[Bio] / Sprout / SproutLoad.pm Repository:
ViewVC logotype

Diff of /Sprout/SproutLoad.pm

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 1.26, Mon Jan 30 21:57:02 2006 UTC revision 1.70, Wed Sep 27 12:58:18 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                # 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 330  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 365  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 401  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 436  Line 459 
459      FeatureTranslation      FeatureTranslation
460      FeatureUpstream      FeatureUpstream
461      IsLocatedIn      IsLocatedIn
462        HasFeature
463        HasRoleInSubsystem
464    
465  =over 4  =over 4
466    
# Line 461  Line 486 
486      my $loadFeatureLink = $self->_TableLoader('FeatureLink');      my $loadFeatureLink = $self->_TableLoader('FeatureLink');
487      my $loadFeatureTranslation = $self->_TableLoader('FeatureTranslation');      my $loadFeatureTranslation = $self->_TableLoader('FeatureTranslation');
488      my $loadFeatureUpstream = $self->_TableLoader('FeatureUpstream');      my $loadFeatureUpstream = $self->_TableLoader('FeatureUpstream');
489        my $loadHasFeature = $self->_TableLoader('HasFeature', $self->PrimaryOnly);
490        my $loadHasRoleInSubsystem = $self->_TableLoader('HasRoleInSubsystem', $self->PrimaryOnly);
491      # 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
492      # locations.      # locations.
493      my $chunkSize = $self->{sprout}->MaxSegment();      my $chunkSize = $self->{sprout}->MaxSegment();
# Line 474  Line 501 
501              $loadFeature->Add("genomeIn");              $loadFeature->Add("genomeIn");
502              # Get the feature list for this genome.              # Get the feature list for this genome.
503              my $features = $fig->all_features_detailed($genomeID);              my $features = $fig->all_features_detailed($genomeID);
504                # Sort and count the list.
505                my @featureTuples = sort { $a->[0] cmp $b->[0] } @{$features};
506                my $count = scalar @featureTuples;
507                Trace("$count features found for genome $genomeID.") if T(3);
508                # Set up for our duplicate-feature check.
509                my $oldFeatureID = "";
510              # Loop through the features.              # Loop through the features.
511              for my $featureData (@{$features}) {              for my $featureTuple (@featureTuples) {
                 $loadFeature->Add("featureIn");  
512                  # Split the tuple.                  # Split the tuple.
513                  my ($featureID, $locations, undef, $type) = @{$featureData};                  my ($featureID, $locations, undef, $type) = @{$featureTuple};
514                    # Check for duplicates.
515                    if ($featureID eq $oldFeatureID) {
516                        Trace("Duplicate feature $featureID found.") if T(1);
517                    } else {
518                        $oldFeatureID = $featureID;
519                        # Count this feature.
520                        $loadFeature->Add("featureIn");
521                        # Get the functional assignment.
522                        my $assignment = $fig->function_of($featureID);
523                  # Create the feature record.                  # Create the feature record.
524                  $loadFeature->Put($featureID, 1, $type);                      $loadFeature->Put($featureID, 1, $type, $assignment);
525                        # Link it to the parent genome.
526                        $loadHasFeature->Put($genomeID, $featureID, $type);
527                  # Create the aliases.                  # Create the aliases.
528                  for my $alias ($fig->feature_aliases($featureID)) {                  for my $alias ($fig->feature_aliases($featureID)) {
529                      $loadFeatureAlias->Put($featureID, $alias);                      $loadFeatureAlias->Put($featureID, $alias);
# Line 503  Line 546 
546                          $loadFeatureUpstream->Put($featureID, $upstream);                          $loadFeatureUpstream->Put($featureID, $upstream);
547                      }                      }
548                  }                  }
549                        # Now we need to find the subsystems this feature participates in.
550                        my @subsystems = $fig->peg_to_subsystems($featureID);
551                        for my $subsystem (@subsystems) {
552                            $loadHasRoleInSubsystem->Put($featureID, $genomeID, $type, $subsystem);
553                        }
554                  # 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
555                  # 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
556                  # the maximum segment size. This simplifies the genes_in_region processing                  # the maximum segment size. This simplifies the genes_in_region processing
# Line 532  Line 580 
580              }              }
581          }          }
582      }      }
583        }
584      # Finish the loads.      # Finish the loads.
