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revision 1.61, Sun Jul 30 01:41:34 2006 UTC revision 1.75, Sun Oct 22 05:17:10 2006 UTC
# Line 120  Line 120 
120                      # an omitted access code can be defaulted to 1.                      # an omitted access code can be defaulted to 1.
121                      for my $genomeLine (@genomeList) {                      for my $genomeLine (@genomeList) {
122                          my ($genomeID, $accessCode) = split("\t", $genomeLine);                          my ($genomeID, $accessCode) = split("\t", $genomeLine);
123                          if (undef $accessCode) {                          if (! defined($accessCode)) {
124                              $accessCode = 1;                              $accessCode = 1;
125                          }                          }
126                          $genomes{$genomeID} = $accessCode;                          $genomes{$genomeID} = $accessCode;
# Line 163  Line 163 
163                  Confess("Invalid subsystem parameter in SproutLoad constructor.");                  Confess("Invalid subsystem parameter in SproutLoad constructor.");
164              }              }
165          }          }
166            # Go through the subsys hash again, creating the keyword list for each subsystem.
167            for my $subsystem (keys %subsystems) {
168                my $name = $subsystem;
169                $name =~ s/_/ /g;
170                my $classes = $fig->subsystem_classification($subsystem);
171                my @classList = map { " $_" } @{$classes};
172                $name .= join("", @classList);
173                $subsystems{$subsystem} = $name;
174            }
175      }      }
176      # Get the data directory from the Sprout object.      # Get the data directory from the Sprout object.
177      my ($directory) = $sprout->LoadInfo();      my ($directory) = $sprout->LoadInfo();
# Line 266  Line 275 
275              my $extra = join " ", @extraData;              my $extra = join " ", @extraData;
276              # Get the full taxonomy.              # Get the full taxonomy.
277              my $taxonomy = $fig->taxonomy_of($genomeID);              my $taxonomy = $fig->taxonomy_of($genomeID);
278                # Open the NMPDR group file for this genome.
279                my $group;
280                if (open(TMP, "<$FIG_Config::organisms/$genomeID/NMPDR") &&
281                    defined($group = <TMP>)) {
282                    # Clean the line ending.
283                    chomp $group;
284                } else {
285                    # No group, so use the default.
286                    $group = $FIG_Config::otherGroup;
287                }
288                close TMP;
289              # Output the genome record.              # Output the genome record.
290              $loadGenome->Put($genomeID, $accessCode, $fig->is_complete($genomeID), $genus,              $loadGenome->Put($genomeID, $accessCode, $fig->is_complete($genomeID), $genus,
291                               $species, $extra, $taxonomy);                               $group, $species, $extra, $taxonomy);
292              # Now we loop through each of the genome's contigs.              # Now we loop through each of the genome's contigs.
293              my @contigs = $fig->all_contigs($genomeID);              my @contigs = $fig->all_contigs($genomeID);
294              for my $contigID (@contigs) {              for my $contigID (@contigs) {
# Line 449  Line 469 
469      FeatureUpstream      FeatureUpstream
470      IsLocatedIn      IsLocatedIn
471      HasFeature      HasFeature
472        HasRoleInSubsystem
473    
474  =over 4  =over 4
475    
# Line 463  Line 484 
484  sub LoadFeatureData {  sub LoadFeatureData {
485      # Get this object instance.      # Get this object instance.
486      my ($self) = @_;      my ($self) = @_;
487      # Get the FIG object.      # Get the FIG and Sprout objects.
488      my $fig = $self->{fig};      my $fig = $self->{fig};
489        my $sprout = $self->{sprout};
490      # Get the table of genome IDs.      # Get the table of genome IDs.
491      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
492      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
# Line 474  Line 496 
496      my $loadFeatureLink = $self->_TableLoader('FeatureLink');      my $loadFeatureLink = $self->_TableLoader('FeatureLink');
497      my $loadFeatureTranslation = $self->_TableLoader('FeatureTranslation');      my $loadFeatureTranslation = $self->_TableLoader('FeatureTranslation');
498      my $loadFeatureUpstream = $self->_TableLoader('FeatureUpstream');      my $loadFeatureUpstream = $self->_TableLoader('FeatureUpstream');
499      my $loadHasFeature = $self->_TableLoader('HasFeature');      my $loadHasFeature = $self->_TableLoader('HasFeature', $self->PrimaryOnly);
500        my $loadHasRoleInSubsystem = $self->_TableLoader('HasRoleInSubsystem', $self->PrimaryOnly);
501        # Get the subsystem hash.
502        my $subHash = $self->{subsystems};
503      # Get the maximum sequence size. We need this later for splitting up the      # Get the maximum sequence size. We need this later for splitting up the
504      # locations.      # locations.
505      my $chunkSize = $self->{sprout}->MaxSegment();      my $chunkSize = $self->{sprout}->MaxSegment();
# Line 505  Line 530 
530                      $oldFeatureID = $featureID;                      $oldFeatureID = $featureID;
531                      # Count this feature.                      # Count this feature.
532                      $loadFeature->Add("featureIn");                      $loadFeature->Add("featureIn");
533                      # Create the feature record.                      # Begin building the keywords.
534                      $loadFeature->Put($featureID, 1, $type);                      my @keywords = ($genomeID);
