sprout->LoadInfo();
178      # Create the Sprout load object.      # Create the Sprout load object.
# Line 162  Line 182 
182                    subsystems => \%subsystems,                    subsystems => \%subsystems,
183                    sprout => $sprout,                    sprout => $sprout,
184                    loadDirectory => $directory,                    loadDirectory => $directory,
185                    erdb => $sprout->{_erdb},                    erdb => $sprout,
186                    loaders => [],                    loaders => [],
187                    options => $options                    options => $options
188                   };                   };
# Line 250  Line 270 
270              $loadGenome->Add("genomeIn");              $loadGenome->Add("genomeIn");
271              # The access code comes in via the genome hash.              # The access code comes in via the genome hash.
272              my $accessCode = $genomeHash->{$genomeID};              my $accessCode = $genomeHash->{$genomeID};
273              # 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.  
274              my ($genus, $species, @extraData) = split / /, $self->{fig}->genus_species($genomeID);              my ($genus, $species, @extraData) = split / /, $self->{fig}->genus_species($genomeID);
275              my $extra = join " ", @extraData, "[$genomeID]";              my $extra = join " ", @extraData;
276              # Get the full taxonomy.              # Get the full taxonomy.
277              my $taxonomy = $fig->taxonomy_of($genomeID);              my $taxonomy = $fig->taxonomy_of($genomeID);
278                # Open the NMPDR group file for this genome.
279                my $group;
280                if (open(TMP, "<$FIG_Config::organisms/$genomeID/NMPDR") &&
281                    defined($group = <TMP>)) {
282                    # Clean the line ending.
283                    chomp $group;
284                } else {
285                    # No group, so use the default.
286                    $group = $FIG_Config::otherGroup;
287                }
288                close TMP;
289              # Output the genome record.              # Output the genome record.
290              $loadGenome->Put($genomeID, $accessCode, $fig->is_complete($genomeID), $genus,              $loadGenome->Put($genomeID, $accessCode, $fig->is_complete($genomeID), $genus,
291                               $species, $extra, $taxonomy);                               $group, $species, $extra, $taxonomy);
292              # Now we loop through each of the genome's contigs.              # Now we loop through each of the genome's contigs.
293              my @contigs = $fig->all_contigs($genomeID);              my @contigs = $fig->all_contigs($genomeID);
294              for my $contigID (@contigs) {              for my $contigID (@contigs) {
# Line 330  Line 360 
360      my $fig = $self->{fig};      my $fig = $self->{fig};
361      # Get the genome hash.      # Get the genome hash.
362      my $genomeFilter = $self->{genomes};      my $genomeFilter = $self->{genomes};
363      my $genomeCount = (keys %{$genomeFilter});      # Set up an ID counter for the PCHs.
364      my $featureCount = $genomeCount * 4000;      my $pchID = 0;
365      # Start the loads.      # Start the loads.
366      my $loadCoupling = $self->_TableLoader('Coupling');      my $loadCoupling = $self->_TableLoader('Coupling');
367      my $loadIsEvidencedBy = $self->_TableLoader('IsEvidencedBy', $self->PrimaryOnly);      my $loadIsEvidencedBy = $self->_TableLoader('IsEvidencedBy', $self->PrimaryOnly);
# Line 365  Line 395 
395                  for my $coupleData (@couplings) {                  for my $coupleData (@couplings) {
396                      my ($peg2, $score) = @{$coupleData};                      my ($peg2, $score) = @{$coupleData};
397                      # Compute the coupling ID.                      # Compute the coupling ID.
398                      my $coupleID = Sprout::CouplingID($peg1, $peg2);                      my $coupleID = $self->{erdb}->CouplingID($peg1, $peg2);
399                      if (! exists $dupHash{$coupleID}) {                      if (! exists $dupHash{$coupleID}) {
400                          $loadCoupling->Add("couplingIn");                          $loadCoupling->Add("couplingIn");
401                          # 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 401  Line 431 
431                              }                              }
432                          }                          }
433                          for my $evidenceID (keys %evidenceMap) {                          for my $evidenceID (keys %evidenceMap) {
434                                # Get the ID for this evidence.
435                                $pchID++;
436                              # Create the evidence record.                              # Create the evidence record.
