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revision 1.62, Sun Jul 30 05:44:57 2006 UTC revision 1.81, Wed Feb 21 13:21:42 2007 UTC
# Line 80  Line 80 
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 NMPDR subsystems will be  to a list of subsystem names. If nothing is specified, all NMPDR subsystems will be
82  considered trusted. (A subsystem is considered NMPDR if it has a file named C<NMPDR>  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.  in its data directory.) Only subsystem data related to the NMPDR subsystems is loaded.
84    
85  =item options  =item options
86    
# 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 138  Line 138 
138          if (! defined $subsysFile || $subsysFile eq '') {          if (! defined $subsysFile || $subsysFile eq '') {
139              # Here we want all the usable subsystems. First we get the whole list.              # Here we want all the usable subsystems. First we get the whole list.
140              my @subs = $fig->all_subsystems();              my @subs = $fig->all_subsystems();
141              # Loop through, checking for usability.              # Loop through, checking for the NMPDR file.
142              for my $sub (@subs) {              for my $sub (@subs) {
143                  if ($fig->usable_subsystem($sub)) {                  if ($fig->nmpdr_subsystem($sub)) {
144                      $subsystems{$sub} = 1;                      $subsystems{$sub} = 1;
145                  }                  }
146              }              }
# Line 163  Line 163 
163                  Confess("Invalid subsystem parameter in SproutLoad constructor.");                  Confess("Invalid subsystem parameter in SproutLoad constructor.");
164              }              }
165          }          }
166            # Go through the subsys hash again, creating the keyword list for each subsystem.
167            for my $subsystem (keys %subsystems) {
168                my $name = $subsystem;
169                $name =~ s/_/ /g;
170                my $classes = $fig->subsystem_classification($subsystem);
171                $name .= " " . join(" ", @{$classes});
172                $subsystems{$subsystem} = $name;
173            }
174      }      }
175      # Get the data directory from the Sprout object.      # Get the data directory from the Sprout object.
176      my ($directory) = $sprout->LoadInfo();      my ($directory) = $sprout->LoadInfo();
# Line 266  Line 274 
274              my $extra = join " ", @extraData;              my $extra = join " ", @extraData;
275              # Get the full taxonomy.              # Get the full taxonomy.
276              my $taxonomy = $fig->taxonomy_of($genomeID);              my $taxonomy = $fig->taxonomy_of($genomeID);
277                # Open the NMPDR group file for this genome.
278                my $group;
279                if (open(TMP, "<$FIG_Config::organisms/$genomeID/NMPDR") &&
280                    defined($group = <TMP>)) {
281                    # Clean the line ending.
282                    chomp $group;
283                } else {
284                    # No group, so use the default.
285                    $group = $FIG_Config::otherGroup;
286                }
287                close TMP;
288              # Output the genome record.              # Output the genome record.
289              $loadGenome->Put($genomeID, $accessCode, $fig->is_complete($genomeID), $genus,              $loadGenome->Put($genomeID, $accessCode, $fig->is_complete($genomeID), $genus,
290                               $species, $extra, $taxonomy);                               $group, $species, $extra, $taxonomy);
291              # Now we loop through each of the genome's contigs.              # Now we loop through each of the genome's contigs.
292              my @contigs = $fig->all_contigs($genomeID);              my @contigs = $fig->all_contigs($genomeID);
293              for my $contigID (@contigs) {              for my $contigID (@contigs) {
# Line 449  Line 468 
468      FeatureUpstream      FeatureUpstream
469      IsLocatedIn      IsLocatedIn
470      HasFeature      HasFeature
471        HasRoleInSubsystem
472        FeatureEssential
473        FeatureVirulent
474        FeatureIEDB
475    
476  =over 4  =over 4
477    
# Line 463  Line 486 
486  sub LoadFeatureData {  sub LoadFeatureData {
487      # Get this object instance.      # Get this object instance.
488      my ($self) = @_;      my ($self) = @_;
489      # Get the FIG object.      # Get the FIG and Sprout objects.
490      my $fig = $self->{fig};      my $fig = $self->{fig};
491        my $sprout = $self->{sprout};
492      # Get the table of genome IDs.      # Get the table of genome IDs.