535                      # Link it to the parent genome.                      # Get the functional assignment and aliases. This
536                      $loadHasFeature->Put($genomeID, $featureID, $type);                      # depends on the feature type.
537                        my $assignment;
538                        if ($type eq "peg") {
539                            $assignment = $fig->function_of($featureID);
540                      # Create the aliases.                      # Create the aliases.
541                      for my $alias ($fig->feature_aliases($featureID)) {                      for my $alias ($fig->feature_aliases($featureID)) {
542                          $loadFeatureAlias->Put($featureID, $alias);                          $loadFeatureAlias->Put($featureID, $alias);
543                                push @keywords, $alias;
544                      }                      }
545                        } else {
546                            # For other types, the assignment is the first (and ONLY) alias.
547                            ($assignment) = $fig->feature_aliases($featureID);
548                        }
549                        Trace("Assignment for $featureID is: $assignment") if T(4);
550                        # Break the assignment into words and shove it onto the
551                        # keyword list.
552                        push @keywords, split(/\s+/, $assignment);
553                        # Link this feature to the parent genome.
554                        $loadHasFeature->Put($genomeID, $featureID, $type);
555                      # Get the links.                      # Get the links.
556                      my @links = $fig->fid_links($featureID);                      my @links = $fig->fid_links($featureID);
557                      for my $link (@links) {                      for my $link (@links) {
# Line 531  Line 570 
570                              $loadFeatureUpstream->Put($featureID, $upstream);                              $loadFeatureUpstream->Put($featureID, $upstream);
571                          }                          }
572                      }                      }
573                        # Now we need to find the subsystems this feature participates in.
574                        # We also add the subsystems to the keyword list. Before we do that,
575                        # we must convert underscores to spaces and tack on the classifications.
576                        my @subsystems = $fig->peg_to_subsystems($featureID);
577                        for my $subsystem (@subsystems) {
578                            # Only proceed if we like this subsystem.
579                            if (exists $subHash->{$subsystem}) {
580                                # Store the has-role link.
581                                $loadHasRoleInSubsystem->Put($featureID, $subsystem, $genomeID, $type);
582                                # Save the subsystem's keyword data.
583                                my $subKeywords = $subHash->{$subsystem};
584                                push @keywords, split /\s+/, $subKeywords;
585                                # Now we need to get this feature's role in the subsystem.
586                                my $subObject = $fig->get_subsystem($subsystem);
587                                my @roleColumns = $subObject->get_peg_roles($featureID);
588                                my @allRoles = $subObject->get_roles();
589                                for my $col (@roleColumns) {
590                                    my $role = $allRoles[$col];
591                                    push @keywords, split /\s+/, $role;
592                                    push @keywords, $subObject->get_role_abbr($col);
593                                }
594                            }
595                        }
596                        # The final task is to add virulence and essentiality attributes.
597                        if ($fig->virulent($featureID)) {
598                            push @keywords, "virulent";
599                        }
600                        if ($fig->essential($featureID)) {
601                            push @keywords, "essential";
602                        }
603                        # Now we need to bust up hyphenated words in the keyword
604                        # list.
605                        my $keywordString = "";
606                        for my $keyword (@keywords) {
607                            if (length $keyword >= 4) {
608                                $keywordString .= " $keyword";
609                                if ($keyword =~ /-/) {
610                                    my @words = grep { length($_) >= 4 } split /-/, $keyword;
611                                    $keywordString .= join(" ", "", @words);
612                                }
613                            }
614                        }
615                        # Clean the keyword list.
616                        my $cleanWords = $sprout->CleanKeywords($keywordString);
617                        Trace("Keyword string for $featureID: $cleanWords") if T(4);
618                        # Create the feature record.
619                        $loadFeature->Put($featureID, 1, $type, $assignment, $cleanWords);
620                      # 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
621                      # 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
622                      # the maximum segment size. This simplifies the genes_in_region processing                      # the maximum segment size. This simplifies the genes_in_region processing
# Line 566  Line 652 
652      return $retVal;      return $retVal;
653  }  }
654    
 =head3 LoadBBHData  
   