437                              my ($peg3, $peg4, $usage) = @{$evidenceMap{$evidenceID}};                              my ($peg3, $peg4, $usage) = @{$evidenceMap{$evidenceID}};
438                              $loadPCH->Put($evidenceID, $usage);                              $loadPCH->Put($pchID, $usage);
439                              # Connect it to the coupling.                              # Connect it to the coupling.
440                              $loadIsEvidencedBy->Put($coupleID, $evidenceID);                              $loadIsEvidencedBy->Put($coupleID, $pchID);
441                              # Connect it to the features.                              # Connect it to the features.
442                              $loadUsesAsEvidence->Put($evidenceID, $peg3, 1);                              $loadUsesAsEvidence->Put($pchID, $peg3, 1);
443                              $loadUsesAsEvidence->Put($evidenceID, $peg4, 2);                              $loadUsesAsEvidence->Put($pchID, $peg4, 2);
444                          }                          }
445                      }                      }
446                  }                  }
# Line 436  Line 468 
468      FeatureTranslation      FeatureTranslation
469      FeatureUpstream      FeatureUpstream
470      IsLocatedIn      IsLocatedIn
471        HasFeature
472        HasRoleInSubsystem
473    
474  =over 4  =over 4
475    
# Line 450  Line 484 
484  sub LoadFeatureData {  sub LoadFeatureData {
485      # Get this object instance.      # Get this object instance.
486      my ($self) = @_;      my ($self) = @_;
487      # Get the FIG object.      # Get the FIG and Sprout objects.
488      my $fig = $self->{fig};      my $fig = $self->{fig};
489        my $sprout = $self->{sprout};
490      # Get the table of genome IDs.      # Get the table of genome IDs.
491      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
492      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
# Line 461  Line 496 
496      my $loadFeatureLink = $self->_TableLoader('FeatureLink');      my $loadFeatureLink = $self->_TableLoader('FeatureLink');
497      my $loadFeatureTranslation = $self->_TableLoader('FeatureTranslation');      my $loadFeatureTranslation = $self->_TableLoader('FeatureTranslation');
498      my $loadFeatureUpstream = $self->_TableLoader('FeatureUpstream');      my $loadFeatureUpstream = $self->_TableLoader('FeatureUpstream');
499        my $loadHasFeature = $self->_TableLoader('HasFeature', $self->PrimaryOnly);
500        my $loadHasRoleInSubsystem = $self->_TableLoader('HasRoleInSubsystem', $self->PrimaryOnly);
501        # Get the subsystem hash.
502        my $subHash = $self->{subsystems};
503      # 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
504      # locations.      # locations.
505      my $chunkSize = $self->{sprout}->MaxSegment();      my $chunkSize = $self->{sprout}->MaxSegment();
# Line 474  Line 513 
513              $loadFeature->Add("genomeIn");              $loadFeature->Add("genomeIn");
514              # Get the feature list for this genome.              # Get the feature list for this genome.
515              my $features = $fig->all_features_detailed($genomeID);              my $features = $fig->all_features_detailed($genomeID);
516                # Sort and count the list.
517                my @featureTuples = sort { $a->[0] cmp $b->[0] } @{$features};
518                my $count = scalar @featureTuples;
519                Trace("$count features found for genome $genomeID.") if T(3);
520                # Set up for our duplicate-feature check.
521                my $oldFeatureID = "";
522              # Loop through the features.              # Loop through the features.
523              for my $featureData (@{$features}) {              for my $featureTuple (@featureTuples) {
                 $loadFeature->Add("featureIn");  
524                  # Split the tuple.                  # Split the tuple.
525                  my ($featureID, $locations, undef, $type) = @{$featureData};                  my ($featureID, $locations, undef, $type) = @{$featureTuple};
526                  # Create the feature record.                  # Check for duplicates.
527                  $loadFeature->Put($featureID, 1, $type);                  if ($featureID eq $oldFeatureID) {
528                        Trace("Duplicate feature $featureID found.") if T(1);
529                    } else {
530                        $oldFeatureID = $featureID;
531                        # Count this feature.
532                        $loadFeature->Add("featureIn");
533                        # Get the functional assignment.