585      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
586      return $retVal;      return $retVal;
# Line 580  Line 629 
629              Trace("Processing features for genome $genomeID.") if T(3);              Trace("Processing features for genome $genomeID.") if T(3);
630              # Get the feature list for this genome.              # Get the feature list for this genome.
631              my $features = $fig->all_features_detailed($genomeID);              my $features = $fig->all_features_detailed($genomeID);
632                # Count the BBHs we find.
633                my $bbhCount = 0;
634              # Loop through the features.              # Loop through the features.
635              for my $featureData (@{$features}) {              for my $featureData (@{$features}) {
636                  # Split the tuple.                  # Split the tuple.
# Line 595  Line 646 
646                      if ($genomeHash->{$targetGenomeID}) {                      if ($genomeHash->{$targetGenomeID}) {
647                          $loadIsBidirectionalBestHitOf->Put($featureID, $targetID, $targetGenomeID,                          $loadIsBidirectionalBestHitOf->Put($featureID, $targetID, $targetGenomeID,
648                                                             $score);                                                             $score);
649                            $bbhCount++;
650                      }                      }
651                  }                  }
652              }              }
653                Trace("$bbhCount BBHs found for $genomeID.") if T(3);
654          }          }
655      }      }
656      # Finish the loads.      # Finish the loads.
# Line 620  Line 673 
673  The following relations are loaded by this method.  The following relations are loaded by this method.
674    
675      Subsystem      Subsystem
676        SubsystemClass
677      Role      Role
678      RoleEC      RoleEC
679      SSCell      SSCell
# Line 682  Line 736 
736      my $loadConsistsOfGenomes = $self->_TableLoader('ConsistsOfGenomes', $self->PrimaryOnly);      my $loadConsistsOfGenomes = $self->_TableLoader('ConsistsOfGenomes', $self->PrimaryOnly);
737      my $loadHasRoleSubset = $self->_TableLoader('HasRoleSubset', $self->PrimaryOnly);      my $loadHasRoleSubset = $self->_TableLoader('HasRoleSubset', $self->PrimaryOnly);
738      my $loadHasGenomeSubset = $self->_TableLoader('HasGenomeSubset', $self->PrimaryOnly);      my $loadHasGenomeSubset = $self->_TableLoader('HasGenomeSubset', $self->PrimaryOnly);
739        my $loadSubsystemClass = $self->_TableLoader('SubsystemClass', $self->PrimaryOnly);
740      if ($self->{options}->{loadOnly}) {      if ($self->{options}->{loadOnly}) {
741          Trace("Loading from existing files.") if T(2);          Trace("Loading from existing files.") if T(2);
742      } else {      } else {
# Line 697  Line 752 
752          my ($genomeID, $roleID);          my ($genomeID, $roleID);
753          my %roleData = ();          my %roleData = ();
754          for my $subsysID (@subsysIDs) {          for my $subsysID (@subsysIDs) {
             Trace("Creating subsystem $subsysID.") if T(3);  
             $loadSubsystem->Add("subsystemIn");  
755              # Get the subsystem object.              # Get the subsystem object.
756              my $sub = $fig->get_subsystem($subsysID);              my $sub = $fig->get_subsystem($subsysID);
757                # Only proceed if the subsystem has a spreadsheet.
758                if (! $sub->{empty_ss}) {
759                    Trace("Creating subsystem $subsysID.") if T(3);
760                    $loadSubsystem->Add("subsystemIn");
761              # Create the subsystem record.              # Create the subsystem record.
762              my $curator = $sub->get_curator();              my $curator = $sub->get_curator();
763              my $notes = $sub->get_notes();              my $notes = $sub->get_notes();
764              $loadSubsystem->Put($subsysID, $curator, $notes);              $loadSubsystem->Put($subsysID, $curator, $notes);
765                    my $classList = $fig->subsystem_classification($subsysID);
766                    my @classes = @$classList;
767                    if (@classes) {
768                        for my $class (@classes) {
769                            $loadSubsystemClass->Put($subsysID, $class);
770                        }
771                    }
772              # 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.
