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revision 1.26, Mon Jan 30 21:57:02 2006 UTC revision 1.65, Sun Aug 27 00:05:45 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 250  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              # Output the genome record.              # Output the genome record.
# Line 330  Line 340 
340      my $fig = $self->{fig};      my $fig = $self->{fig};
341      # Get the genome hash.      # Get the genome hash.
342      my $genomeFilter = $self->{genomes};      my $genomeFilter = $self->{genomes};
343      my $genomeCount = (keys %{$genomeFilter});      # Set up an ID counter for the PCHs.
344      my $featureCount = $genomeCount * 4000;      my $pchID = 0;
345      # Start the loads.      # Start the loads.
346      my $loadCoupling = $self->_TableLoader('Coupling');      my $loadCoupling = $self->_TableLoader('Coupling');
347      my $loadIsEvidencedBy = $self->_TableLoader('IsEvidencedBy', $self->PrimaryOnly);      my $loadIsEvidencedBy = $self->_TableLoader('IsEvidencedBy', $self->PrimaryOnly);
# Line 365  Line 375 
375                  for my $coupleData (@couplings) {                  for my $coupleData (@couplings) {
376                      my ($peg2, $score) = @{$coupleData};                      my ($peg2, $score) = @{$coupleData};
377                      # Compute the coupling ID.                      # Compute the coupling ID.
378                      my $coupleID = Sprout::CouplingID($peg1, $peg2);                      my $coupleID = $self->{erdb}->CouplingID($peg1, $peg2);
379                      if (! exists $dupHash{$coupleID}) {                      if (! exists $dupHash{$coupleID}) {
380                          $loadCoupling->Add("couplingIn");                          $loadCoupling->Add("couplingIn");
381                          # 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 411 
411                              }                              }
412                          }                          }
413                          for my $evidenceID (keys %evidenceMap) {                          for my $evidenceID (keys %evidenceMap) {
414                                # Get the ID for this evidence.
415                                $pchID++;
416                              # Create the evidence record.                              # Create the evidence record.
417                              my ($peg3, $peg4, $usage) = @{$evidenceMap{$evidenceID}};                              my ($peg3, $peg4, $usage) = @{$evidenceMap{$evidenceID}};
418                              $loadPCH->Put($evidenceID, $usage);                              $loadPCH->Put($pchID, $usage);
419                              # Connect it to the coupling.                              # Connect it to the coupling.
420                              $loadIsEvidencedBy->Put($coupleID, $evidenceID);                              $loadIsEvidencedBy->Put($coupleID, $pchID);
421                              # Connect it to the features.                              # Connect it to the features.
422                              $loadUsesAsEvidence->Put($evidenceID, $peg3, 1);                              $loadUsesAsEvidence->Put($pchID, $peg3, 1);
423                              $loadUsesAsEvidence->Put($evidenceID, $peg4, 2);                              $loadUsesAsEvidence->Put($pchID, $peg4, 2);
424                          }                          }
425                      }                      }
426                  }                  }
# Line 436  Line 448 
448      FeatureTranslation      FeatureTranslation
449      FeatureUpstream      FeatureUpstream
450      IsLocatedIn      IsLocatedIn
451        HasFeature
452    
453  =over 4  =over 4
454    
# Line 461  Line 474 
474      my $loadFeatureLink = $self->_TableLoader('FeatureLink');      my $loadFeatureLink = $self->_TableLoader('FeatureLink');
475      my $loadFeatureTranslation = $self->_TableLoader('FeatureTranslation');      my $loadFeatureTranslation = $self->_TableLoader('FeatureTranslation');
476      my $loadFeatureUpstream = $self->_TableLoader('FeatureUpstream');      my $loadFeatureUpstream = $self->_TableLoader('FeatureUpstream');
477        my $loadHasFeature = $self->_TableLoader('HasFeature');
478      # 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
479      # locations.      # locations.
480      my $chunkSize = $self->{sprout}->MaxSegment();      my $chunkSize = $self->{sprout}->MaxSegment();
# Line 474  Line 488 
488              $loadFeature->Add("genomeIn");              $loadFeature->Add("genomeIn");
489              # Get the feature list for this genome.              # Get the feature list for this genome.
490              my $features = $fig->all_features_detailed($genomeID);              my $features = $fig->all_features_detailed($genomeID);
491                # Sort and count the list.
492                my @featureTuples = sort { $a->[0] cmp $b->[0] } @{$features};
493                my $count = scalar @featureTuples;
494                Trace("$count features found for genome $genomeID.") if T(3);
495                # Set up for our duplicate-feature check.
496                my $oldFeatureID = "";
497              # Loop through the features.              # Loop through the features.