534                        my $assignment = $fig->function_of($featureID);
535                        # Begin building the keywords.
536                        my $keywords = "$assignment $genomeID";
537                        # Link this feature to the parent genome.
538                        $loadHasFeature->Put($genomeID, $featureID, $type);
539                  # Create the aliases.                  # Create the aliases.
540                  for my $alias ($fig->feature_aliases($featureID)) {                  for my $alias ($fig->feature_aliases($featureID)) {
541                      $loadFeatureAlias->Put($featureID, $alias);                      $loadFeatureAlias->Put($featureID, $alias);
542                            $keywords .= " $alias";
543                  }                  }
544                  # Get the links.                  # Get the links.
545                  my @links = $fig->fid_links($featureID);                  my @links = $fig->fid_links($featureID);
# Line 503  Line 559 
559                          $loadFeatureUpstream->Put($featureID, $upstream);                          $loadFeatureUpstream->Put($featureID, $upstream);
560                      }                      }
561                  }                  }
562                        # Now we need to find the subsystems this feature participates in.
563                        # We also add the subsystems to the keyword list. Before we do that,
564                        # we must convert underscores to spaces and tack on the classifications.
565                        my @subsystems = $fig->peg_to_subsystems($featureID);
566                        for my $subsystem (@subsystems) {
567                            # Only proceed if we like this subsystem.
568                            if (exists $subHash->{$subsystem}) {
569                                # Store the has-role link.
570                                $loadHasRoleInSubsystem->Put($featureID, $subsystem, $genomeID, $type);
571                                # Save the subsystem's keyword data.
572                                my $subKeywords = $subHash->{$subsystem};
573                                $keywords .= " $subKeywords";
574                            }
575                        }
576                        # The final task is to add virulence and essentiality attributes.
577                        if ($fig->virulent($featureID)) {
578                            $keywords .= " virulent";
579                        }
580                        if ($fig->essential($featureID)) {
581                            $keywords .= " essential";
582                        }
583                        # Clean the keyword list.
584                        my $cleanWords = $sprout->CleanKeywords($keywords);
585                        # Create the feature record.
586                        $loadFeature->Put($featureID, 1, $type, $assignment, $cleanWords);
587                  # 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
588                  # 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
589                  # the maximum segment size. This simplifies the genes_in_region processing                  # the maximum segment size. This simplifies the genes_in_region processing
# Line 532  Line 613 
613              }              }
614          }          }
615      }      }
     # Finish the loads.  
     my $retVal = $self->_FinishAll();  
     return $retVal;  
 }  
   
 =head3 LoadBBHData  
   
 C<< my $stats = $spl->LoadBBHData(); >>  
   
 Load the bidirectional best hit data from FIG into Sprout.  
   
 Sprout does not store information on similarities. Instead, it has only the  
 bi-directional best hits. Even so, the BBH table is one of the largest in  
 the database.  
   
 The following relations are loaded by this method.  
   
     IsBidirectionalBestHitOf  
   
 =over 4  
   
 =item RETURNS  
   
 Returns a statistics object for the loads.  
   
 =back  
   
 =cut  
 #: Return Type $%;  
 sub LoadBBHData {  
     # Get this object instance.  
     my ($self) = @_;  
     # Get the FIG object.  
     my $fig = $self->{fig};  
     # Get the table of genome IDs.  
     my $genomeHash = $self->{genomes};  
     # Create load objects for each of the tables we're loading.  
     my $loadIsBidirectionalBestHitOf = $self->_TableLoader('IsBidirectionalBestHitOf');  
     if ($self->{options}->{loadOnly}) {  
         Trace("Loading from existing files.") if T(2);  
     } else {  
         Trace("Generating BBH data.") if T(2);  
         # Now we loop through the genomes, generating the data for each one.  
         for my $genomeID (sort keys %{$genomeHash}) {  
             $loadIsBidirectionalBestHitOf->Add("genomeIn");  
             Trace("Processing features for genome $genomeID.") if T(3);  
             # Get the feature list for this genome.  
             my $features = $fig->all_features_detailed($genomeID);  