493      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
494      # 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 498 
498      my $loadFeatureLink = $self->_TableLoader('FeatureLink');      my $loadFeatureLink = $self->_TableLoader('FeatureLink');
499      my $loadFeatureTranslation = $self->_TableLoader('FeatureTranslation');      my $loadFeatureTranslation = $self->_TableLoader('FeatureTranslation');
500      my $loadFeatureUpstream = $self->_TableLoader('FeatureUpstream');      my $loadFeatureUpstream = $self->_TableLoader('FeatureUpstream');
501      my $loadHasFeature = $self->_TableLoader('HasFeature');      my $loadHasFeature = $self->_TableLoader('HasFeature', $self->PrimaryOnly);
502        my $loadHasRoleInSubsystem = $self->_TableLoader('HasRoleInSubsystem', $self->PrimaryOnly);
503        my $loadFeatureEssential = $self->_TableLoader('FeatureEssential');
504        my $loadFeatureVirulent = $self->_TableLoader('FeatureVirulent');
505        my $loadFeatureIEDB = $self->_TableLoader('FeatureIEDB');
506        # Get the subsystem hash.
507        my $subHash = $self->{subsystems};
508      # 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
509      # locations.      # locations.
510      my $chunkSize = $self->{sprout}->MaxSegment();      my $chunkSize = $self->{sprout}->MaxSegment();
# Line 491  Line 521 
521              # Sort and count the list.              # Sort and count the list.
522              my @featureTuples = sort { $a->[0] cmp $b->[0] } @{$features};              my @featureTuples = sort { $a->[0] cmp $b->[0] } @{$features};
523              my $count = scalar @featureTuples;              my $count = scalar @featureTuples;
524                my @fids = map { $_->[0] } @featureTuples;
525              Trace("$count features found for genome $genomeID.") if T(3);              Trace("$count features found for genome $genomeID.") if T(3);
526                # Get the attributes for this genome and put them in a hash by feature ID.
527                my $attributes = GetGenomeAttributes($fig, $genomeID, \@fids);
528              # Set up for our duplicate-feature check.              # Set up for our duplicate-feature check.
529              my $oldFeatureID = "";              my $oldFeatureID = "";
530              # Loop through the features.              # Loop through the features.
# Line 505  Line 538 
538                      $oldFeatureID = $featureID;                      $oldFeatureID = $featureID;
539                      # Count this feature.                      # Count this feature.
540                      $loadFeature->Add("featureIn");                      $loadFeature->Add("featureIn");
541                      # Create the feature record.                      # Begin building the keywords. We start with the genome ID, the
542                      $loadFeature->Put($featureID, 1, $type);                      # feature ID, the taxonomy, and the organism name.
543                      # Link it to the parent genome.                      my @keywords = ($genomeID, $featureID, $fig->genus_species($genomeID),
544                      $loadHasFeature->Put($genomeID, $featureID, $type);                                      $fig->taxonomy_of($genomeID));
545                        # Get the functional assignment and aliases.
546                        my $assignment = $fig->function_of($featureID);
547                      # Create the aliases.                      # Create the aliases.
548                      for my $alias ($fig->feature_aliases($featureID)) {                      for my $alias ($fig->feature_aliases($featureID)) {
549                          $loadFeatureAlias->Put($featureID, $alias);                          $loadFeatureAlias->Put($featureID, $alias);
550                            push @keywords, $alias;
551                      }                      }
552                        Trace("Assignment for $featureID is: $assignment") if T(4);
553                        # Break the assignment into words and shove it onto the
554                        # keyword list.
555                        push @keywords, split(/\s+/, $assignment);
556                        # Link this feature to the parent genome.
557                        $loadHasFeature->Put($genomeID, $featureID, $type);
558                      # Get the links.                      # Get the links.
559                      my @links = $fig->fid_links($featureID);                      my @links = $fig->fid_links($featureID);
560                      for my $link (@links) {                      for my $link (@links) {
# Line 531  Line 573 
573                              $loadFeatureUpstream->Put($featureID, $upstream);                              $loadFeatureUpstream->Put($featureID, $upstream);
574                          }                          }
575                      }                      }
576                        # Now we need to find the subsystems this feature participates in.
577                        # We also add the subsystems to the keyword list. Before we do that,
578                        # we must convert underscores to spaces and tack on the classifications.