498              for my $featureData (@{$features}) {              for my $featureTuple (@featureTuples) {
                 $loadFeature->Add("featureIn");  
499                  # Split the tuple.                  # Split the tuple.
500                  my ($featureID, $locations, undef, $type) = @{$featureData};                  my ($featureID, $locations, undef, $type) = @{$featureTuple};
501                    # Check for duplicates.
502                    if ($featureID eq $oldFeatureID) {
503                        Trace("Duplicate feature $featureID found.") if T(1);
504                    } else {
505                        $oldFeatureID = $featureID;
506                        # Count this feature.
507                        $loadFeature->Add("featureIn");
508                  # Create the feature record.                  # Create the feature record.
509                  $loadFeature->Put($featureID, 1, $type);                  $loadFeature->Put($featureID, 1, $type);
510                        # Link it to the parent genome.
511                        $loadHasFeature->Put($genomeID, $featureID, $type);
512                  # Create the aliases.                  # Create the aliases.
513                  for my $alias ($fig->feature_aliases($featureID)) {                  for my $alias ($fig->feature_aliases($featureID)) {
514                      $loadFeatureAlias->Put($featureID, $alias);                      $loadFeatureAlias->Put($featureID, $alias);
# Line 532  Line 560 
560              }              }
561          }          }
562      }      }
563        }
564      # Finish the loads.      # Finish the loads.
565      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
566      return $retVal;      return $retVal;
# Line 580  Line 609 
609              Trace("Processing features for genome $genomeID.") if T(3);              Trace("Processing features for genome $genomeID.") if T(3);
610              # Get the feature list for this genome.              # Get the feature list for this genome.
611              my $features = $fig->all_features_detailed($genomeID);              my $features = $fig->all_features_detailed($genomeID);
612                # Count the BBHs we find.
613                my $bbhCount = 0;
614              # Loop through the features.              # Loop through the features.
615              for my $featureData (@{$features}) {              for my $featureData (@{$features}) {
616                  # Split the tuple.                  # Split the tuple.
# Line 595  Line 626 
626                      if ($genomeHash->{$targetGenomeID}) {                      if ($genomeHash->{$targetGenomeID}) {
627                          $loadIsBidirectionalBestHitOf->Put($featureID, $targetID, $targetGenomeID,                          $loadIsBidirectionalBestHitOf->Put($featureID, $targetID, $targetGenomeID,
628                                                             $score);                                                             $score);
629                            $bbhCount++;
630                      }                      }
631                  }                  }
632              }              }
633                Trace("$bbhCount BBHs found for $genomeID.") if T(3);
634          }          }
635      }      }
636      # Finish the loads.      # Finish the loads.
# Line 620  Line 653 
653  The following relations are loaded by this method.  The following relations are loaded by this method.
654    
655      Subsystem      Subsystem
656        SubsystemClass
657      Role      Role
658      RoleEC      RoleEC
659      SSCell      SSCell
# Line 682  Line 716 
716      my $loadConsistsOfGenomes = $self->_TableLoader('ConsistsOfGenomes', $self->PrimaryOnly);      my $loadConsistsOfGenomes = $self->_TableLoader('ConsistsOfGenomes', $self->PrimaryOnly);
717      my $loadHasRoleSubset = $self->_TableLoader('HasRoleSubset', $self->PrimaryOnly);      my $loadHasRoleSubset = $self->_TableLoader('HasRoleSubset', $self->PrimaryOnly);
718      my $loadHasGenomeSubset = $self->_TableLoader('HasGenomeSubset', $self->PrimaryOnly);      my $loadHasGenomeSubset = $self->_TableLoader('HasGenomeSubset', $self->PrimaryOnly);
719        my $loadSubsystemClass = $self->_TableLoader('SubsystemClass', $self->PrimaryOnly);
720      if ($self->{options}->{loadOnly}) {      if ($self->{options}->{loadOnly}) {
721          Trace("Loading from existing files.") if T(2);          Trace("Loading from existing files.") if T(2);
722      } else {      } else {
# Line 697  Line 732 
732          my ($genomeID, $roleID);          my ($genomeID, $roleID);
733          my %roleData = ();          my %roleData = ();
734          for my $subsysID (@subsysIDs) {          for my $subsysID (@subsysIDs) {
             Trace("Creating subsystem $subsysID.") if T(3);  
             $loadSubsystem->Add("subsystemIn");  
735              # Get the subsystem object.              # Get the subsystem object.
736              my $sub = $fig->get_subsystem($subsysID);              my $sub = $fig->get_subsystem($subsysID);
737                # Only proceed if the subsystem has a spreadsheet.
738                if (! $sub->{empty_ss}) {
739                    Trace("Creating subsystem $subsysID.") if T(3);
740                    $loadSubsystem->Add("subsystemIn");
741              # Create the subsystem record.              # Create the subsystem record.