 C<< my $stats = $spl->LoadBBHData(); >>  
   
 Load the bidirectional best hit data from FIG into Sprout.  
   
 Sprout does not store information on similarities. Instead, it has only the  
 bi-directional best hits. Even so, the BBH table is one of the largest in  
 the database.  
   
 The following relations are loaded by this method.  
   
     IsBidirectionalBestHitOf  
   
 =over 4  
   
 =item RETURNS  
   
 Returns a statistics object for the loads.  
   
 =back  
   
 =cut  
 #: Return Type $%;  
 sub LoadBBHData {  
     # Get this object instance.  
     my ($self) = @_;  
     # Get the FIG object.  
     my $fig = $self->{fig};  
     # Get the table of genome IDs.  
     my $genomeHash = $self->{genomes};  
     # Create load objects for each of the tables we're loading.  
     my $loadIsBidirectionalBestHitOf = $self->_TableLoader('IsBidirectionalBestHitOf');  
     if ($self->{options}->{loadOnly}) {  
         Trace("Loading from existing files.") if T(2);  
     } else {  
         Trace("Generating BBH data.") if T(2);  
         # Now we loop through the genomes, generating the data for each one.  
         for my $genomeID (sort keys %{$genomeHash}) {  
             $loadIsBidirectionalBestHitOf->Add("genomeIn");  
             Trace("Processing features for genome $genomeID.") if T(3);  
             # Get the feature list for this genome.  
             my $features = $fig->all_features_detailed($genomeID);  
             # Loop through the features.  
             for my $featureData (@{$features}) {  
                 # Split the tuple.  
                 my ($featureID, $locations, $aliases, $type) = @{$featureData};  
                 # Get the bi-directional best hits.  
                 my @bbhList = $fig->bbhs($featureID);  
                 for my $bbhEntry (@bbhList) {  
                     # Get the target feature ID and the score.  
                     my ($targetID, $score) = @{$bbhEntry};  
                     # Check the target feature's genome.  
                     my $targetGenomeID = $fig->genome_of($targetID);  
                     # Only proceed if it's one of our genomes.  
                     if ($genomeHash->{$targetGenomeID}) {  
                         $loadIsBidirectionalBestHitOf->Put($featureID, $targetID, $targetGenomeID,  
                                                            $score);  
                     }  
                 }  
             }  
         }  
     }  
     # Finish the loads.  
     my $retVal = $self->_FinishAll();  
     return $retVal;  
 }  
   