579                        my @subsystems = $fig->peg_to_subsystems($featureID);
580                        for my $subsystem (@subsystems) {
581                            # Only proceed if we like this subsystem.
582                            if (exists $subHash->{$subsystem}) {
583                                # Store the has-role link.
584                                $loadHasRoleInSubsystem->Put($featureID, $subsystem, $genomeID, $type);
585                                # Save the subsystem's keyword data.
586                                my $subKeywords = $subHash->{$subsystem};
587                                push @keywords, split /\s+/, $subKeywords;
588                                # Now we need to get this feature's role in the subsystem.
589                                my $subObject = $fig->get_subsystem($subsystem);
590                                my @roleColumns = $subObject->get_peg_roles($featureID);
591                                my @allRoles = $subObject->get_roles();
592                                for my $col (@roleColumns) {
593                                    my $role = $allRoles[$col];
594                                    push @keywords, split /\s+/, $role;
595                                    push @keywords, $subObject->get_role_abbr($col);
596                                }
597                            }
598                        }
599                        # There are three special attributes computed from property
600                        # data that we build next. If the special attribute is non-empty,
601                        # its name will be added to the keyword list. First, we get all
602                        # the attributes for this feature. They will come back as
603                        # 4-tuples: [peg, name, value, URL]. We use a 3-tuple instead:
604                        # [name, value, value with URL]. (We don't need the PEG, since
605                        # we already know it.)
606                        my @attributes = map { [$_->[1], $_->[2], Tracer::CombineURL($_->[2], $_->[3])] }
607                                             @{$attributes->{$featureID}};
608                        # Now we process each of the special attributes.
609                        if (SpecialAttribute($featureID, \@attributes,
610                                             1, [0,2], '^(essential|potential_essential)$',
611                                             $loadFeatureEssential)) {
612                            push @keywords, 'essential';
613                            $loadFeature->Add('essential');
614                        }
615                        if (SpecialAttribute($featureID, \@attributes,
616                                             0, [2], '^virulen',
617                                             $loadFeatureVirulent)) {
618                            push @keywords, 'virulent';
619                            $loadFeature->Add('virulent');
620                        }
621                        if (SpecialAttribute($featureID, \@attributes,
622                                             0, [0,2], '^iedb_',
623                                             $loadFeatureIEDB)) {
624                            push @keywords, 'iedb';
625                            $loadFeature->Add('iedb');
626                        }
627                        # Now we need to bust up hyphenated words in the keyword
628                        # list. We keep them separate and put them at the end so
629                        # the original word order is available.
630                        my $keywordString = "";
631                        my $bustedString = "";
632                        for my $keyword (@keywords) {
633                            if (length $keyword >= 3) {
634                                $keywordString .= " $keyword";
635                                if ($keyword =~ /-/) {
636                                    my @words = split /-/, $keyword;
637                                    $bustedString .= join(" ", "", @words);
638                                }
639                            }
640                        }
641                        $keywordString .= $bustedString;
642                        # Get rid of annoying punctuation.
643                        $keywordString =~ s/[();]//g;
644                        # Clean the keyword list.
645                        my $cleanWords = $sprout->CleanKeywords($keywordString);
646                        Trace("Keyword string for $featureID: $cleanWords") if T(4);
647                        # Create the feature record.
648                        $loadFeature->Put($featureID, 1, $type, $assignment, $cleanWords);
649                      # 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
650                      # 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
651                      # 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 681 
681      return $retVal;      return $retVal;
682  }  }
683    
 =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;  
 }  
   
684  =head3 LoadSubsystemData  =head3 LoadSubsystemData
685    
686  C<< my $stats = $spl->LoadSubsystemData(); >>  C<< my $stats = $spl->LoadSubsystemData(); >>
# Line 738  Line 785 
785                  my $curator = $sub->get_curator();                  my $curator = $sub->get_curator();
786                  my $notes = $sub->get_notes();                  my $notes = $sub->get_notes();
787                  $loadSubsystem->Put($subsysID, $curator, $notes);                  $loadSubsystem->Put($subsysID, $curator, $notes);
788                  my $class = $fig->subsystem_classification($subsysID);                  # Now for the classification string. This comes back as a list
789                  if ($class) {                  # reference and we convert it to a space-delimited string.