             # Loop through the features.  
             for my $featureData (@{$features}) {  
                 # Split the tuple.  
                 my ($featureID, $locations, $aliases, $type) = @{$featureData};  
                 # Get the bi-directional best hits.  
                 my @bbhList = $fig->bbhs($featureID);  
                 for my $bbhEntry (@bbhList) {  
                     # Get the target feature ID and the score.  
                     my ($targetID, $score) = @{$bbhEntry};  
                     # Check the target feature's genome.  
                     my $targetGenomeID = $fig->genome_of($targetID);  
                     # Only proceed if it's one of our genomes.  
                     if ($genomeHash->{$targetGenomeID}) {  
                         $loadIsBidirectionalBestHitOf->Put($featureID, $targetID, $targetGenomeID,  
                                                            $score);  
                     }  
                 }  
             }  
         }  
616      }      }
617      # Finish the loads.      # Finish the loads.
618      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
# Line 620  Line 634 
634  The following relations are loaded by this method.  The following relations are loaded by this method.
635    
636      Subsystem      Subsystem
637        SubsystemClass
638      Role      Role
639      RoleEC      RoleEC
640      SSCell      SSCell
# Line 682  Line 697 
697      my $loadConsistsOfGenomes = $self->_TableLoader('ConsistsOfGenomes', $self->PrimaryOnly);      my $loadConsistsOfGenomes = $self->_TableLoader('ConsistsOfGenomes', $self->PrimaryOnly);
698      my $loadHasRoleSubset = $self->_TableLoader('HasRoleSubset', $self->PrimaryOnly);      my $loadHasRoleSubset = $self->_TableLoader('HasRoleSubset', $self->PrimaryOnly);
699      my $loadHasGenomeSubset = $self->_TableLoader('HasGenomeSubset', $self->PrimaryOnly);      my $loadHasGenomeSubset = $self->_TableLoader('HasGenomeSubset', $self->PrimaryOnly);
700        my $loadSubsystemClass = $self->_TableLoader('SubsystemClass', $self->PrimaryOnly);
701      if ($self->{options}->{loadOnly}) {      if ($self->{options}->{loadOnly}) {
702          Trace("Loading from existing files.") if T(2);          Trace("Loading from existing files.") if T(2);
703      } else {      } else {
# Line 697  Line 713 
713          my ($genomeID, $roleID);          my ($genomeID, $roleID);
714          my %roleData = ();          my %roleData = ();
715          for my $subsysID (@subsysIDs) {          for my $subsysID (@subsysIDs) {
             Trace("Creating subsystem $subsysID.") if T(3);  
             $loadSubsystem->Add("subsystemIn");  
716              # Get the subsystem object.              # Get the subsystem object.
717              my $sub = $fig->get_subsystem($subsysID);              my $sub = $fig->get_subsystem($subsysID);
718                # Only proceed if the subsystem has a spreadsheet.
719                if (! $sub->{empty_ss}) {
720                    Trace("Creating subsystem $subsysID.") if T(3);
721                    $loadSubsystem->Add("subsystemIn");
722              # Create the subsystem record.              # Create the subsystem record.
723              my $curator = $sub->get_curator();              my $curator = $sub->get_curator();
724              my $notes = $sub->get_notes();              my $notes = $sub->get_notes();
725              $loadSubsystem->Put($subsysID, $curator, $notes);              $loadSubsystem->Put($subsysID, $curator, $notes);
726                    # Now for the classification string. This comes back as a list
727                    # reference and we convert it to a space-delimited string.
728                    my $classList = $fig->subsystem_classification($subsysID);
729                    my $classString = join(" : ", grep { $_ } @$classList);
730                    $loadSubsystemClass->Put($subsysID, $classString);
731              # 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.
732              for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {              for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {
733                  # Connect to this role.                  # Connect to this role.
# Line 748  Line 771 
771                      # part of the spreadsheet cell ID.                      # part of the spreadsheet cell ID.
772                      for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {                      for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {
773                          # Get the features in the spreadsheet cell for this genome and role.                          # Get the features in the spreadsheet cell for this genome and role.
774                          my @pegs = $sub->get_pegs_from_cell($row, $col);                              my @pegs = grep { !$fig->is_deleted_fid($_) } $sub->get_pegs_from_cell($row, $col);
775                          # Only proceed if features exist.                          # Only proceed if features exist.
