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revision 1.62, Sun Jul 30 05:44:57 2006 UTC revision 1.78, Wed Nov 15 12:15:30 2006 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 505  Line 535 
535                      $oldFeatureID = $featureID;                      $oldFeatureID = $featureID;
536                      # Count this feature.                      # Count this feature.
537                      $loadFeature->Add("featureIn");                      $loadFeature->Add("featureIn");
538                      # Create the feature record.                      # Begin building the keywords. We start with the genome ID, the
539                      $loadFeature->Put($featureID, 1, $type);                      # feature ID, and the organism name.
540                      # Link it to the parent genome.                      my @keywords = ($genomeID, $featureID, $fig->genus_species($genomeID));
541                      $loadHasFeature->Put($genomeID, $featureID, $type);                      # Get the functional assignment and aliases. This
542                        # depends on the feature type.
543                        my $assignment;
544                        if ($type eq "peg") {
545                            $assignment = $fig->function_of($featureID);
546                      # Create the aliases.                      # Create the aliases.
547                      for my $alias ($fig->feature_aliases($featureID)) {                      for my $alias ($fig->feature_aliases($featureID)) {
548                          $loadFeatureAlias->Put($featureID, $alias);                          $loadFeatureAlias->Put($featureID, $alias);
549                                push @keywords, $alias;
550                      }                      }
551                        } else {
552                            # For other types, the assignment is the first (and ONLY) alias.
553                            ($assignment) = $fig->feature_aliases($featureID);
554                        }
555                        Trace("Assignment for $featureID is: $assignment") if T(4);
556                        # Break the assignment into words and shove it onto the
557                        # keyword list.
558                        push @keywords, split(/\s+/, $assignment);
559                        # Link this feature to the parent genome.
560                        $loadHasFeature->Put($genomeID, $featureID, $type);
561                      # Get the links.                      # Get the links.
562                      my @links = $fig->fid_links($featureID);                      my @links = $fig->fid_links($featureID);
563                      for my $link (@links) {                      for my $link (@links) {
# Line 531  Line 576 
576                              $loadFeatureUpstream->Put($featureID, $upstream);                              $loadFeatureUpstream->Put($featureID, $upstream);
577                          }                          }
578                      }                      }
579                        # Now we need to find the subsystems this feature participates in.
580                        # We also add the subsystems to the keyword list. Before we do that,
581                        # we must convert underscores to spaces and tack on the classifications.
582                        my @subsystems = $fig->peg_to_subsystems($featureID);
583                        for my $subsystem (@subsystems) {
584                            # Only proceed if we like this subsystem.
585                            if (exists $subHash->{$subsystem}) {
586                                # Store the has-role link.
587                                $loadHasRoleInSubsystem->Put($featureID, $subsystem, $genomeID, $type);
588                                # Save the subsystem's keyword data.
589                                my $subKeywords = $subHash->{$subsystem};
590                                push @keywords, split /\s+/, $subKeywords;
591                                # Now we need to get this feature's role in the subsystem.
592                                my $subObject = $fig->get_subsystem($subsystem);
593                                my @roleColumns = $subObject->get_peg_roles($featureID);
594                                my @allRoles = $subObject->get_roles();
595                                for my $col (@roleColumns) {
596                                    my $role = $allRoles[$col];
597                                    push @keywords, split /\s+/, $role;
598                                    push @keywords, $subObject->get_role_abbr($col);
599                                }
600                            }
601                        }
602                        # There are three special attributes computed from property
603                        # data that we build next. If the special attribute is non-empty,
604                        # its name will be added to the keyword list. First, we get all
605                        # the attributes for this feature. They will come back as
606                        # 4-tuples: [peg, name, value, URL]. We use a 3-tuple instead:
607                        # [name, value, value with URL]. (We don't need the PEG, since
608                        # we already know it.)
609                        my @attributes = map { [$_->[1], $_->[2], Tracer::CombineURL($_->[2], $_->[3])] }
610                                             $fig->get_attributes($featureID);
611                        # Now we process each of the special attributes.
