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revision 1.30, Sun Mar 26 12:35:21 2006 UTC revision 1.68, Sun Sep 24 17:14:16 2006 UTC
# Line 30  Line 30 
30      $stats->Accumulate($spl->LoadFeatureData());      $stats->Accumulate($spl->LoadFeatureData());
31      print $stats->Show();      print $stats->Show();
32    
 This module makes use of the internal Sprout property C<_erdb>.  
   
33  It is worth noting that the FIG object does not need to be a real one. Any object  It is worth noting that the FIG object does not need to be a real one. Any object
34  that implements the FIG methods for data retrieval could be used. So, for example,  that implements the FIG methods for data retrieval could be used. So, for example,
35  this object could be used to copy data from one Sprout database to another, or  this object could be used to copy data from one Sprout database to another, or
# Line 80  Line 78 
78  =item subsysFile  =item subsysFile
79    
80  Either the name of the file containing the list of trusted subsystems or a reference  Either the name of the file containing the list of trusted subsystems or a reference
81  to a list of subsystem names. If nothing is specified, all known subsystems will be  to a list of subsystem names. If nothing is specified, all NMPDR subsystems will be
82  considered trusted. Only subsystem data related to the trusted subsystems is loaded.  considered trusted. (A subsystem is considered NMPDR if it has a file named C<NMPDR>
83    in its data directory.) Only subsystem data related to the trusted subsystems is loaded.
84    
85  =item options  =item options
86    
# Line 94  Line 93 
93  sub new {  sub new {
94      # Get the parameters.      # Get the parameters.
95      my ($class, $sprout, $fig, $genomeFile, $subsysFile, $options) = @_;      my ($class, $sprout, $fig, $genomeFile, $subsysFile, $options) = @_;
96      # Load the list of genomes into a hash.      # Create the genome hash.
97      my %genomes;      my %genomes = ();
98        # We only need it if load-only is NOT specified.
99        if (! $options->{loadOnly}) {
100      if (! defined($genomeFile) || $genomeFile eq '') {      if (! defined($genomeFile) || $genomeFile eq '') {
101          # Here we want all the complete genomes and an access code of 1.          # Here we want all the complete genomes and an access code of 1.
102          my @genomeList = $fig->genomes(1);          my @genomeList = $fig->genomes(1);
# Line 119  Line 120 
120                  # an omitted access code can be defaulted to 1.                  # an omitted access code can be defaulted to 1.
121                  for my $genomeLine (@genomeList) {                  for my $genomeLine (@genomeList) {
122                      my ($genomeID, $accessCode) = split("\t", $genomeLine);                      my ($genomeID, $accessCode) = split("\t", $genomeLine);
123                      if (undef $accessCode) {                          if (! defined($accessCode)) {
124                          $accessCode = 1;                          $accessCode = 1;
125                      }                      }
126                      $genomes{$genomeID} = $accessCode;                      $genomes{$genomeID} = $accessCode;
# Line 129  Line 130 
130              Confess("Invalid genome parameter ($type) in SproutLoad constructor.");              Confess("Invalid genome parameter ($type) in SproutLoad constructor.");
131          }          }
132      }      }
133        }
134      # Load the list of trusted subsystems.      # Load the list of trusted subsystems.
135      my %subsystems = ();      my %subsystems = ();
136        # We only need it if load-only is NOT specified.
137        if (! $options->{loadOnly}) {
138      if (! defined $subsysFile || $subsysFile eq '') {      if (! defined $subsysFile || $subsysFile eq '') {
139          # Here we want all the subsystems.              # Here we want all the usable subsystems. First we get the whole list.
140          %subsystems = map { $_ => 1 } $fig->all_subsystems();              my @subs = $fig->all_subsystems();
141                # Loop through, checking for usability.
142                for my $sub (@subs) {
143                    if ($fig->usable_subsystem($sub)) {
144                        $subsystems{$sub} = 1;
145                    }
146                }
147      } else {      } else {
148          my $type = ref $subsysFile;          my $type = ref $subsysFile;
149          if ($type eq 'ARRAY') {          if ($type eq 'ARRAY') {
# Line 153  Line 163 
163              Confess("Invalid subsystem parameter in SproutLoad constructor.");              Confess("Invalid subsystem parameter in SproutLoad constructor.");
164          }          }
165      }      }
166        }
167      # Get the data directory from the Sprout object.      # Get the data directory from the Sprout object.