773              for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {              for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {
774                  # Connect to this role.                  # Connect to this role.
# Line 748  Line 812 
812                      # part of the spreadsheet cell ID.                      # part of the spreadsheet cell ID.
813                      for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {                      for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {
814                          # Get the features in the spreadsheet cell for this genome and role.                          # Get the features in the spreadsheet cell for this genome and role.
815                          my @pegs = $sub->get_pegs_from_cell($row, $col);                              my @pegs = grep { !$fig->is_deleted_fid($_) } $sub->get_pegs_from_cell($row, $col);
816                          # Only proceed if features exist.                          # Only proceed if features exist.
817                          if (@pegs > 0) {                          if (@pegs > 0) {
818                              # Create the spreadsheet cell.                              # Create the spreadsheet cell.
# Line 769  Line 833 
833                      if ($pegCount > 0) {                      if ($pegCount > 0) {
834                          Trace("$pegCount PEGs in $cellCount cells for $genomeID.") if T(3);                          Trace("$pegCount PEGs in $cellCount cells for $genomeID.") if T(3);
835                          $loadParticipatesIn->Put($genomeID, $subsysID, $variantCode);                          $loadParticipatesIn->Put($genomeID, $subsysID, $variantCode);
                         # Partition the PEGs found into clusters.  
                         my @clusters = $fig->compute_clusters(\@pegsFound, $sub);  
836                          # Create a hash mapping PEG IDs to cluster numbers.                          # Create a hash mapping PEG IDs to cluster numbers.
837                          # We default to -1 for all of them.                          # We default to -1 for all of them.
838                          my %clusterOf = map { $_ => -1 } @pegsFound;                          my %clusterOf = map { $_ => -1 } @pegsFound;
839                                # Partition the PEGs found into clusters.
840                                my @clusters = $fig->compute_clusters([keys %clusterOf], $sub);
841                          for (my $i = 0; $i <= $#clusters; $i++) {                          for (my $i = 0; $i <= $#clusters; $i++) {
842                              my $subList = $clusters[$i];                              my $subList = $clusters[$i];
843                              for my $peg (@{$subList}) {                              for my $peg (@{$subList}) {
# Line 801  Line 865 
865                  # Connect the subset to the subsystem.                  # Connect the subset to the subsystem.
866                  $loadHasRoleSubset->Put($subsysID, $actualID);                  $loadHasRoleSubset->Put($subsysID, $actualID);
867                  # Connect the subset to its roles.                  # Connect the subset to its roles.
868                  my @roles = $sub->get_subset($subsetID);                      my @roles = $sub->get_subsetC_roles($subsetID);
869                  for my $roleID (@roles) {                  for my $roleID (@roles) {
870                      $loadConsistsOfRoles->Put($actualID, $roleID);                      $loadConsistsOfRoles->Put($actualID, $roleID);
871                  }                  }
# Line 821  Line 885 
885                  }                  }
886              }              }
887          }          }
888            }
889          # 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
890          # 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
891          # in subsystems (and therefore appear in the %ecToRoles hash) are          # in subsystems (and therefore appear in the %ecToRoles hash) are
# Line 906  Line 971 
971          my %propertyKeys = ();          my %propertyKeys = ();
972          my $nextID = 1;          my $nextID = 1;
973          # Loop through the genomes.          # Loop through the genomes.
974          for my $genomeID (keys %{$genomeHash}) {          for my $genomeID (sort keys %{$genomeHash}) {
975              $loadProperty->Add("genomeIn");              $loadProperty->Add("genomeIn");
976              Trace("Generating properties for $genomeID.") if T(3);              Trace("Generating properties for $genomeID.") if T(3);
977              # 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 1015  Line 1080 
1080          # Loop through the genomes.          # Loop through the genomes.
1081          for my $genomeID (sort keys %{$genomeHash}) {          for my $genomeID (sort keys %{$genomeHash}) {
1082              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);  
1083                  # 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
1084                  # from showing up for a single PEG's annotations.                  # from showing up for a single PEG's annotations.
1085                  my %seenTimestamps = ();                  my %seenTimestamps = ();
1086                  # Loop through the annotations.              # Get the genome's annotations.