776                          if (@pegs > 0) {                          if (@pegs > 0) {
777                              # Create the spreadsheet cell.                              # Create the spreadsheet cell.
# Line 769  Line 792 
792                      if ($pegCount > 0) {                      if ($pegCount > 0) {
793                          Trace("$pegCount PEGs in $cellCount cells for $genomeID.") if T(3);                          Trace("$pegCount PEGs in $cellCount cells for $genomeID.") if T(3);
794                          $loadParticipatesIn->Put($genomeID, $subsysID, $variantCode);                          $loadParticipatesIn->Put($genomeID, $subsysID, $variantCode);
                         # Partition the PEGs found into clusters.  
                         my @clusters = $fig->compute_clusters(\@pegsFound, $sub);  
795                          # Create a hash mapping PEG IDs to cluster numbers.                          # Create a hash mapping PEG IDs to cluster numbers.
796                          # We default to -1 for all of them.                          # We default to -1 for all of them.
797                          my %clusterOf = map { $_ => -1 } @pegsFound;                          my %clusterOf = map { $_ => -1 } @pegsFound;
798                                # Partition the PEGs found into clusters.
799                                my @clusters = $fig->compute_clusters([keys %clusterOf], $sub);
800                          for (my $i = 0; $i <= $#clusters; $i++) {                          for (my $i = 0; $i <= $#clusters; $i++) {
801                              my $subList = $clusters[$i];                              my $subList = $clusters[$i];
802                              for my $peg (@{$subList}) {                              for my $peg (@{$subList}) {
# Line 801  Line 824 
824                  # Connect the subset to the subsystem.                  # Connect the subset to the subsystem.
825                  $loadHasRoleSubset->Put($subsysID, $actualID);                  $loadHasRoleSubset->Put($subsysID, $actualID);
826                  # Connect the subset to its roles.                  # Connect the subset to its roles.
827                  my @roles = $sub->get_subset($subsetID);                      my @roles = $sub->get_subsetC_roles($subsetID);
828                  for my $roleID (@roles) {                  for my $roleID (@roles) {
829                      $loadConsistsOfRoles->Put($actualID, $roleID);                      $loadConsistsOfRoles->Put($actualID, $roleID);
830                  }                  }
# Line 821  Line 844 
844                  }                  }
845              }              }
846          }          }
847            }
848          # 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
849          # 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
850          # in subsystems (and therefore appear in the %ecToRoles hash) are          # in subsystems (and therefore appear in the %ecToRoles hash) are
# Line 906  Line 930 
930          my %propertyKeys = ();          my %propertyKeys = ();
931          my $nextID = 1;          my $nextID = 1;
932          # Loop through the genomes.          # Loop through the genomes.
933          for my $genomeID (keys %{$genomeHash}) {          for my $genomeID (sort keys %{$genomeHash}) {
934              $loadProperty->Add("genomeIn");              $loadProperty->Add("genomeIn");
935              Trace("Generating properties for $genomeID.") if T(3);              Trace("Generating properties for $genomeID.") if T(3);
936              # 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 920  Line 944 
944                  # 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
945                  # to insure we do not get any genome attributes.                  # to insure we do not get any genome attributes.
946                  my @attributeList = $fig->get_attributes($fid, '', '', '');                  my @attributeList = $fig->get_attributes($fid, '', '', '');
947                    # Add essentiality and virulence attributes.
948                    if ($fig->essential($fid)) {
949                        push @attributeList, [$fid, 'essential', 1, ''];
950                    }
951                    if ($fig->virulent($fid)) {
952                        push @attributeList, [$fid, 'virulent', 1, ''];
953                    }
954                  if (scalar @attributeList) {                  if (scalar @attributeList) {
955                      $featureCount++;                      $featureCount++;
956                  }                  }
# Line 1015  Line 1046 
1046          # Loop through the genomes.          # Loop through the genomes.
1047          for my $genomeID (sort keys %{$genomeHash}) {          for my $genomeID (sort keys %{$genomeHash}) {
1048              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);  
1049                  # 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
1050                  # from showing up for a single PEG's annotations.                  # from showing up for a single PEG's annotations.