168      my ($directory) = $sprout->LoadInfo();      my ($directory) = $sprout->LoadInfo();
169      # Create the Sprout load object.      # Create the Sprout load object.
# Line 162  Line 173 
173                    subsystems => \%subsystems,                    subsystems => \%subsystems,
174                    sprout => $sprout,                    sprout => $sprout,
175                    loadDirectory => $directory,                    loadDirectory => $directory,
176                    erdb => $sprout->{_erdb},                    erdb => $sprout,
177                    loaders => [],                    loaders => [],
178                    options => $options                    options => $options
179                   };                   };
# Line 255  Line 266 
266              my $extra = join " ", @extraData;              my $extra = join " ", @extraData;
267              # Get the full taxonomy.              # Get the full taxonomy.
268              my $taxonomy = $fig->taxonomy_of($genomeID);              my $taxonomy = $fig->taxonomy_of($genomeID);
269                # Open the NMPDR group file for this genome.
270                my $group;
271                if (open(TMP, "<$FIG_Config::organisms/$genomeID/NMPDR") &&
272                    defined($group = <TMP>)) {
273                    # Clean the line ending.
274                    chomp $group;
275                } else {
276                    # No group, so use the default.
277                    $group = $FIG_Config::otherGroup;
278                }
279                close TMP;
280              # Output the genome record.              # Output the genome record.
281              $loadGenome->Put($genomeID, $accessCode, $fig->is_complete($genomeID), $genus,              $loadGenome->Put($genomeID, $accessCode, $fig->is_complete($genomeID), $genus,
282                               $species, $extra, $taxonomy);                               $group, $species, $extra, $taxonomy);
283              # Now we loop through each of the genome's contigs.              # Now we loop through each of the genome's contigs.
284              my @contigs = $fig->all_contigs($genomeID);              my @contigs = $fig->all_contigs($genomeID);
285              for my $contigID (@contigs) {              for my $contigID (@contigs) {
# Line 329  Line 351 
351      my $fig = $self->{fig};      my $fig = $self->{fig};
352      # Get the genome hash.      # Get the genome hash.
353      my $genomeFilter = $self->{genomes};      my $genomeFilter = $self->{genomes};
354      my $genomeCount = (keys %{$genomeFilter});      # Set up an ID counter for the PCHs.
355      my $featureCount = $genomeCount * 4000;      my $pchID = 0;
356      # Start the loads.      # Start the loads.
357      my $loadCoupling = $self->_TableLoader('Coupling');      my $loadCoupling = $self->_TableLoader('Coupling');
358      my $loadIsEvidencedBy = $self->_TableLoader('IsEvidencedBy', $self->PrimaryOnly);      my $loadIsEvidencedBy = $self->_TableLoader('IsEvidencedBy', $self->PrimaryOnly);
# Line 364  Line 386 
386                  for my $coupleData (@couplings) {                  for my $coupleData (@couplings) {
387                      my ($peg2, $score) = @{$coupleData};                      my ($peg2, $score) = @{$coupleData};
388                      # Compute the coupling ID.                      # Compute the coupling ID.
389                      my $coupleID = Sprout::CouplingID($peg1, $peg2);                      my $coupleID = $self->{erdb}->CouplingID($peg1, $peg2);
390                      if (! exists $dupHash{$coupleID}) {                      if (! exists $dupHash{$coupleID}) {
391                          $loadCoupling->Add("couplingIn");                          $loadCoupling->Add("couplingIn");
392                          # Here we have a new coupling to store in the load files.                          # Here we have a new coupling to store in the load files.
# Line 400  Line 422 
422                              }                              }
423                          }                          }
424                          for my $evidenceID (keys %evidenceMap) {                          for my $evidenceID (keys %evidenceMap) {
425                                # Get the ID for this evidence.
426                                $pchID++;
427                              # Create the evidence record.                              # Create the evidence record.
428                              my ($peg3, $peg4, $usage) = @{$evidenceMap{$evidenceID}};                              my ($peg3, $peg4, $usage) = @{$evidenceMap{$evidenceID}};
429                              $loadPCH->Put($evidenceID, $usage);                              $loadPCH->Put($pchID, $usage);
430                              # Connect it to the coupling.                              # Connect it to the coupling.
431                              $loadIsEvidencedBy->Put($coupleID, $evidenceID);                              $loadIsEvidencedBy->Put($coupleID, $pchID);
432                              # Connect it to the features.                              # Connect it to the features.