790                      $loadSubsystemClass->Put($subsysID, $class);                  my $classList = $fig->subsystem_classification($subsysID);
791                  }                  my $classString = join($FIG_Config::splitter, grep { $_ } @$classList);
792                    $loadSubsystemClass->Put($subsysID, $classString);
793                  # 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.
794                  for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {                  for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {
795                      # Connect to this role.                      # Connect to this role.
# Line 944  Line 992 
992          my %propertyKeys = ();          my %propertyKeys = ();
993          my $nextID = 1;          my $nextID = 1;
994          # Loop through the genomes.          # Loop through the genomes.
995          for my $genomeID (keys %{$genomeHash}) {          for my $genomeID (sort keys %{$genomeHash}) {
996              $loadProperty->Add("genomeIn");              $loadProperty->Add("genomeIn");
997              Trace("Generating properties for $genomeID.") if T(3);              Trace("Generating properties for $genomeID.") if T(3);
998              # 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 953  Line 1001 
1001              my @features = map { $_->[0] } @{$fig->all_features_detailed($genomeID)};              my @features = map { $_->[0] } @{$fig->all_features_detailed($genomeID)};
1002              my $featureCount = 0;              my $featureCount = 0;
1003              my $propertyCount = 0;              my $propertyCount = 0;
1004                # Get the properties for this genome's features.
1005                my $attributes = GetGenomeAttributes($fig, $genomeID, \@features);
1006                Trace("Property hash built for $genomeID.") if T(3);
1007              # Loop through the features, creating HasProperty records.              # Loop through the features, creating HasProperty records.
1008              for my $fid (@features) {              for my $fid (@features) {
1009                  # 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
1010                  # to insure we do not get any genome attributes.                  # to insure we do not get any genome attributes.
1011                  my @attributeList = $fig->get_attributes($fid, '', '', '');                  my @attributeList = @{$attributes->{$fid}};
1012                  if (scalar @attributeList) {                  if (scalar @attributeList) {
1013                      $featureCount++;                      $featureCount++;
1014                  }                  }
# Line 1370  Line 1421 
1421    
1422      GenomeGroups      GenomeGroups
1423    
1424  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,
1425    butThere is no direct support for genome groups in FIG, so we access the SEED
1426  files directly.  files directly.
1427    
1428  =over 4  =over 4
# Line 1396  Line 1448 
1448          Trace("Loading from existing files.") if T(2);          Trace("Loading from existing files.") if T(2);
1449      } else {      } else {
1450          Trace("Generating group data.") if T(2);          Trace("Generating group data.") if T(2);
1451          # 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;  
         }  
1452      }      }
1453      # Finish the load.      # Finish the load.
1454      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
# Line 1506  Line 1544 
1544  The following relations are loaded by this method.  The following relations are loaded by this method.
1545    
1546      Family      Family
1547      ContainsFeature      IsFamilyForFeature
1548    
1549  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>,
1550  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 1568 
1568      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
1569      # Create load objects for the tables we're loading.      # Create load objects for the tables we're loading.
1570      my $loadFamily = $self->_TableLoader('Family');      my $loadFamily = $self->_TableLoader('Family');
1571      my $loadContainsFeature = $self->_TableLoader('ContainsFeature');      my $loadIsFamilyForFeature = $self->_TableLoader('IsFamilyForFeature');
1572      if ($self->{options}->{loadOnly}) {      if ($self->{options}->{loadOnly}) {
1573          Trace("Loading from existing files.") if T(2);          Trace("Loading from existing files.") if T(2);
1574      } else {      } else {
# Line 1542  Line 1580 
1580              Trace("Processing features for $genomeID.") if T(2);              Trace("Processing features for $genomeID.") if T(2);
1581              # Loop through this genome's PEGs.              # Loop through this genome's PEGs.
1582              for my $fid ($fig->all_features($genomeID, "peg")) {              for my $fid ($fig->all_features($genomeID, "peg")) {
1583                  $loadContainsFeature->Add("features", 1);                  $loadIsFamilyForFeature->Add("features", 1);
1584                  # Get this feature's families.                  # Get this feature's families.