612                        if (SpecialAttribute($featureID, \@attributes,
613                                             1, [0,2], '^(essential|potential_essential)$',
614                                             $loadFeatureEssential)) {
615                            push @keywords, 'essential';
616                            $loadFeature->Add('essential');
617                        }
618                        if (SpecialAttribute($featureID, \@attributes,
619                                             0, [2], '^virulen',
620                                             $loadFeatureVirulent)) {
621                            push @keywords, 'virulent';
622                            $loadFeature->Add('virulent');
623                        }
624                        if (SpecialAttribute($featureID, \@attributes,
625                                             0, [0,2], '^iedb_',
626                                             $loadFeatureIEDB)) {
627                            push @keywords, 'iedb';
628                            $loadFeature->Add('iedb');
629                        }
630                        # Now we need to bust up hyphenated words in the keyword
631                        # list.
632                        my $keywordString = "";
633                        for my $keyword (@keywords) {
634                            if (length $keyword >= 4) {
635                                $keywordString .= " $keyword";
636                                if ($keyword =~ /-/) {
637                                    my @words = grep { length($_) >= 4 } split /-/, $keyword;
638                                    $keywordString .= join(" ", "", @words);
639                                }
640                            }
641                        }
642                        # Clean the keyword list.
643                        my $cleanWords = $sprout->CleanKeywords($keywordString);
644                        Trace("Keyword string for $featureID: $cleanWords") if T(4);
645                        # Create the feature record.
646                        $loadFeature->Put($featureID, 1, $type, $assignment, $cleanWords);
647                      # 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
648                      # 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
649                      # 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 679 
679      return $retVal;      return $retVal;
680  }  }
681    
 =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;  
 }  
   
682  =head3 LoadSubsystemData  =head3 LoadSubsystemData
683    
684  C<< my $stats = $spl->LoadSubsystemData(); >>  C<< my $stats = $spl->LoadSubsystemData(); >>
# Line 738  Line 783 
783                  my $curator = $sub->get_curator();                  my $curator = $sub->get_curator();
784                  my $notes = $sub->get_notes();                  my $notes = $sub->get_notes();
785                  $loadSubsystem->Put($subsysID, $curator, $notes);                  $loadSubsystem->Put($subsysID, $curator, $notes);
786                  my $class = $fig->subsystem_classification($subsysID);                  # Now for the classification string. This comes back as a list
787                  if ($class) {                  # reference and we convert it to a space-delimited string.
788                      $loadSubsystemClass->Put($subsysID, $class);                  my $classList = $fig->subsystem_classification($subsysID);
789                  }                  my $classString = join($FIG_Config::splitter, grep { $_ } @$classList);
790                    $loadSubsystemClass->Put($subsysID, $classString);
791                  # 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.
792                  for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {                  for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {
793                      # Connect to this role.                      # Connect to this role.
# Line 944  Line 990 
990          my %propertyKeys = ();          my %propertyKeys = ();
991          my $nextID = 1;          my $nextID = 1;
992          # Loop through the genomes.          # Loop through the genomes.
993          for my $genomeID (keys %{$genomeHash}) {          for my $genomeID (sort keys %{$genomeHash}) {
994              $loadProperty->Add("genomeIn");              $loadProperty->Add("genomeIn");
995              Trace("Generating properties for $genomeID.") if T(3);              Trace("Generating properties for $genomeID.") if T(3);
996              # 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 957  Line 1003 
1003              for my $fid (@features) {              for my $fid (@features) {
1004                  # 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
1005                  # to insure we do not get any genome attributes.                  # to insure we do not get any genome attributes.
1006                  my @attributeList = $fig->get_attributes($fid, '', '', '');                  my @attributeList = $fig->get_attributes($fid);
1007                    # Add essentiality and virulence attributes.
1008                    if ($fig->essential($fid)) {
1009                        push @attributeList, [$fid, 'essential', 1, ''];
1010                    }
1011                    if ($fig->virulent($fid)) {
1012                        push @attributeList, [$fid, 'virulent', 1, ''];
1013                    }
1014                  if (scalar @attributeList) {                  if (scalar @attributeList) {
1015                      $featureCount++;                      $featureCount++;
1016                  }                  }
# Line 1370  Line 1423 
1423    
1424      GenomeGroups      GenomeGroups
1425    
1426  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,
1427    butThere is no direct support for genome groups in FIG, so we access the SEED
1428  files directly.  files directly.
1429    
1430  =over 4  =over 4
# Line 1396  Line 1450 
1450          Trace("Loading from existing files.") if T(2);          Trace("Loading from existing files.") if T(2);
1451      } else {      } else {
1452          Trace("Generating group data.") if T(2);          Trace("Generating group data.") if T(2);
1453          # 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;  
         }  
1454      }      }
1455      # Finish the load.      # Finish the load.