1051                  my %seenTimestamps = ();                  my %seenTimestamps = ();
1052                  # Loop through the annotations.              # Get the genome's annotations.
1053                  for my $tuple ($fig->feature_annotations($peg, "raw")) {              my @annotations = $fig->read_all_annotations($genomeID);
1054                      my ($fid, $timestamp, $user, $text) = @{$tuple};              Trace("Processing annotations.") if T(2);
1055                for my $tuple (@annotations) {
1056                    # Get the annotation tuple.
1057                    my ($peg, $timestamp, $user, $text) = @{$tuple};
1058                      # Here we fix up the annotation text. "\r" is removed,                      # Here we fix up the annotation text. "\r" is removed,
1059                      # and "\t" and "\n" are escaped. Note we use the "s"                  # and "\t" and "\n" are escaped. Note we use the "gs"
1060                      # modifier so that new-lines inside the text do not                      # modifier so that new-lines inside the text do not
1061                      # stop the substitution search.                      # stop the substitution search.
1062                      $text =~ s/\r//gs;                      $text =~ s/\r//gs;
# Line 1039  Line 1069 
1069                          # 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
1070                          # the key is unique.                          # the key is unique.
1071                          my $keyStamp = $timestamp;                          my $keyStamp = $timestamp;
1072                          while ($seenTimestamps{$keyStamp}) {                      while ($seenTimestamps{"$peg:$keyStamp"}) {
1073                              $keyStamp++;                              $keyStamp++;
1074                          }                          }
                         $seenTimestamps{$keyStamp} = 1;  
1075                          my $annotationID = "$peg:$keyStamp";                          my $annotationID = "$peg:$keyStamp";
1076                        $seenTimestamps{$annotationID} = 1;
1077                          # Insure the user exists.                          # Insure the user exists.
1078                          if (! $users{$user}) {                          if (! $users{$user}) {
1079                              $loadSproutUser->Put($user, "SEED user");                              $loadSproutUser->Put($user, "SEED user");
# Line 1061  Line 1091 
1091                  }                  }
1092              }              }
1093          }          }
     }  
1094      # Finish the load.      # Finish the load.
1095      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
1096      return $retVal;      return $retVal;
# Line 1190  Line 1219 
1219      } else {      } else {
1220          Trace("Generating external data.") if T(2);          Trace("Generating external data.") if T(2);
1221          # We loop through the files one at a time. First, the organism file.          # We loop through the files one at a time. First, the organism file.
1222          Open(\*ORGS, "<$FIG_Config::global/ext_org.table");          Open(\*ORGS, "sort +0 -1 -u -t\"\t\" $FIG_Config::global/ext_org.table |");
1223          my $orgLine;          my $orgLine;
1224          while (defined($orgLine = <ORGS>)) {          while (defined($orgLine = <ORGS>)) {
1225              # Clean the input line.              # Clean the input line.
# Line 1202  Line 1231 
1231          close ORGS;          close ORGS;
1232          # Now the function file.          # Now the function file.
1233          my $funcLine;          my $funcLine;
1234          Open(\*FUNCS, "<$FIG_Config::global/ext_func.table");          Open(\*FUNCS, "sort +0 -1 -u -t\"\t\" $FIG_Config::global/ext_func.table |");
1235          while (defined($funcLine = <FUNCS>)) {          while (defined($funcLine = <FUNCS>)) {
1236              # Clean the line ending.              # Clean the line ending.
1237              chomp $funcLine;              chomp $funcLine;
# Line 1334  Line 1363 
1363    
1364      GenomeGroups      GenomeGroups
1365    
1366  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,
1367    butThere is no direct support for genome groups in FIG, so we access the SEED
1368  files directly.  files directly.
1369    
1370  =over 4  =over 4
# Line 1360  Line 1390 
1390          Trace("Loading from existing files.") if T(2);          Trace("Loading from existing files.") if T(2);
1391      } else {      } else {
1392          Trace("Generating group data.") if T(2);          Trace("Generating group data.") if T(2);
1393            # Currently there are no groups.
1394        }
1395        # Finish the load.