742              my $curator = $sub->get_curator();              my $curator = $sub->get_curator();
743              my $notes = $sub->get_notes();              my $notes = $sub->get_notes();
744              $loadSubsystem->Put($subsysID, $curator, $notes);              $loadSubsystem->Put($subsysID, $curator, $notes);
745                    my $classList = $fig->subsystem_classification($subsysID);
746                    my @classes = @$classList;
747                    if (@classes) {
748                        for my $class (@classes) {
749                            $loadSubsystemClass->Put($subsysID, $class);
750                        }
751                    }
752              # 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.
753              for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {              for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {
754                  # Connect to this role.                  # Connect to this role.
# Line 748  Line 792 
792                      # part of the spreadsheet cell ID.                      # part of the spreadsheet cell ID.
793                      for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {                      for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {
794                          # Get the features in the spreadsheet cell for this genome and role.                          # Get the features in the spreadsheet cell for this genome and role.
795                          my @pegs = $sub->get_pegs_from_cell($row, $col);                              my @pegs = grep { !$fig->is_deleted_fid($_) } $sub->get_pegs_from_cell($row, $col);
796                          # Only proceed if features exist.                          # Only proceed if features exist.
797                          if (@pegs > 0) {                          if (@pegs > 0) {
798                              # Create the spreadsheet cell.                              # Create the spreadsheet cell.
# Line 769  Line 813 
813                      if ($pegCount > 0) {                      if ($pegCount > 0) {
814                          Trace("$pegCount PEGs in $cellCount cells for $genomeID.") if T(3);                          Trace("$pegCount PEGs in $cellCount cells for $genomeID.") if T(3);
815                          $loadParticipatesIn->Put($genomeID, $subsysID, $variantCode);                          $loadParticipatesIn->Put($genomeID, $subsysID, $variantCode);
                         # Partition the PEGs found into clusters.  
                         my @clusters = $fig->compute_clusters(\@pegsFound, $sub);  
816                          # Create a hash mapping PEG IDs to cluster numbers.                          # Create a hash mapping PEG IDs to cluster numbers.
817                          # We default to -1 for all of them.                          # We default to -1 for all of them.
818                          my %clusterOf = map { $_ => -1 } @pegsFound;                          my %clusterOf = map { $_ => -1 } @pegsFound;
819                                # Partition the PEGs found into clusters.
820                                my @clusters = $fig->compute_clusters([keys %clusterOf], $sub);
821                          for (my $i = 0; $i <= $#clusters; $i++) {                          for (my $i = 0; $i <= $#clusters; $i++) {
822                              my $subList = $clusters[$i];                              my $subList = $clusters[$i];
823                              for my $peg (@{$subList}) {                              for my $peg (@{$subList}) {
# Line 801  Line 845 
845                  # Connect the subset to the subsystem.                  # Connect the subset to the subsystem.
846                  $loadHasRoleSubset->Put($subsysID, $actualID);                  $loadHasRoleSubset->Put($subsysID, $actualID);
847                  # Connect the subset to its roles.                  # Connect the subset to its roles.
848                  my @roles = $sub->get_subset($subsetID);                      my @roles = $sub->get_subsetC_roles($subsetID);
849                  for my $roleID (@roles) {                  for my $roleID (@roles) {
850                      $loadConsistsOfRoles->Put($actualID, $roleID);                      $loadConsistsOfRoles->Put($actualID, $roleID);
851                  }                  }
# Line 821  Line 865 
865                  }                  }
866              }              }
867          }          }
868            }
869          # 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
870          # 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
871          # in subsystems (and therefore appear in the %ecToRoles hash) are          # in subsystems (and therefore appear in the %ecToRoles hash) are
# Line 1015  Line 1060 
1060          # Loop through the genomes.          # Loop through the genomes.
1061          for my $genomeID (sort keys %{$genomeHash}) {          for my $genomeID (sort keys %{$genomeHash}) {
1062              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);  
1063                  # 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
1064                  # from showing up for a single PEG's annotations.                  # from showing up for a single PEG's annotations.
1065                  my %seenTimestamps = ();                  my %seenTimestamps = ();
1066                  # Loop through the annotations.              # Get the genome's annotations.
1067                  for my $tuple ($fig->feature_annotations($peg, "raw")) {              my @annotations = $fig->read_all_annotations($genomeID);
1068                      my ($fid, $timestamp, $user, $text) = @{$tuple};              Trace("Processing annotations.") if T(2);
1069                for my $tuple (@annotations) {
1070                    # Get the annotation tuple.