1456      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
# Line 1506  Line 1546 
1546  The following relations are loaded by this method.  The following relations are loaded by this method.
1547    
1548      Family      Family
1549      ContainsFeature      IsFamilyForFeature
1550    
1551  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>,
1552  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 1570 
1570      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
1571      # Create load objects for the tables we're loading.      # Create load objects for the tables we're loading.
1572      my $loadFamily = $self->_TableLoader('Family');      my $loadFamily = $self->_TableLoader('Family');
1573      my $loadContainsFeature = $self->_TableLoader('ContainsFeature');      my $loadIsFamilyForFeature = $self->_TableLoader('IsFamilyForFeature');
1574      if ($self->{options}->{loadOnly}) {      if ($self->{options}->{loadOnly}) {
1575          Trace("Loading from existing files.") if T(2);          Trace("Loading from existing files.") if T(2);
1576      } else {      } else {
# Line 1542  Line 1582 
1582              Trace("Processing features for $genomeID.") if T(2);              Trace("Processing features for $genomeID.") if T(2);
1583              # Loop through this genome's PEGs.              # Loop through this genome's PEGs.
1584              for my $fid ($fig->all_features($genomeID, "peg")) {              for my $fid ($fig->all_features($genomeID, "peg")) {
1585                  $loadContainsFeature->Add("features", 1);                  $loadIsFamilyForFeature->Add("features", 1);
1586                  # Get this feature's families.                  # Get this feature's families.
1587                  my @families = $fig->families_for_protein($fid);                  my @families = $fig->families_for_protein($fid);
1588                  # Loop through the families, connecting them to the feature.                  # Loop through the families, connecting them to the feature.
1589                  for my $family (@families) {                  for my $family (@families) {
1590                      $loadContainsFeature->Put($family, $fid);                      $loadIsFamilyForFeature->Put($family, $fid);
1591                      # If this is a new family, create a record for it.                      # If this is a new family, create a record for it.
1592                      if (! exists $familyHash{$family}) {                      if (! exists $familyHash{$family}) {
1593                          $familyHash{$family} = 1;                          $familyHash{$family} = 1;
# Line 1565  Line 1605 
1605      return $retVal;      return $retVal;
1606  }  }
1607    
1608    =head3 LoadDrugData
1609    
1610    C<< my $stats = $spl->LoadDrugData(); >>
1611    
1612    Load the drug target data into Sprout.
1613    
1614    The following relations are loaded by this method.
1615    
1616        DrugProject
1617        ContainsTopic
1618        DrugTopic
1619        ContainsAnalysisOf
1620        PDB
1621        IncludesBound
1622        IsBoundIn
1623        BindsWith
1624        Ligand
1625        DescribesProteinForFeature
1626        FeatureConservation
1627    
1628    The source information for these relations is taken from flat files in the
1629    C<$FIG_Config::drug_directory>. The file C<master_tables.list> contains
1630    a list of drug project names paired with file names. The named file (in the
1631    same directory) contains all the data for the project.
1632    
1633    =over 4
1634    
1635    =item RETURNS
1636    
1637    Returns a statistics object for the loads.
1638    
1639    =back
1640    
1641    =cut
1642    #: Return Type $%;
1643    sub LoadDrugData {
1644        # Get this object instance.
1645        my ($self) = @_;
1646        # Get the FIG object.
1647        my $fig = $self->{fig};
1648        # Get the genome hash.
1649        my $genomeHash = $self->{genomes};
1650        # Create load objects for the tables we're loading.
1651        my $loadDrugProject = $self->_TableLoader('DrugProject');
1652        my $loadContainsTopic = $self->_TableLoader('ContainsTopic');
1653        my $loadDrugTopic = $self->_TableLoader('DrugTopic');
1654        my $loadContainsAnalysisOf = $self->_TableLoader('ContainsAnalysisOf');
1655        my $loadPDB = $self->_TableLoader('PDB');
1656        my $loadIncludesBound = $self->_TableLoader('IncludesBound');
1657        my $loadIsBoundIn = $self->_TableLoader('IsBoundIn');
1658        my $loadBindsWith = $self->_TableLoader('BindsWith');
1659        my $loadLigand = $self->_TableLoader('Ligand');
1660        my $loadDescribesProteinForFeature = $self->_TableLoader('DescribesProteinForFeature');
1661        my $loadFeatureConservation = $self->_TableLoader('FeatureConservation');
1662        if ($self->{options}->{loadOnly}) {
1663            Trace("Loading from existing files.") if T(2);
1664        } else {
1665            Trace("Generating drug target data.") if T(2);
1666            # Load the project list. The file comes in as a list of chomped lines,
1667            # and we split them on the TAB character to make the project name the
1668            # key and the file name the value of the resulting hash.
