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revision 1.40, Thu Jun 8 15:37:32 2006 UTC revision 1.74, Sat Oct 21 06:44:17 2006 UTC
# Line 120  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 136  Line 136 
136      # We only need it if load-only is NOT specified.      # We only need it if load-only is NOT specified.
137      if (! $options->{loadOnly}) {      if (! $options->{loadOnly}) {
138          if (! defined $subsysFile || $subsysFile eq '') {          if (! defined $subsysFile || $subsysFile eq '') {
139              # Here we want all the NMPDR subsystems. First we get the whole list.              # Here we want all the usable subsystems. First we get the whole list.
140              my @subs = $fig->all_subsystems();              my @subs = $fig->all_subsystems();
141              # Loop through, checking for the NMPDR file.              # Loop through, checking for usability.
142              for my $sub (@subs) {              for my $sub (@subs) {
143                  if (-e "$FIG_Config::data/Subsystems/$sub/NMPDR") {                  if ($fig->usable_subsystem($sub)) {
144                      $subsystems{$sub} = 1;                      $subsystems{$sub} = 1;
145                  }                  }
146              }              }
# Line 163  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();
# Line 266  Line 275 
275              my $extra = join " ", @extraData;              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 340  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 375  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 411  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, $peg4, 2);
444                          }                          }
445                      }                      }
446                  }                  }
# Line 447  Line 469 
469      FeatureUpstream      FeatureUpstream
470      IsLocatedIn      IsLocatedIn
471      HasFeature      HasFeature
472        HasRoleInSubsystem
473    
474  =over 4  =over 4
475    
# Line 461  Line 484 
484  sub LoadFeatureData {  sub LoadFeatureData {
485      # Get this object instance.      # Get this object instance.
486      my ($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 472  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');      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 486  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                  # Link it to the parent genome.                      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);                  $loadHasFeature->Put($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 517  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 546  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 634  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 696  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 721  Line 723 
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)); $col++) {
733                      # Connect to this role.                      # Connect to this role.
# Line 785  Line 792 
792                          if ($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 837  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 870  Line 878 
878                  }                  }
879              }              }
880          }          }
     }  
881      # Finish the load.      # Finish the load.
882      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
883      return $retVal;      return $retVal;
# Line 923  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 937  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++;                      $featureCount++;
956                  }                  }
# Line 1042  Line 1056 
1056                  # Get the annotation tuple.                  # Get the annotation tuple.
1057                  my ($peg, $timestamp, $user, $text) = @{$tuple};                  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;                  $text =~ s/\r//gs;
# Line 1205  Line 1219 
1219      } else {      } else {
1220          Trace("Generating external data.") if T(2);          Trace("Generating external data.") if T(2);
1221          # We loop through the files one at a time. First, the organism file.          # We loop through the files one at a time. First, the organism file.
1222          Open(\*ORGS, "<$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 1217  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 1349  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 1375  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 1396  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 1463  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 1475  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                $loaderHash{$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 ($self->{options}->{dbLoad}) {              if ($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);
# Line 1485  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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