1087                  for my $tuple ($fig->feature_annotations($peg, "raw")) {              my @annotations = $fig->read_all_annotations($genomeID);
1088                      my ($fid, $timestamp, $user, $text) = @{$tuple};              Trace("Processing annotations.") if T(2);
1089                for my $tuple (@annotations) {
1090                    # Get the annotation tuple.
1091                    my ($peg, $timestamp, $user, $text) = @{$tuple};
1092                      # Here we fix up the annotation text. "\r" is removed,                      # Here we fix up the annotation text. "\r" is removed,
1093                      # and "\t" and "\n" are escaped. Note we use the "s"                  # and "\t" and "\n" are escaped. Note we use the "gs"
1094                      # modifier so that new-lines inside the text do not                      # modifier so that new-lines inside the text do not
1095                      # stop the substitution search.                      # stop the substitution search.
1096                      $text =~ s/\r//gs;                      $text =~ s/\r//gs;
# Line 1039  Line 1103 
1103                          # 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
1104                          # the key is unique.                          # the key is unique.
1105                          my $keyStamp = $timestamp;                          my $keyStamp = $timestamp;
1106                          while ($seenTimestamps{$keyStamp}) {                      while ($seenTimestamps{"$peg:$keyStamp"}) {
1107                              $keyStamp++;                              $keyStamp++;
1108                          }                          }
                         $seenTimestamps{$keyStamp} = 1;  
1109                          my $annotationID = "$peg:$keyStamp";                          my $annotationID = "$peg:$keyStamp";
1110                        $seenTimestamps{$annotationID} = 1;
1111                          # Insure the user exists.                          # Insure the user exists.
1112                          if (! $users{$user}) {                          if (! $users{$user}) {
1113                              $loadSproutUser->Put($user, "SEED user");                              $loadSproutUser->Put($user, "SEED user");
# Line 1061  Line 1125 
1125                  }                  }
1126              }              }
1127          }          }
     }  
1128      # Finish the load.      # Finish the load.
1129      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
1130      return $retVal;      return $retVal;
# Line 1190  Line 1253 
1253      } else {      } else {
1254          Trace("Generating external data.") if T(2);          Trace("Generating external data.") if T(2);
1255          # We loop through the files one at a time. First, the organism file.          # We loop through the files one at a time. First, the organism file.
1256          Open(\*ORGS, "<$FIG_Config::global/ext_org.table");          Open(\*ORGS, "sort +0 -1 -u -t\"\t\" $FIG_Config::global/ext_org.table |");
1257          my $orgLine;          my $orgLine;
1258          while (defined($orgLine = <ORGS>)) {          while (defined($orgLine = <ORGS>)) {
1259              # Clean the input line.              # Clean the input line.
# Line 1202  Line 1265 
1265          close ORGS;          close ORGS;
1266          # Now the function file.          # Now the function file.
1267          my $funcLine;          my $funcLine;
1268          Open(\*FUNCS, "<$FIG_Config::global/ext_func.table");          Open(\*FUNCS, "sort +0 -1 -u -t\"\t\" $FIG_Config::global/ext_func.table |");
1269          while (defined($funcLine = <FUNCS>)) {          while (defined($funcLine = <FUNCS>)) {
1270              # Clean the line ending.              # Clean the line ending.
1271              chomp $funcLine;              chomp $funcLine;
# Line 1334  Line 1397 
1397    
1398      GenomeGroups      GenomeGroups
1399    
1400  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,
1401    butThere is no direct support for genome groups in FIG, so we access the SEED
1402  files directly.  files directly.
1403    
1404  =over 4  =over 4
# Line 1360  Line 1424 
1424          Trace("Loading from existing files.") if T(2);          Trace("Loading from existing files.") if T(2);
1425      } else {      } else {
1426          Trace("Generating group data.") if T(2);          Trace("Generating group data.") if T(2);
1427            # Currently there are no groups.
1428        }
1429        # Finish the load.