1396        my $retVal = $self->_FinishAll();
1397        return $retVal;
1398    }
1399    
1400    =head3 LoadSynonymData
1401    
1402    C<< my $stats = $spl->LoadSynonymData(); >>
1403    
1404    Load the synonym groups into Sprout.
1405    
1406    The following relations are loaded by this method.
1407    
1408        SynonymGroup
1409        IsSynonymGroupFor
1410    
1411    The source information for these relations is taken from the C<maps_to_id> method
1412    of the B<FIG> object. Unfortunately, to make this work, we need to use direct
1413    SQL against the FIG database.
1414    
1415    =over 4
1416    
1417    =item RETURNS
1418    
1419    Returns a statistics object for the loads.
1420    
1421    =back
1422    
1423    =cut
1424    #: Return Type $%;
1425    sub LoadSynonymData {
1426        # Get this object instance.
1427        my ($self) = @_;
1428        # Get the FIG object.
1429        my $fig = $self->{fig};
1430        # Get the genome hash.
1431        my $genomeHash = $self->{genomes};
1432        # Create a load object for the table we're loading.
1433        my $loadSynonymGroup = $self->_TableLoader('SynonymGroup');
1434        my $loadIsSynonymGroupFor = $self->_TableLoader('IsSynonymGroupFor');
1435        if ($self->{options}->{loadOnly}) {
1436            Trace("Loading from existing files.") if T(2);
1437        } else {
1438            Trace("Generating synonym group data.") if T(2);
1439            # Get the database handle.
1440            my $dbh = $fig->db_handle();
1441            # Ask for the synonyms.
1442            my $sth = $dbh->prepare_command("SELECT maps_to, syn_id FROM peg_synonyms ORDER BY maps_to");
1443            my $result = $sth->execute();
1444            if (! defined($result)) {
1445                Confess("Database error in Synonym load: " . $sth->errstr());
1446            } else {
1447                # Remember the current synonym.
1448                my $current_syn = "";
1449                # Count the features.
1450                my $featureCount = 0;
1451                # Loop through the synonym/peg pairs.
1452                while (my @row = $sth->fetchrow()) {
1453                    # Get the synonym ID and feature ID.
1454                    my ($syn_id, $peg) = @row;
1455                    # Insure it's for one of our genomes.
1456                    my $genomeID = FIG::genome_of($peg);
1457                    if (exists $genomeHash->{$genomeID}) {
1458                        # Verify the synonym.
1459                        if ($syn_id ne $current_syn) {
1460                            # It's new, so put it in the group table.
1461                            $loadSynonymGroup->Put($syn_id);
1462                            $current_syn = $syn_id;
1463                        }
1464                        # Connect the synonym to the peg.
1465                        $loadIsSynonymGroupFor->Put($syn_id, $peg);
1466                        # Count this feature.
1467                        $featureCount++;
1468                        if ($featureCount % 1000 == 0) {
1469                            Trace("$featureCount features processed.") if T(3);
1470                        }
1471                    }
1472                }
1473            }
1474        }
1475        # Finish the load.
1476        my $retVal = $self->_FinishAll();
1477        return $retVal;
1478    }
1479    
1480    =head3 LoadFamilyData
1481    
1482    C<< my $stats = $spl->LoadFamilyData(); >>
1483    
1484    Load the protein families into Sprout.
1485    
1486    The following relations are loaded by this method.
1487    
1488        Family
1489        IsFamilyForFeature
1490    
1491    The source information for these relations is taken from the C<families_for_protein>,
1492    C<family_function>, and C<sz_family> methods of the B<FIG> object.
1493    
1494    =over 4
1495    
1496    =item RETURNS
1497    
1498    Returns a statistics object for the loads.
1499    
1500    =back
1501    
1502    =cut
1503    #: Return Type $%;
1504    sub LoadFamilyData {
1505        # Get this object instance.
1506        my ($self) = @_;
1507        # Get the FIG object.
1508        my $fig = $self->{fig};
1509        # Get the genome hash.
1510        my $genomeHash = $self->{genomes};
1511        # Create load objects for the tables we're loading.
1512        my $loadFamily = $self->_TableLoader('Family');
1513        my $loadIsFamilyForFeature = $self->_TableLoader('IsFamilyForFeature');
1514        if ($self->{options}->{loadOnly}) {
1515            Trace("Loading from existing files.") if T(2);
1516        } else {
1517            Trace("Generating family data.") if T(2);
1518            # Create a hash for the family IDs.