1585                  my @families = $fig->families_for_protein($fid);                  my @families = $fig->families_for_protein($fid);
1586                  # Loop through the families, connecting them to the feature.                  # Loop through the families, connecting them to the feature.
1587                  for my $family (@families) {                  for my $family (@families) {
1588                      $loadContainsFeature->Put($family, $fid);                      $loadIsFamilyForFeature->Put($family, $fid);
1589                      # If this is a new family, create a record for it.                      # If this is a new family, create a record for it.
1590                      if (! exists $familyHash{$family}) {                      if (! exists $familyHash{$family}) {
1591                          $familyHash{$family} = 1;                          $familyHash{$family} = 1;
# Line 1565  Line 1603 
1603      return $retVal;      return $retVal;
1604  }  }
1605    
1606    =head3 LoadDrugData
1607    
1608    C<< my $stats = $spl->LoadDrugData(); >>
1609    
1610    Load the drug target data into Sprout.
1611    
1612    The following relations are loaded by this method.
1613    
1614        DrugProject
1615        ContainsTopic
1616        DrugTopic
1617        ContainsAnalysisOf
1618        PDB
1619        IncludesBound
1620        IsBoundIn
1621        BindsWith
1622        Ligand
1623        DescribesProteinForFeature
1624        FeatureConservation
1625    
1626    The source information for these relations is taken from flat files in the
1627    C<$FIG_Config::drug_directory>. The file C<master_tables.list> contains
1628    a list of drug project names paired with file names. The named file (in the
1629    same directory) contains all the data for the project.
1630    
1631    =over 4
1632    
1633    =item RETURNS
1634    
1635    Returns a statistics object for the loads.
1636    
1637    =back
1638    
1639    =cut
1640    #: Return Type $%;
1641    sub LoadDrugData {
1642        # Get this object instance.
1643        my ($self) = @_;
1644        # Get the FIG object.
1645        my $fig = $self->{fig};
1646        # Get the genome hash.
1647        my $genomeHash = $self->{genomes};
1648        # Create load objects for the tables we're loading.
1649        my $loadDrugProject = $self->_TableLoader('DrugProject');
1650        my $loadContainsTopic = $self->_TableLoader('ContainsTopic');
1651        my $loadDrugTopic = $self->_TableLoader('DrugTopic');
1652        my $loadContainsAnalysisOf = $self->_TableLoader('ContainsAnalysisOf');
1653        my $loadPDB = $self->_TableLoader('PDB');
1654        my $loadIncludesBound = $self->_TableLoader('IncludesBound');
1655        my $loadIsBoundIn = $self->_TableLoader('IsBoundIn');
1656        my $loadBindsWith = $self->_TableLoader('BindsWith');
1657        my $loadLigand = $self->_TableLoader('Ligand');
1658        my $loadDescribesProteinForFeature = $self->_TableLoader('DescribesProteinForFeature');
1659        my $loadFeatureConservation = $self->_TableLoader('FeatureConservation');
1660        if ($self->{options}->{loadOnly}) {
1661            Trace("Loading from existing files.") if T(2);
1662        } else {
1663            Trace("Generating drug target data.") if T(2);
1664            # Load the project list. The file comes in as a list of chomped lines,
1665            # and we split them on the TAB character to make the project name the
1666            # key and the file name the value of the resulting hash.
1667            my %projects = map { split /\t/, $_ } Tracer::GetFile("$FIG_Config::drug_directory/master_tables.list");
1668            # Create hashes for the derived objects: PDBs, Features, and Ligands. These objects
1669            # may occur multiple times in a single project file or even in multiple project
1670            # files.
1671            my %ligands = ();
1672            my %pdbs = ();
1673            my %features = ();
1674            my %bindings = ();
1675            # Set up a counter for drug topics. This will be used as the key.
1676            my $topicCounter = 0;
1677            # Loop through the projects. We sort the keys not because we need them sorted, but
1678            # because it makes it easier to infer our progress from trace messages.
1679            for my $project (sort keys %projects) {
1680                Trace("Processing project $project.") if T(3);
1681                # Only proceed if the download file exists.
1682                my $projectFile = "$FIG_Config::drug_directory/$projects{$project}";
1683                if (! -f $projectFile) {
1684                    Trace("Project file $projectFile not found.") if T(0);
1685                } else {
1686                    # Create the project record.