433                              $loadUsesAsEvidence->Put($evidenceID, $peg3, 1);                              $loadUsesAsEvidence->Put($pchID, $peg3, 1);
434                              $loadUsesAsEvidence->Put($evidenceID, $peg4, 2);                              $loadUsesAsEvidence->Put($pchID, $peg4, 2);
435                          }                          }
436                      }                      }
437                  }                  }
# Line 475  Line 499 
499              $loadFeature->Add("genomeIn");              $loadFeature->Add("genomeIn");
500              # Get the feature list for this genome.              # Get the feature list for this genome.
501              my $features = $fig->all_features_detailed($genomeID);              my $features = $fig->all_features_detailed($genomeID);
502                # Sort and count the list.
503                my @featureTuples = sort { $a->[0] cmp $b->[0] } @{$features};
504                my $count = scalar @featureTuples;
505                Trace("$count features found for genome $genomeID.") if T(3);
506                # Set up for our duplicate-feature check.
507                my $oldFeatureID = "";
508              # Loop through the features.              # Loop through the features.
509              for my $featureData (@{$features}) {              for my $featureTuple (@featureTuples) {
                 $loadFeature->Add("featureIn");  
510                  # Split the tuple.                  # Split the tuple.
511                  my ($featureID, $locations, undef, $type) = @{$featureData};                  my ($featureID, $locations, undef, $type) = @{$featureTuple};
512                    # Check for duplicates.
513                    if ($featureID eq $oldFeatureID) {
514                        Trace("Duplicate feature $featureID found.") if T(1);
515                    } else {
516                        $oldFeatureID = $featureID;
517                        # Count this feature.
518                        $loadFeature->Add("featureIn");
519                        # Get the functional assignment.
520                        my $assignment = $fig->function_of($featureID);
521                  # Create the feature record.                  # Create the feature record.
522                  $loadFeature->Put($featureID, 1, $type);                      $loadFeature->Put($featureID, 1, $type, $assignment);
523                  # Link it to the parent genome.                  # Link it to the parent genome.
524                  $loadHasFeature->Put($genomeID, $featureID, $type);                  $loadHasFeature->Put($genomeID, $featureID, $type);
525                  # Create the aliases.                  # Create the aliases.
# Line 535  Line 573 
573              }              }
574          }          }
575      }      }
576        }
577      # Finish the loads.      # Finish the loads.
578      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
579      return $retVal;      return $retVal;
# Line 583  Line 622 
622              Trace("Processing features for genome $genomeID.") if T(3);              Trace("Processing features for genome $genomeID.") if T(3);
623              # Get the feature list for this genome.              # Get the feature list for this genome.
624              my $features = $fig->all_features_detailed($genomeID);              my $features = $fig->all_features_detailed($genomeID);
625                # Count the BBHs we find.
626                my $bbhCount = 0;
627              # Loop through the features.              # Loop through the features.
628              for my $featureData (@{$features}) {              for my $featureData (@{$features}) {
629                  # Split the tuple.                  # Split the tuple.
# Line 598  Line 639 
639                      if ($genomeHash->{$targetGenomeID}) {                      if ($genomeHash->{$targetGenomeID}) {
640                          $loadIsBidirectionalBestHitOf->Put($featureID, $targetID, $targetGenomeID,                          $loadIsBidirectionalBestHitOf->Put($featureID, $targetID, $targetGenomeID,
641                                                             $score);                                                             $score);
642                            $bbhCount++;
643                      }                      }
644                  }                  }
645              }              }
646                Trace("$bbhCount BBHs found for $genomeID.") if T(3);
647          }          }
648      }      }
649      # Finish the loads.      # Finish the loads.