1519            my %familyHash = ();
1520          # Loop through the genomes.          # Loop through the genomes.
1521          my $line;          for my $genomeID (sort keys %{$genomeHash}) {
1522          for my $genomeID (keys %{$genomeHash}) {              Trace("Processing features for $genomeID.") if T(2);
1523              Trace("Processing $genomeID.") if T(3);              # Loop through this genome's PEGs.
1524              # Open the NMPDR group file for this genome.              for my $fid ($fig->all_features($genomeID, "peg")) {
1525              if (open(TMP, "<$FIG_Config::organisms/$genomeID/NMPDR") &&                  $loadIsFamilyForFeature->Add("features", 1);
1526                  defined($line = <TMP>)) {                  # Get this feature's families.
1527                  # Clean the line ending.                  my @families = $fig->families_for_protein($fid);
1528                  chomp $line;                  # Loop through the families, connecting them to the feature.
1529                  # Add the group to the table. Note that there can only be one group                  for my $family (@families) {
1530                  # per genome.                      $loadIsFamilyForFeature->Put($family, $fid);
1531                  $loadGenomeGroups->Put($genomeID, $line);                      # If this is a new family, create a record for it.
1532                        if (! exists $familyHash{$family}) {
1533                            $familyHash{$family} = 1;
1534                            $loadFamily->Add("families", 1);
1535                            my $size = $fig->sz_family($family);
1536                            my $func = $fig->family_function($family);
1537                            $loadFamily->Put($family, $size, $func);
1538                        }
1539                    }
1540              }              }
             close TMP;  
1541          }          }
1542      }      }
1543      # Finish the load.      # Finish the load.
# Line 1381  Line 1545 
1545      return $retVal;      return $retVal;
1546  }  }
1547    
1548    
1549    
1550  =head2 Internal Utility Methods  =head2 Internal Utility Methods
1551    
1552  =head3 TableLoader  =head3 TableLoader
# Line 1448  Line 1614 
1614      my $retVal = Stats->new();      my $retVal = Stats->new();
1615      # Get the loader list.      # Get the loader list.
1616      my $loadList = $self->{loaders};      my $loadList = $self->{loaders};
1617        # Create a hash to hold the statistics objects, keyed on relation name.
1618        my %loaderHash = ();
1619      # 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
1620      # 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.
1621      while (my $loader = pop @{$loadList}) {      while (my $loader = pop @{$loadList}) {
1622          # Get the relation name.          # Get the relation name.
1623          my $relName = $loader->RelName;          my $relName = $loader->RelName;
# Line 1460  Line 1628 
1628              # Here we really need to finish.              # Here we really need to finish.
1629              Trace("Finishing $relName.") if T(2);              Trace("Finishing $relName.") if T(2);
1630              my $stats = $loader->Finish();              my $stats = $loader->Finish();
1631              if ($self->{options}->{dbLoad} && ! $loader->Ignore) {              $loaderHash{$relName} = $stats;
1632            }
1633        }
1634        # Now we loop through again, actually loading the tables. We want to finish before
1635        # loading so that if something goes wrong at this point, all the load files are usable
1636        # and we don't have to redo all that work.
1637        for my $relName (sort keys %loaderHash) {
1638            # Get the statistics for this relation.
1639            my $stats = $loaderHash{$relName};
1640            # Check for a database load.
1641            if ($self->{options}->{dbLoad}) {
1642                  # 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.
1643                  Trace("Loading relation $relName.") if T(2);                  Trace("Loading relation $relName.") if T(2);
1644                  my $newStats = $self->{sprout}->LoadUpdate(1, [$relName]);                  my $newStats = $self->{sprout}->LoadUpdate(1, [$relName]);
# Line 1470  Line 1648 
1648              $retVal->Accumulate($stats);              $retVal->Accumulate($stats);
1649              Trace("Statistics for $relName:\n" . $stats->Show()) if T(2);              Trace("Statistics for $relName:\n" . $stats->Show()) if T(2);
1650          }          }
     }  
1651      # Return the load statistics.      # Return the load statistics.
1652      return $retVal;      return $retVal;
1653  }  }

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