1430        my $retVal = $self->_FinishAll();
1431        return $retVal;
1432    }
1433    
1434    =head3 LoadSynonymData
1435    
1436    C<< my $stats = $spl->LoadSynonymData(); >>
1437    
1438    Load the synonym groups into Sprout.
1439    
1440    The following relations are loaded by this method.
1441    
1442        SynonymGroup
1443        IsSynonymGroupFor
1444    
1445    The source information for these relations is taken from the C<maps_to_id> method
1446    of the B<FIG> object. Unfortunately, to make this work, we need to use direct
1447    SQL against the FIG database.
1448    
1449    =over 4
1450    
1451    =item RETURNS
1452    
1453    Returns a statistics object for the loads.
1454    
1455    =back
1456    
1457    =cut
1458    #: Return Type $%;
1459    sub LoadSynonymData {
1460        # Get this object instance.
1461        my ($self) = @_;
1462        # Get the FIG object.
1463        my $fig = $self->{fig};
1464        # Get the genome hash.
1465        my $genomeHash = $self->{genomes};
1466        # Create a load object for the table we're loading.
1467        my $loadSynonymGroup = $self->_TableLoader('SynonymGroup');
1468        my $loadIsSynonymGroupFor = $self->_TableLoader('IsSynonymGroupFor');
1469        if ($self->{options}->{loadOnly}) {
1470            Trace("Loading from existing files.") if T(2);
1471        } else {
1472            Trace("Generating synonym group data.") if T(2);
1473            # Get the database handle.
1474            my $dbh = $fig->db_handle();
1475            # Ask for the synonyms.
1476            my $sth = $dbh->prepare_command("SELECT maps_to, syn_id FROM peg_synonyms ORDER BY maps_to");
1477            my $result = $sth->execute();
1478            if (! defined($result)) {
1479                Confess("Database error in Synonym load: " . $sth->errstr());
1480            } else {
1481                # Remember the current synonym.
1482                my $current_syn = "";
1483                # Count the features.
1484                my $featureCount = 0;
1485                # Loop through the synonym/peg pairs.
1486                while (my @row = $sth->fetchrow()) {
1487                    # Get the synonym ID and feature ID.
1488                    my ($syn_id, $peg) = @row;
1489                    # Insure it's for one of our genomes.
1490                    my $genomeID = FIG::genome_of($peg);
1491                    if (exists $genomeHash->{$genomeID}) {
1492                        # Verify the synonym.
1493                        if ($syn_id ne $current_syn) {
1494                            # It's new, so put it in the group table.
1495                            $loadSynonymGroup->Put($syn_id);
1496                            $current_syn = $syn_id;
1497                        }
1498                        # Connect the synonym to the peg.
1499                        $loadIsSynonymGroupFor->Put($syn_id, $peg);
1500                        # Count this feature.
1501                        $featureCount++;
1502                        if ($featureCount % 1000 == 0) {
1503                            Trace("$featureCount features processed.") if T(3);
1504                        }
1505                    }
1506                }
1507            }
1508        }
1509        # Finish the load.
1510        my $retVal = $self->_FinishAll();
1511        return $retVal;
1512    }
1513    
1514    =head3 LoadFamilyData
1515    
1516    C<< my $stats = $spl->LoadFamilyData(); >>
1517    
1518    Load the protein families into Sprout.
1519    
1520    The following relations are loaded by this method.
1521    
1522        Family
1523        IsFamilyForFeature
1524    
1525    The source information for these relations is taken from the C<families_for_protein>,
1526    C<family_function>, and C<sz_family> methods of the B<FIG> object.
1527    
1528    =over 4
1529    
1530    =item RETURNS
1531    
1532    Returns a statistics object for the loads.
1533    
1534    =back
1535    
1536    =cut
1537    #: Return Type $%;
1538    sub LoadFamilyData {
1539        # Get this object instance.
1540        my ($self) = @_;
1541        # Get the FIG object.
1542        my $fig = $self->{fig};
1543        # Get the genome hash.
1544        my $genomeHash = $self->{genomes};
1545        # Create load objects for the tables we're loading.
1546        my $loadFamily = $self->_TableLoader('Family');
1547        my $loadIsFamilyForFeature = $self->_TableLoader('IsFamilyForFeature');
1548        if ($self->{options}->{loadOnly}) {
1549            Trace("Loading from existing files.") if T(2);
1550        } else {
1551            Trace("Generating family data.") if T(2);
1552            # Create a hash for the family IDs.