1687                    $loadDrugProject->Put($project);
1688                    # Create a hash for the topics. Each project has one or more topics. The
1689                    # topic is identified by a URL, a category, and an identifier.
1690                    my %topics = ();
1691                    # Now we can open the project file.
1692                    Trace("Reading project file $projectFile.") if T(3);
1693                    Open(\*PROJECT, "<$projectFile");
1694                    # Get the first record, which is a list of column headers. We don't use this
1695                    # for anything, but it may be useful for debugging.
1696                    my $headerLine = <PROJECT>;
1697                    # Loop through the rest of the records.
1698                    while (! eof PROJECT) {
1699                        # Get the current line of data. Note that not all lines will have all
1700                        # the fields. In particular, the CLIBE data is fairly rare.
1701                        my ($authorOrganism, $category, $tag, $refURL, $peg, $conservation,
1702                            $pdbBound, $pdbBoundEval, $pdbFree, $pdbFreeEval, $pdbFreeTitle,
1703                            $protDistInfo, $passAspInfo, $passAspFile, $passWeightInfo,
1704                            $passWeightFile, $clibeInfo, $clibeURL, $clibeTotalEnergy,
1705                            $clibeVanderwaals, $clibeHBonds, $clibeEI, $clibeSolvationE)
1706                           = Tracer::GetLine(\*PROJECT);
1707                        # The tag contains an identifier for the current line of data followed
1708                        # by a text statement that generally matches a property name in the
1709                        # main database. We split it up, since the identifier goes with
1710                        # the PDB data and the text statement is part of the topic.
1711                        my ($lineID, $topicTag) = split /\s*,\s*/, $tag;
1712                        $loadDrugProject->Add("data line");
1713                        # Check for a new topic.
1714                        my $topicData = "$category\t$topicTag\t$refURL";
1715                        if (! exists $topics{$topicData}) {
1716                            # Here we have a new topic. Compute its ID.
1717                            $topicCounter++;
1718                            $topics{$topicData} = $topicCounter;
1719                            # Create its database record.
1720                            $loadDrugTopic->Put($topicCounter, $refURL, $category, $authorOrganism,
1721                                                $topicTag);
1722                            # Connect it to the project.
1723                            $loadContainsTopic->Put($project, $topicCounter);
1724                            $loadDrugTopic->Add("topic");
1725                        }
1726                        # Now we know the topic ID exists in the hash and the topic will
1727                        # appear in the database, so we get this topic's ID.
1728                        my $topicID = $topics{$topicData};
1729                        # If the feature in this line is new, we need to save its conservation
1730                        # number.
1731                        if (! exists $features{$peg}) {
1732                            $loadFeatureConservation->Put($peg, $conservation);
1733                            $features{$peg} = 1;
1734                        }
1735                        # Now we have two PDBs to deal with-- a bound PDB and a free PDB.
1736                        # The free PDB will have data about docking points; the bound PDB
1737                        # will have data about docking. We store both types as PDBs, and
1738                        # the special data comes from relationships. First we process the
1739                        # bound PDB.
1740                        if ($pdbBound) {
1741                            $loadPDB->Add("bound line");
1742                            # Insure this PDB is in the database.
1743                            $self->CreatePDB($pdbBound, lc "$pdbFreeTitle (bound)", "bound", \%pdbs, $loadPDB);
1744                            # Connect it to this topic.
1745                            $loadIncludesBound->Put($topicID, $pdbBound);
1746                            # Check for CLIBE data.
1747                            if ($clibeInfo) {
1748                                $loadLigand->Add("clibes");
1749                                # We have CLIBE data, so we create a ligand and relate it to the PDB.
1750                                if (! exists $ligands{$clibeInfo}) {
1751                                    # This is a new ligand, so create its record.
1752                                    $loadLigand->Put($clibeInfo);
1753                                    $loadLigand->Add("ligand");
1754                                    # Make sure we know this ligand already exists.
1755                                    $ligands{$clibeInfo} = 1;
1756                                }
1757                                # Now connect the PDB to the ligand using the CLIBE data.