1669            my %projects = map { split /\t/, $_ } Tracer::GetFile("$FIG_Config::drug_directory/master_tables.list");
1670            # Create hashes for the derived objects: PDBs, Features, and Ligands. These objects
1671            # may occur multiple times in a single project file or even in multiple project
1672            # files.
1673            my %ligands = ();
1674            my %pdbs = ();
1675            my %features = ();
1676            my %bindings = ();
1677            # Set up a counter for drug topics. This will be used as the key.
1678            my $topicCounter = 0;
1679            # Loop through the projects. We sort the keys not because we need them sorted, but
1680            # because it makes it easier to infer our progress from trace messages.
1681            for my $project (sort keys %projects) {
1682                Trace("Processing project $project.") if T(3);
1683                # Only proceed if the download file exists.
1684                my $projectFile = "$FIG_Config::drug_directory/$projects{$project}";
1685                if (! -f $projectFile) {
1686                    Trace("Project file $projectFile not found.") if T(0);
1687                } else {
1688                    # Create the project record.
1689                    $loadDrugProject->Put($project);
1690                    # Create a hash for the topics. Each project has one or more topics. The
1691                    # topic is identified by a URL, a category, and an identifier.
1692                    my %topics = ();
1693                    # Now we can open the project file.
1694                    Trace("Reading project file $projectFile.") if T(3);
1695                    Open(\*PROJECT, "<$projectFile");
1696                    # Get the first record, which is a list of column headers. We don't use this
1697                    # for anything, but it may be useful for debugging.
1698                    my $headerLine = <PROJECT>;
1699                    # Loop through the rest of the records.
1700                    while (! eof PROJECT) {
1701                        # Get the current line of data. Note that not all lines will have all
1702                        # the fields. In particular, the CLIBE data is fairly rare.
1703                        my ($authorOrganism, $category, $tag, $refURL, $peg, $conservation,
1704                            $pdbBound, $pdbBoundEval, $pdbFree, $pdbFreeEval, $pdbFreeTitle,
1705                            $protDistInfo, $passAspInfo, $passAspFile, $passWeightInfo,
1706                            $passWeightFile, $clibeInfo, $clibeURL, $clibeTotalEnergy,
1707                            $clibeVanderwaals, $clibeHBonds, $clibeEI, $clibeSolvationE)
1708                           = Tracer::GetLine(\*PROJECT);
1709                        # The tag contains an identifier for the current line of data followed
1710                        # by a text statement that generally matches a property name in the
1711                        # main database. We split it up, since the identifier goes with
1712                        # the PDB data and the text statement is part of the topic.
1713                        my ($lineID, $topicTag) = split /\s*,\s*/, $tag;
1714                        $loadDrugProject->Add("data line");
1715                        # Check for a new topic.
1716                        my $topicData = "$category\t$topicTag\t$refURL";
1717                        if (! exists $topics{$topicData}) {
1718                            # Here we have a new topic. Compute its ID.
1719                            $topicCounter++;
1720                            $topics{$topicData} = $topicCounter;
1721                            # Create its database record.
1722                            $loadDrugTopic->Put($topicCounter, $refURL, $category, $authorOrganism,
1723                                                $topicTag);
1724                            # Connect it to the project.
1725                            $loadContainsTopic->Put($project, $topicCounter);
1726                            $loadDrugTopic->Add("topic");
1727                        }
1728                        # Now we know the topic ID exists in the hash and the topic will
1729                        # appear in the database, so we get this topic's ID.
1730                        my $topicID = $topics{$topicData};
1731                        # If the feature in this line is new, we need to save its conservation
1732                        # number.
1733                        if (! exists $features{$peg}) {
1734                            $loadFeatureConservation->Put($peg, $conservation);
1735                            $features{$peg} = 1;
1736                        }
1737                        # Now we have two PDBs to deal with-- a bound PDB and a free PDB.