1071                    my ($peg, $timestamp, $user, $text) = @{$tuple};
1072                      # Here we fix up the annotation text. "\r" is removed,                      # Here we fix up the annotation text. "\r" is removed,
1073                      # and "\t" and "\n" are escaped. Note we use the "s"                  # and "\t" and "\n" are escaped. Note we use the "gs"
1074                      # modifier so that new-lines inside the text do not                      # modifier so that new-lines inside the text do not
1075                      # stop the substitution search.                      # stop the substitution search.
1076                      $text =~ s/\r//gs;                      $text =~ s/\r//gs;
# Line 1039  Line 1083 
1083                          # 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
1084                          # the key is unique.                          # the key is unique.
1085                          my $keyStamp = $timestamp;                          my $keyStamp = $timestamp;
1086                          while ($seenTimestamps{$keyStamp}) {                      while ($seenTimestamps{"$peg:$keyStamp"}) {
1087                              $keyStamp++;                              $keyStamp++;
1088                          }                          }
                         $seenTimestamps{$keyStamp} = 1;  
1089                          my $annotationID = "$peg:$keyStamp";                          my $annotationID = "$peg:$keyStamp";
1090                        $seenTimestamps{$annotationID} = 1;
1091                          # Insure the user exists.                          # Insure the user exists.
1092                          if (! $users{$user}) {                          if (! $users{$user}) {
1093                              $loadSproutUser->Put($user, "SEED user");                              $loadSproutUser->Put($user, "SEED user");
# Line 1061  Line 1105 
1105                  }                  }
1106              }              }
1107          }          }
     }  
1108      # Finish the load.      # Finish the load.
1109      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
1110      return $retVal;      return $retVal;
# Line 1190  Line 1233 
1233      } else {      } else {
1234          Trace("Generating external data.") if T(2);          Trace("Generating external data.") if T(2);
1235          # We loop through the files one at a time. First, the organism file.          # We loop through the files one at a time. First, the organism file.
1236          Open(\*ORGS, "<$FIG_Config::global/ext_org.table");          Open(\*ORGS, "sort +0 -1 -u -t\"\t\" $FIG_Config::global/ext_org.table |");
1237          my $orgLine;          my $orgLine;
1238          while (defined($orgLine = <ORGS>)) {          while (defined($orgLine = <ORGS>)) {
1239              # Clean the input line.              # Clean the input line.
# Line 1202  Line 1245 
1245          close ORGS;          close ORGS;
1246          # Now the function file.          # Now the function file.
1247          my $funcLine;          my $funcLine;
1248          Open(\*FUNCS, "<$FIG_Config::global/ext_func.table");          Open(\*FUNCS, "sort +0 -1 -u -t\"\t\" $FIG_Config::global/ext_func.table |");
1249          while (defined($funcLine = <FUNCS>)) {          while (defined($funcLine = <FUNCS>)) {
1250              # Clean the line ending.              # Clean the line ending.
1251              chomp $funcLine;              chomp $funcLine;
# Line 1381  Line 1424 
1424      return $retVal;      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.
1548            for my $genomeID (sort keys %{$genomeHash}) {
1549                Trace("Processing features for $genomeID.") if T(2);
1550                # Loop through this genome's PEGs.
1551                for my $fid ($fig->all_features($genomeID, "peg")) {
1552                    $loadIsFamilyForFeature->Add("features", 1);
1553                    # Get this feature's families.
1554                    my @families = $fig->families_for_protein($fid);
1555                    # Loop through the families, connecting them to the feature.
1556                    for my $family (@families) {
1557                        $loadIsFamilyForFeature->Put($family, $fid);
1558                        # 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                }
1568            }
1569        }
1570        # Finish the load.
1571        my $retVal = $self->_FinishAll();
1572        return $retVal;
1573    }
1574    
1575  =head2 Internal Utility Methods  =head2 Internal Utility Methods
1576    
1577  =head3 TableLoader  =head3 TableLoader
# Line 1448  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          # Get the relation name.          # Get the relation name.
1648          my $relName = $loader->RelName;          my $relName = $loader->RelName;
# Line 1460  Line 1653 
1653              # Here we really need to finish.              # 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 = $loader->Finish();
1656              if ($self->{options}->{dbLoad} && ! $loader->Ignore) {              $loaderHash{$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}) {
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);
1669                  my $newStats = $self->{sprout}->LoadUpdate(1, [$relName]);                  my $newStats = $self->{sprout}->LoadUpdate(1, [$relName]);
# Line 1470  Line 1673 
1673              $retVal->Accumulate($stats);              $retVal->Accumulate($stats);
1674              Trace("Statistics for $relName:\n" . $stats->Show()) if T(2);              Trace("Statistics for $relName:\n" . $stats->Show()) if T(2);
1675          }          }
     }  
1676      # Return the load statistics.      # Return the load statistics.
1677      return $retVal;      return $retVal;
1678  }  }

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