1758                                $loadBindsWith->Put($pdbBound, $clibeInfo, $clibeURL, $clibeHBonds, $clibeEI,
1759                                                    $clibeSolvationE, $clibeVanderwaals);
1760                            }
1761                            # Connect this PDB to the feature.
1762                            $loadDescribesProteinForFeature->Put($pdbBound, $peg, $protDistInfo, $pdbBoundEval);
1763                        }
1764                        # Next is the free PDB.
1765                        if ($pdbFree) {
1766                            $loadPDB->Add("free line");
1767                            # Insure this PDB is in the database.
1768                            $self->CreatePDB($pdbFree, lc $pdbFreeTitle, "free", \%pdbs, $loadPDB);
1769                            # Connect it to this topic.
1770                            $loadContainsAnalysisOf->Put($topicID, $pdbFree, $passAspInfo,
1771                                                         $passWeightFile, $passWeightInfo, $passAspFile);
1772                            # Connect this PDB to the feature.
1773                            $loadDescribesProteinForFeature->Put($pdbFree, $peg, $protDistInfo, $pdbFreeEval);
1774                        }
1775                        # If we have both PDBs, we may need to link them.
1776                        if ($pdbFree && $pdbBound) {
1777                            $loadIsBoundIn->Add("connection");
1778                            # Insure we only link them once.
1779                            my $bindingKey =  "$pdbFree\t$pdbBound";
1780                            if (! exists $bindings{$bindingKey}) {
1781                                $loadIsBoundIn->Add("newConnection");
1782                                $loadIsBoundIn->Put($pdbFree, $pdbBound);
1783                                $bindings{$bindingKey} = 1;
1784                            }
1785                        }
1786                    }
1787                    # Close off this project.
1788                    close PROJECT;
1789                }
1790            }
1791        }
1792        # Finish the load.
1793        my $retVal = $self->_FinishAll();
1794        return $retVal;
1795    }
1796    
1797    
1798  =head2 Internal Utility Methods  =head2 Internal Utility Methods
1799    
1800    =head3 SpecialAttribute
1801    
1802    C<< my $count = SproutLoad::SpecialAttribute($id, \@attributes, $idxMatch, \@idxValues, $pattern, $loader); >>
1803    
1804    Look for special attributes of a given type. A special attribute is found by comparing one of
1805    the columns of the incoming attribute list to a search pattern. If a match is found, then
1806    a set of columns is put into an output table connected to the specified ID.
1807    
1808    For example, when processing features, the attribute list we look at has three columns: attribute
1809    name, attribute value, and attribute value HTML. The IEDB attribute exists if the attribute name
1810    begins with C<iedb_>. The call signature is therefore
1811    
1812        my $found = SpecialAttribute($fid, \@attributeList, 0, [0,2], '^iedb_', $loadFeatureIEDB);
1813    
1814    The pattern is matched against column 0, and if we have a match, then column 2's value is put
1815    to the output along with the specified feature ID.
1816    
1817    =over 4
1818    
1819    =item id
1820    
1821    ID of the object whose special attributes are being loaded. This forms the first column of the
1822    output.
1823    
1824    =item attributes
1825    
1826    Reference to a list of tuples.
1827    
1828    =item idxMatch
1829    
1830    Index in each tuple of the column to be matched against the pattern. If the match is
1831    successful, an output record will be generated.
1832    
1833    =item idxValues
1834    
1835    Reference to a list containing the indexes in each tuple of the columns to be put as
1836    the second column of the output.
1837    
1838    =item pattern
1839    
1840    Pattern to be matched against the specified column. The match will be case-insensitive.
1841    
1842    =item loader
1843    
1844    An object to which each output record will be put. Usually this is an B<ERDBLoad> object,
1845    but technically it could be anything with a C<Put> method.
1846    
1847    =item RETURN
1848    
1849    Returns a count of the matches found.
1850    
1851    =item
1852    
1853    =back
1854    
1855    =cut
1856    
1857    sub SpecialAttribute {
1858        # Get the parameters.
1859        my ($id, $attributes, $idxMatch, $idxValues, $pattern, $loader) = @_;
1860        # Declare the return variable.
1861        my $retVal = 0;
1862        # Loop through the attribute rows.
1863        for my $row (@{$attributes}) {
1864            # Check for a match.