# Line 623  Line 666 
666  The following relations are loaded by this method.  The following relations are loaded by this method.
667    
668      Subsystem      Subsystem
669        SubsystemClass
670      Role      Role
671      RoleEC      RoleEC
672      SSCell      SSCell
# Line 685  Line 729 
729      my $loadConsistsOfGenomes = $self->_TableLoader('ConsistsOfGenomes', $self->PrimaryOnly);      my $loadConsistsOfGenomes = $self->_TableLoader('ConsistsOfGenomes', $self->PrimaryOnly);
730      my $loadHasRoleSubset = $self->_TableLoader('HasRoleSubset', $self->PrimaryOnly);      my $loadHasRoleSubset = $self->_TableLoader('HasRoleSubset', $self->PrimaryOnly);
731      my $loadHasGenomeSubset = $self->_TableLoader('HasGenomeSubset', $self->PrimaryOnly);      my $loadHasGenomeSubset = $self->_TableLoader('HasGenomeSubset', $self->PrimaryOnly);
732        my $loadSubsystemClass = $self->_TableLoader('SubsystemClass', $self->PrimaryOnly);
733      if ($self->{options}->{loadOnly}) {      if ($self->{options}->{loadOnly}) {
734          Trace("Loading from existing files.") if T(2);          Trace("Loading from existing files.") if T(2);
735      } else {      } else {
# Line 700  Line 745 
745          my ($genomeID, $roleID);          my ($genomeID, $roleID);
746          my %roleData = ();          my %roleData = ();
747          for my $subsysID (@subsysIDs) {          for my $subsysID (@subsysIDs) {
             Trace("Creating subsystem $subsysID.") if T(3);  
             $loadSubsystem->Add("subsystemIn");  
748              # Get the subsystem object.              # Get the subsystem object.
749              my $sub = $fig->get_subsystem($subsysID);              my $sub = $fig->get_subsystem($subsysID);
750                # Only proceed if the subsystem has a spreadsheet.
751                if (! $sub->{empty_ss}) {
752                    Trace("Creating subsystem $subsysID.") if T(3);
753                    $loadSubsystem->Add("subsystemIn");
754              # Create the subsystem record.              # Create the subsystem record.
755              my $curator = $sub->get_curator();              my $curator = $sub->get_curator();
756              my $notes = $sub->get_notes();              my $notes = $sub->get_notes();
757              $loadSubsystem->Put($subsysID, $curator, $notes);              $loadSubsystem->Put($subsysID, $curator, $notes);
758                    my $classList = $fig->subsystem_classification($subsysID);
759                    my @classes = @$classList;
760                    if (@classes) {
761                        for my $class (@classes) {
762                            $loadSubsystemClass->Put($subsysID, $class);
763                        }
764                    }
765              # Connect it to its roles. Each role is a column in the subsystem spreadsheet.              # Connect it to its roles. Each role is a column in the subsystem spreadsheet.
766              for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {              for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {
767                  # Connect to this role.                  # Connect to this role.
# Line 751  Line 805 
805                      # part of the spreadsheet cell ID.                      # part of the spreadsheet cell ID.
806                      for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {                      for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {
807                          # Get the features in the spreadsheet cell for this genome and role.                          # Get the features in the spreadsheet cell for this genome and role.
808                          my @pegs = $sub->get_pegs_from_cell($row, $col);                              my @pegs = grep { !$fig->is_deleted_fid($_) } $sub->get_pegs_from_cell($row, $col);
809                          # Only proceed if features exist.                          # Only proceed if features exist.
810                          if (@pegs > 0) {                          if (@pegs > 0) {
811                              # Create the spreadsheet cell.                              # Create the spreadsheet cell.
# Line 772  Line 826 
826                      if ($pegCount > 0) {                      if ($pegCount > 0) {
827                          Trace("$pegCount PEGs in $cellCount cells for $genomeID.") if T(3);                          Trace("$pegCount PEGs in $cellCount cells for $genomeID.") if T(3);
828                          $loadParticipatesIn->Put($genomeID, $subsysID, $variantCode);                          $loadParticipatesIn->Put($genomeID, $subsysID, $variantCode);
                         # Partition the PEGs found into clusters.  
                         my @clusters = $fig->compute_clusters(\@pegsFound, $sub);  
829                          # Create a hash mapping PEG IDs to cluster numbers.                          # Create a hash mapping PEG IDs to cluster numbers.
830                          # We default to -1 for all of them.                          # We default to -1 for all of them.
831                          my %clusterOf = map { $_ => -1 } @pegsFound;                          my %clusterOf = map { $_ => -1 } @pegsFound;
832                                # Partition the PEGs found into clusters.