1553            my %familyHash = ();
1554          # Loop through the genomes.          # Loop through the genomes.
1555          my $line;          for my $genomeID (sort keys %{$genomeHash}) {
1556          for my $genomeID (keys %{$genomeHash}) {              Trace("Processing features for $genomeID.") if T(2);
1557              Trace("Processing $genomeID.") if T(3);              # Loop through this genome's PEGs.
1558              # Open the NMPDR group file for this genome.              for my $fid ($fig->all_features($genomeID, "peg")) {
1559              if (open(TMP, "<$FIG_Config::organisms/$genomeID/NMPDR") &&                  $loadIsFamilyForFeature->Add("features", 1);
1560                  defined($line = <TMP>)) {                  # Get this feature's families.
1561                  # Clean the line ending.                  my @families = $fig->families_for_protein($fid);
1562                  chomp $line;                  # Loop through the families, connecting them to the feature.
1563                  # Add the group to the table. Note that there can only be one group                  for my $family (@families) {
1564                  # per genome.                      $loadIsFamilyForFeature->Put($family, $fid);
1565                  $loadGenomeGroups->Put($genomeID, $line);                      # If this is a new family, create a record for it.
1566                        if (! exists $familyHash{$family}) {
1567                            $familyHash{$family} = 1;
1568                            $loadFamily->Add("families", 1);
1569                            my $size = $fig->sz_family($family);
1570                            my $func = $fig->family_function($family);
1571                            $loadFamily->Put($family, $size, $func);
1572                        }
1573                    }
1574              }              }
             close TMP;  
1575          }          }
1576      }      }
1577      # Finish the load.      # Finish the load.
# Line 1381  Line 1579 
1579      return $retVal;      return $retVal;
1580  }  }
1581    
1582    
1583    
1584  =head2 Internal Utility Methods  =head2 Internal Utility Methods
1585    
1586  =head3 TableLoader  =head3 TableLoader
# Line 1448  Line 1648 
1648      my $retVal = Stats->new();      my $retVal = Stats->new();
1649      # Get the loader list.      # Get the loader list.
1650      my $loadList = $self->{loaders};      my $loadList = $self->{loaders};
1651        # Create a hash to hold the statistics objects, keyed on relation name.
1652        my %loaderHash = ();
1653      # 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
1654      # 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.
1655      while (my $loader = pop @{$loadList}) {      while (my $loader = pop @{$loadList}) {
1656          # Get the relation name.          # Get the relation name.
1657          my $relName = $loader->RelName;          my $relName = $loader->RelName;
# Line 1460  Line 1662 
1662              # Here we really need to finish.              # Here we really need to finish.
1663              Trace("Finishing $relName.") if T(2);              Trace("Finishing $relName.") if T(2);
1664              my $stats = $loader->Finish();              my $stats = $loader->Finish();
1665              if ($self->{options}->{dbLoad} && ! $loader->Ignore) {              $loaderHash{$relName} = $stats;
1666            }
1667        }
1668        # Now we loop through again, actually loading the tables. We want to finish before
1669        # loading so that if something goes wrong at this point, all the load files are usable
1670        # and we don't have to redo all that work.
1671        for my $relName (sort keys %loaderHash) {
1672            # Get the statistics for this relation.
1673            my $stats = $loaderHash{$relName};
1674            # Check for a database load.
1675            if ($self->{options}->{dbLoad}) {
1676                  # 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.
1677                  Trace("Loading relation $relName.") if T(2);                  Trace("Loading relation $relName.") if T(2);
1678                  my $newStats = $self->{sprout}->LoadUpdate(1, [$relName]);                  my $newStats = $self->{sprout}->LoadUpdate(1, [$relName]);
# Line 1470  Line 1682 
1682              $retVal->Accumulate($stats);              $retVal->Accumulate($stats);
1683              Trace("Statistics for $relName:\n" . $stats->Show()) if T(2);              Trace("Statistics for $relName:\n" . $stats->Show()) if T(2);
1684          }          }
     }  
1685      # Return the load statistics.      # Return the load statistics.
1686      return $retVal;      return $retVal;
1687  }  }

Legend:
Removed from v.1.26  
changed lines
  Added in v.1.70

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3