655  =head3 LoadSubsystemData  =head3 LoadSubsystemData
656    
657  C<< my $stats = $spl->LoadSubsystemData(); >>  C<< my $stats = $spl->LoadSubsystemData(); >>
# Line 738  Line 756 
756                  my $curator = $sub->get_curator();                  my $curator = $sub->get_curator();
757                  my $notes = $sub->get_notes();                  my $notes = $sub->get_notes();
758                  $loadSubsystem->Put($subsysID, $curator, $notes);                  $loadSubsystem->Put($subsysID, $curator, $notes);
759                  my $class = $fig->subsystem_classification($subsysID);                  # Now for the classification string. This comes back as a list
760                  if ($class) {                  # reference and we convert it to a space-delimited string.
761                      $loadSubsystemClass->Put($subsysID, $class);                  my $classList = $fig->subsystem_classification($subsysID);
762                  }                  my $classString = join(" : ", grep { $_ } @$classList);
763                    $loadSubsystemClass->Put($subsysID, $classString);
764                  # 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.
765                  for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {                  for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {
766                      # Connect to this role.                      # Connect to this role.
# Line 944  Line 963 
963          my %propertyKeys = ();          my %propertyKeys = ();
964          my $nextID = 1;          my $nextID = 1;
965          # Loop through the genomes.          # Loop through the genomes.
966          for my $genomeID (keys %{$genomeHash}) {          for my $genomeID (sort keys %{$genomeHash}) {
967              $loadProperty->Add("genomeIn");              $loadProperty->Add("genomeIn");
968              Trace("Generating properties for $genomeID.") if T(3);              Trace("Generating properties for $genomeID.") if T(3);
969              # 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 958  Line 977 
977                  # Get all attributes for this feature. We do this one feature at a time                  # Get all attributes for this feature. We do this one feature at a time
978                  # to insure we do not get any genome attributes.                  # to insure we do not get any genome attributes.
979                  my @attributeList = $fig->get_attributes($fid, '', '', '');                  my @attributeList = $fig->get_attributes($fid, '', '', '');
980                    # Add essentiality and virulence attributes.
981                    if ($fig->essential($fid)) {
982                        push @attributeList, [$fid, 'essential', 1, ''];
983                    }
984                    if ($fig->virulent($fid)) {
985                        push @attributeList, [$fid, 'virulent', 1, ''];
986                    }
987                  if (scalar @attributeList) {                  if (scalar @attributeList) {
988                      $featureCount++;                      $featureCount++;
989                  }                  }
# Line 1370  Line 1396 
1396    
1397      GenomeGroups      GenomeGroups
1398    
1399  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,
1400    butThere is no direct support for genome groups in FIG, so we access the SEED
1401  files directly.  files directly.
1402    
1403  =over 4  =over 4
# Line 1396  Line 1423 
1423          Trace("Loading from existing files.") if T(2);          Trace("Loading from existing files.") if T(2);
1424      } else {      } else {
1425          Trace("Generating group data.") if T(2);          Trace("Generating group data.") if T(2);
1426          # Loop through the genomes.          # Currently there are no groups.
         my $line;  
         for my $genomeID (keys %{$genomeHash}) {  
             Trace("Processing $genomeID.") if T(3);  
             # Open the NMPDR group file for this genome.  
             if (open(TMP, "<$FIG_Config::organisms/$genomeID/NMPDR") &&  
                 defined($line = <TMP>)) {  
                 # Clean the line ending.  
                 chomp $line;  
                 # Add the group to the table. Note that there can only be one group  
                 # per genome.  
                 $loadGenomeGroups->Put($genomeID, $line);  
             }  
             close TMP;  
         }  
1427      }      }
1428      # Finish the load.      # Finish the load.
1429      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
# Line 1506  Line 1519 
1519  The following relations are loaded by this method.  The following relations are loaded by this method.
1520    
1521      Family      Family
1522      ContainsFeature      IsFamilyForFeature
1523    
1524  The source information for these relations is taken from the C<families_for_protein>,  The source information for these relations is taken from the C<families_for_protein>,
1525  C<family_function>, and C<sz_family> methods of the B<FIG> object.  C<family_function>, and C<sz_family> methods of the B<FIG> object.
# Line 1530  Line 1543 
1543      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
1544      # Create load objects for the tables we're loading.      # Create load objects for the tables we're loading.
1545      my $loadFamily = $self->_TableLoader('Family');      my $loadFamily = $self->_TableLoader('Family');
1546      my $loadContainsFeature = $self->_TableLoader('ContainsFeature');      my $loadIsFamilyForFeature = $self->_TableLoader('IsFamilyForFeature');
1547      if ($self->{options}->{loadOnly}) {      if ($self->{options}->{loadOnly}) {
1548          Trace("Loading from existing files.") if T(2);          Trace("Loading from existing files.") if T(2);
1549      } else {      } else {
# Line 1542  Line 1555 
1555              Trace("Processing features for $genomeID.") if T(2);              Trace("Processing features for $genomeID.") if T(2);
1556              # Loop through this genome's PEGs.              # Loop through this genome's PEGs.
1557              for my $fid ($fig->all_features($genomeID, "peg")) {              for my $fid ($fig->all_features($genomeID, "peg")) {
1558                  $loadContainsFeature->Add("features", 1);                  $loadIsFamilyForFeature->Add("features", 1);
1559                  # Get this feature's families.                  # Get this feature's families.
1560                  my @families = $fig->families_for_protein($fid);                  my @families = $fig->families_for_protein($fid);
1561                  # Loop through the families, connecting them to the feature.                  # Loop through the families, connecting them to the feature.
1562                  for my $family (@families) {                  for my $family (@families) {
1563                      $loadContainsFeature->Put($family, $fid);                      $loadIsFamilyForFeature->Put($family, $fid);
1564                      # If this is a new family, create a record for it.                      # If this is a new family, create a record for it.
1565                      if (! exists $familyHash{$family}) {                      if (! exists $familyHash{$family}) {
1566                            $familyHash{$family} = 1;
1567                          $loadFamily->Add("families", 1);                          $loadFamily->Add("families", 1);
1568                          my $size = $fig->sz_family($family);                          my $size = $fig->sz_family($family);
1569                          my $func = $fig->family_function($family);                          my $func = $fig->family_function($family);
# Line 1564  Line 1578 
1578      return $retVal;      return $retVal;
1579  }  }
1580    
1581    
1582    
1583  =head2 Internal Utility Methods  =head2 Internal Utility Methods
1584    
1585  =head3 TableLoader  =head3 TableLoader
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