833                                my @clusters = $fig->compute_clusters([keys %clusterOf], $sub);
834                          for (my $i = 0; $i <= $#clusters; $i++) {                          for (my $i = 0; $i <= $#clusters; $i++) {
835                              my $subList = $clusters[$i];                              my $subList = $clusters[$i];
836                              for my $peg (@{$subList}) {                              for my $peg (@{$subList}) {
# Line 824  Line 878 
878                  }                  }
879              }              }
880          }          }
881            }
882          # Now we loop through the diagrams. We need to create the diagram records          # Now we loop through the diagrams. We need to create the diagram records
883          # and link each diagram to its roles. Note that only roles which occur          # and link each diagram to its roles. Note that only roles which occur
884          # in subsystems (and therefore appear in the %ecToRoles hash) are          # in subsystems (and therefore appear in the %ecToRoles hash) are
# Line 909  Line 964 
964          my %propertyKeys = ();          my %propertyKeys = ();
965          my $nextID = 1;          my $nextID = 1;
966          # Loop through the genomes.          # Loop through the genomes.
967          for my $genomeID (keys %{$genomeHash}) {          for my $genomeID (sort keys %{$genomeHash}) {
968              $loadProperty->Add("genomeIn");              $loadProperty->Add("genomeIn");
969              Trace("Generating properties for $genomeID.") if T(3);              Trace("Generating properties for $genomeID.") if T(3);
970              # Get the genome's features. The feature ID is the first field in the              # Get the genome's features. The feature ID is the first field in the
# Line 1018  Line 1073 
1073          # Loop through the genomes.          # Loop through the genomes.
1074          for my $genomeID (sort keys %{$genomeHash}) {          for my $genomeID (sort keys %{$genomeHash}) {
1075              Trace("Processing $genomeID.") if T(3);              Trace("Processing $genomeID.") if T(3);
             # Get the genome's PEGs.  
             my @pegs = $fig->pegs_of($genomeID);  
             for my $peg (@pegs) {  
                 Trace("Processing $peg.") if T(4);  
1076                  # Create a hash of timestamps. We use this to prevent duplicate time stamps                  # Create a hash of timestamps. We use this to prevent duplicate time stamps
1077                  # from showing up for a single PEG's annotations.                  # from showing up for a single PEG's annotations.
1078                  my %seenTimestamps = ();                  my %seenTimestamps = ();
1079                  # Loop through the annotations.              # Get the genome's annotations.
1080                  for my $tuple ($fig->feature_annotations($peg, "raw")) {              my @annotations = $fig->read_all_annotations($genomeID);
1081                      my ($fid, $timestamp, $user, $text) = @{$tuple};              Trace("Processing annotations.") if T(2);
1082                for my $tuple (@annotations) {
1083                    # Get the annotation tuple.
1084                    my ($peg, $timestamp, $user, $text) = @{$tuple};
1085                      # Here we fix up the annotation text. "\r" is removed,                      # Here we fix up the annotation text. "\r" is removed,
1086                      # and "\t" and "\n" are escaped. Note we use the "s"                  # and "\t" and "\n" are escaped. Note we use the "gs"
1087                      # modifier so that new-lines inside the text do not                      # modifier so that new-lines inside the text do not
1088                      # stop the substitution search.                      # stop the substitution search.
1089                      $text =~ s/\r//gs;                      $text =~ s/\r//gs;
# Line 1042  Line 1096 
1096                          # Here it's a number. We need to insure the one we use to form                          # Here it's a number. We need to insure the one we use to form
1097                          # the key is unique.                          # the key is unique.
1098                          my $keyStamp = $timestamp;                          my $keyStamp = $timestamp;
1099                          while ($seenTimestamps{$keyStamp}) {                      while ($seenTimestamps{"$peg:$keyStamp"}) {
1100                              $keyStamp++;                              $keyStamp++;
1101                          }                          }
                         $seenTimestamps{$keyStamp} = 1;  
1102                          my $annotationID = "$peg:$keyStamp";                          my $annotationID = "$peg:$keyStamp";
1103                        $seenTimestamps{$annotationID} = 1;
1104                          # Insure the user exists.                          # Insure the user exists.
1105                          if (! $users{$user}) {                          if (! $users{$user}) {
1106                              $loadSproutUser->Put($user, "SEED user");                              $loadSproutUser->Put($user, "SEED user");
# Line 1064  Line 1118 
1118                  }                  }
1119              }              }
1120          }          }
     }  
1121      # Finish the load.      # Finish the load.
1122      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
1123      return $retVal;      return $retVal;
# Line 1193  Line 1246 
1246      } else {      } else {
1247          Trace("Generating external data.") if T(2);          Trace("Generating external data.") if T(2);
1248          # We loop through the files one at a time. First, the organism file.          # We loop through the files one at a time. First, the organism file.