1865            if ($row->[$idxMatch] =~ m/$pattern/i) {
1866                # We have a match, so output a row. This is a bit tricky, since we may
1867                # be putting out multiple columns of data from the input.
1868                my $value = join(" ", map { $row->[$_] } @{$idxValues});
1869                $loader->Put($id, $value);
1870                $retVal++;
1871            }
1872        }
1873        Trace("$retVal special attributes found for $id and loader " . $loader->RelName() . ".") if T(4) && $retVal;
1874        # Return the number of matches.
1875        return $retVal;
1876    }
1877    
1878    =head3 CreatePDB
1879    
1880    C<< $loader->CreatePDB($pdbID, $title, $type, \%pdbHash); >>
1881    
1882    Insure that a PDB record exists for the identified PDB. If one does not exist, it will be
1883    created.
1884    
1885    =over 4
1886    
1887    =item pdbID
1888    
1889    ID string (usually an unqualified file name) for the desired PDB.
1890    
1891    =item title
1892    
1893    Title to use if the PDB must be created.
1894    
1895    =item type
1896    
1897    Type of PDB: C<free> or C<bound>
1898    
1899    =item pdbHash
1900    
1901    Hash containing the IDs of PDBs that have already been created.
1902    
1903    =item pdbLoader
1904    
1905    Load object for the PDB table.
1906    
1907    =back
1908    
1909    =cut
1910    
1911    sub CreatePDB {
1912        # Get the parameters.
1913        my ($self, $pdbID, $title, $type, $pdbHash, $pdbLoader) = @_;
1914        $pdbLoader->Add("PDB check");
1915        # Check to see if this is a new PDB.
1916        if (! exists $pdbHash->{$pdbID}) {
1917            # It is, so we create it.
1918            $pdbLoader->Put($pdbID, $title, $type);
1919            $pdbHash->{$pdbID} = 1;
1920            # Count it.
1921            $pdbLoader->Add("PDB-$type");
1922        }
1923    }
1924    
1925  =head3 TableLoader  =head3 TableLoader
1926    
1927  Create an ERDBLoad object for the specified table. The object is also added to  Create an ERDBLoad object for the specified table. The object is also added to
# Line 1669  Line 2024 
2024      # Return the load statistics.      # Return the load statistics.
2025      return $retVal;      return $retVal;
2026  }  }
2027    =head3 GetGenomeAttributes
2028    
2029    C<< my $aHashRef = GetGenomeAttributes($fig, $genomeID, \@fids); >>
2030    
2031    Return a hash of attributes keyed on feature ID. This method gets all the attributes
2032    for all the features of a genome in a single call, then organizes them into a hash.
2033    
2034    =over 4
2035    
2036    =item fig
2037    
2038    FIG-like object for accessing attributes.
2039    
2040    =item genomeID
2041    
2042    ID of the genome who's attributes are desired.
2043    
2044    =item fids
2045    
2046    Reference to a list of the feature IDs whose attributes are to be kept.
2047    
2048    =item RETURN
2049    
2050    Returns a reference to a hash. The key of the hash is the feature ID. The value is the
2051    reference to a list of the feature's attribute tuples. Each tuple contains the feature ID,
2052    the attribute key, and one or more attribute values.
2053    
2054    =back
2055    
2056    =cut
2057    
2058    sub GetGenomeAttributes {
2059        # Get the parameters.
2060        my ($fig, $genomeID, $fids) = @_;
2061        # Declare the return variable.
2062        my $retVal = {};
2063        # Get the attributes.
2064        my @aList = $fig->get_attributes("fig|$genomeID%");
2065        # Initialize the hash. This not only enables us to easily determine which FIDs to
2066        # keep, it insures that the caller sees a list reference for every known fid,
2067        # simplifying the logic.
2068        for my $fid (@{$fids}) {
2069            $retVal->{$fid} = [];
2070        }
2071        # Populate the hash.
2072        for my $aListEntry (@aList) {
2073            my $fid = $aListEntry->[0];
2074            if (exists $retVal->{$fid}) {
2075                push @{$retVal->{$fid}}, $aListEntry;
2076            }
2077        }
2078        # Return the result.
2079        return $retVal;
2080    }
2081    
2082  1;  1;

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