1249          Open(\*ORGS, "<$FIG_Config::global/ext_org.table");          Open(\*ORGS, "sort +0 -1 -u -t\"\t\" $FIG_Config::global/ext_org.table |");
1250          my $orgLine;          my $orgLine;
1251          while (defined($orgLine = <ORGS>)) {          while (defined($orgLine = <ORGS>)) {
1252              # Clean the input line.              # Clean the input line.
# Line 1205  Line 1258 
1258          close ORGS;          close ORGS;
1259          # Now the function file.          # Now the function file.
1260          my $funcLine;          my $funcLine;
1261          Open(\*FUNCS, "<$FIG_Config::global/ext_func.table");          Open(\*FUNCS, "sort +0 -1 -u -t\"\t\" $FIG_Config::global/ext_func.table |");
1262          while (defined($funcLine = <FUNCS>)) {          while (defined($funcLine = <FUNCS>)) {
1263              # Clean the line ending.              # Clean the line ending.
1264              chomp $funcLine;              chomp $funcLine;
# Line 1337  Line 1390 
1390    
1391      GenomeGroups      GenomeGroups
1392    
1393  There is no direct support for genome groups in FIG, so we access the SEED  Currently, we do not use groups. We used to use them for NMPDR groups,
1394    butThere is no direct support for genome groups in FIG, so we access the SEED
1395  files directly.  files directly.
1396    
1397  =over 4  =over 4
# Line 1363  Line 1417 
1417          Trace("Loading from existing files.") if T(2);          Trace("Loading from existing files.") if T(2);
1418      } else {      } else {
1419          Trace("Generating group data.") if T(2);          Trace("Generating group data.") if T(2);
1420            # Currently there are no groups.
1421        }
1422        # Finish the load.
1423        my $retVal = $self->_FinishAll();
1424        return $retVal;
1425    }
1426    
1427    =head3 LoadSynonymData
1428    
1429    C<< my $stats = $spl->LoadSynonymData(); >>
1430    
1431    Load the synonym groups into Sprout.
1432    
1433    The following relations are loaded by this method.
1434    
1435        SynonymGroup
1436        IsSynonymGroupFor
1437    
1438    The source information for these relations is taken from the C<maps_to_id> method
1439    of the B<FIG> object. Unfortunately, to make this work, we need to use direct
1440    SQL against the FIG database.
1441    
1442    =over 4
1443    
1444    =item RETURNS
1445    
1446    Returns a statistics object for the loads.
1447    
1448    =back
1449    
1450    =cut
1451    #: Return Type $%;
1452    sub LoadSynonymData {
1453        # Get this object instance.
1454        my ($self) = @_;
1455        # Get the FIG object.
1456        my $fig = $self->{fig};
1457        # Get the genome hash.
1458        my $genomeHash = $self->{genomes};
1459        # Create a load object for the table we're loading.
1460        my $loadSynonymGroup = $self->_TableLoader('SynonymGroup');
1461        my $loadIsSynonymGroupFor = $self->_TableLoader('IsSynonymGroupFor');
1462        if ($self->{options}->{loadOnly}) {
1463            Trace("Loading from existing files.") if T(2);
1464        } else {
1465            Trace("Generating synonym group data.") if T(2);
1466            # Get the database handle.
1467            my $dbh = $fig->db_handle();
1468            # Ask for the synonyms.
1469            my $sth = $dbh->prepare_command("SELECT maps_to, syn_id FROM peg_synonyms ORDER BY maps_to");
1470            my $result = $sth->execute();
1471            if (! defined($result)) {
1472                Confess("Database error in Synonym load: " . $sth->errstr());
1473            } else {
1474                # Remember the current synonym.
1475                my $current_syn = "";
1476                # Count the features.
1477                my $featureCount = 0;
1478                # Loop through the synonym/peg pairs.
1479                while (my @row = $sth->fetchrow()) {
1480                    # Get the synonym ID and feature ID.
1481                    my ($syn_id, $peg) = @row;
1482                    # Insure it's for one of our genomes.
1483                    my $genomeID = FIG::genome_of($peg);
1484                    if (exists $genomeHash->{$genomeID}) {
1485                        # Verify the synonym.
1486                        if ($syn_id ne $current_syn) {
1487                            # It's new, so put it in the group table.
1488                            $loadSynonymGroup->Put($syn_id);
1489                            $current_syn = $syn_id;
1490                        }
1491                        # Connect the synonym to the peg.
1492                        $loadIsSynonymGroupFor->Put($syn_id, $peg);
1493                        # Count this feature.
1494                        $featureCount++;
1495                        if ($featureCount % 1000 == 0) {
1496                            Trace("$featureCount features processed.") if T(3);
1497                        }
1498                    }
1499                }
1500            }
1501        }
1502        # Finish the load.
1503        my $retVal = $self->_FinishAll();
1504        return $retVal;
1505    }
1506    
1507    =head3 LoadFamilyData
1508    
1509    C<< my $stats = $spl->LoadFamilyData(); >>
1510    
1511    Load the protein families into Sprout.
1512    
1513    The following relations are loaded by this method.
1514    
1515        Family
1516        IsFamilyForFeature
1517    
1518    The source information for these relations is taken from the C<families_for_protein>,
1519    C<family_function>, and C<sz_family> methods of the B<FIG> object.
1520    
1521    =over 4
1522    
1523    =item RETURNS
1524    
1525    Returns a statistics object for the loads.
1526    
1527    =back
1528    
1529    =cut
1530    #: Return Type $%;
1531    sub LoadFamilyData {
1532        # Get this object instance.
1533        my ($self) = @_;
1534        # Get the FIG object.
1535        my $fig = $self->{fig};
1536        # Get the genome hash.
1537        my $genomeHash = $self->{genomes};
1538        # Create load objects for the tables we're loading.
1539        my $loadFamily = $self->_TableLoader('Family');
1540        my $loadIsFamilyForFeature = $self->_TableLoader('IsFamilyForFeature');
1541        if ($self->{options}->{loadOnly}) {
1542            Trace("Loading from existing files.") if T(2);
1543        } else {
1544            Trace("Generating family data.") if T(2);
1545            # Create a hash for the family IDs.
1546            my %familyHash = ();
1547          # Loop through the genomes.          # Loop through the genomes.
1548          my $line;          for my $genomeID (sort keys %{$genomeHash}) {
1549          for my $genomeID (keys %{$genomeHash}) {              Trace("Processing features for $genomeID.") if T(2);
1550              Trace("Processing $genomeID.") if T(3);              # Loop through this genome's PEGs.
1551              # Open the NMPDR group file for this genome.              for my $fid ($fig->all_features($genomeID, "peg")) {
1552              if (open(TMP, "<$FIG_Config::organisms/$genomeID/NMPDR") &&                  $loadIsFamilyForFeature->Add("features", 1);
1553                  defined($line = <TMP>)) {                  # Get this feature's families.
1554                  # Clean the line ending.                  my @families = $fig->families_for_protein($fid);
1555                  chomp $line;                  # Loop through the families, connecting them to the feature.
1556                  # Add the group to the table. Note that there can only be one group                  for my $family (@families) {
1557                  # per genome.                      $loadIsFamilyForFeature->Put($family, $fid);
1558                  $loadGenomeGroups->Put($genomeID, $line);                      # If this is a new family, create a record for it.
1559                        if (! exists $familyHash{$family}) {
1560                            $familyHash{$family} = 1;
1561                            $loadFamily->Add("families", 1);
1562                            my $size = $fig->sz_family($family);
1563                            my $func = $fig->family_function($family);
1564                            $loadFamily->Put($family, $size, $func);
1565                        }
1566                    }
1567              }              }
             close TMP;  
1568          }          }
1569      }      }
1570      # Finish the load.      # Finish the load.
# Line 1451  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 1463  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                $loaderHash{$relName} = $stats;
1657            }
1658        }
1659        # Now we loop through again, actually loading the tables. We want to finish before
1660        # loading so that if something goes wrong at this point, all the load files are usable
1661        # and we don't have to redo all that work.
1662        for my $relName (sort keys %loaderHash) {
1663            # Get the statistics for this relation.
1664            my $stats = $loaderHash{$relName};
1665            # Check for a database load.
1666              if ($self->{options}->{dbLoad}) {              if ($self->{options}->{dbLoad}) {
1667                  # Here we want to use the load file just created to load the database.                  # Here we want to use the load file just created to load the database.
1668                  Trace("Loading relation $relName.") if T(2);                  Trace("Loading relation $relName.") if T(2);
# Line 1473  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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