1738                        # The free PDB will have data about docking points; the bound PDB
1739                        # will have data about docking. We store both types as PDBs, and
1740                        # the special data comes from relationships. First we process the
1741                        # bound PDB.
1742                        if ($pdbBound) {
1743                            $loadPDB->Add("bound line");
1744                            # Insure this PDB is in the database.
1745                            $self->CreatePDB($pdbBound, lc "$pdbFreeTitle (bound)", "bound", \%pdbs, $loadPDB);
1746                            # Connect it to this topic.
1747                            $loadIncludesBound->Put($topicID, $pdbBound);
1748                            # Check for CLIBE data.
1749                            if ($clibeInfo) {
1750                                $loadLigand->Add("clibes");
1751                                # We have CLIBE data, so we create a ligand and relate it to the PDB.
1752                                if (! exists $ligands{$clibeInfo}) {
1753                                    # This is a new ligand, so create its record.
1754                                    $loadLigand->Put($clibeInfo);
1755                                    $loadLigand->Add("ligand");
1756                                    # Make sure we know this ligand already exists.
1757                                    $ligands{$clibeInfo} = 1;
1758                                }
1759                                # Now connect the PDB to the ligand using the CLIBE data.
1760                                $loadBindsWith->Put($pdbBound, $clibeInfo, $clibeURL, $clibeHBonds, $clibeEI,
1761                                                    $clibeSolvationE, $clibeVanderwaals);
1762                            }
1763                            # Connect this PDB to the feature.
1764                            $loadDescribesProteinForFeature->Put($pdbBound, $peg, $protDistInfo, $pdbBoundEval);
1765                        }
1766                        # Next is the free PDB.
1767                        if ($pdbFree) {
1768                            $loadPDB->Add("free line");
1769                            # Insure this PDB is in the database.
1770                            $self->CreatePDB($pdbFree, lc $pdbFreeTitle, "free", \%pdbs, $loadPDB);
1771                            # Connect it to this topic.
1772                            $loadContainsAnalysisOf->Put($topicID, $pdbFree, $passAspInfo,
1773                                                         $passWeightFile, $passWeightInfo, $passAspFile);
1774                            # Connect this PDB to the feature.
1775                            $loadDescribesProteinForFeature->Put($pdbFree, $peg, $protDistInfo, $pdbFreeEval);
1776                        }
1777                        # If we have both PDBs, we may need to link them.
1778                        if ($pdbFree && $pdbBound) {
1779                            $loadIsBoundIn->Add("connection");
1780                            # Insure we only link them once.
1781                            my $bindingKey =  "$pdbFree\t$pdbBound";
1782                            if (! exists $bindings{$bindingKey}) {
1783                                $loadIsBoundIn->Add("newConnection");
1784                                $loadIsBoundIn->Put($pdbFree, $pdbBound);
1785                                $bindings{$bindingKey} = 1;
1786                            }
1787                        }
1788                    }
1789                    # Close off this project.
1790                    close PROJECT;
1791                }
1792            }
1793        }
1794        # Finish the load.
1795        my $retVal = $self->_FinishAll();
1796        return $retVal;
1797    }
1798    
1799    
1800  =head2 Internal Utility Methods  =head2 Internal Utility Methods
1801    
1802    =head3 SpecialAttribute
1803    
1804    C<< my $count = SproutLoad::SpecialAttribute($id, \@attributes, $idxMatch, \@idxValues, $pattern, $loader); >>
1805    
1806    Look for special attributes of a given type. A special attribute is found by comparing one of
1807    the columns of the incoming attribute list to a search pattern. If a match is found, then
1808    a set of columns is put into an output table connected to the specified ID.
1809    
1810    For example, when processing features, the attribute list we look at has three columns: attribute
1811    name, attribute value, and attribute value HTML. The IEDB attribute exists if the attribute name
1812    begins with C<iedb_>. The call signature is therefore
1813    
1814        my $found = SpecialAttribute($fid, \@attributeList, 0, [0,2], '^iedb_', $loadFeatureIEDB);
1815    
1816    The pattern is matched against column 0, and if we have a match, then column 2's value is put
1817    to the output along with the specified feature ID.
1818    
1819    =over 4
1820    
1821    =item id
1822    
1823    ID of the object whose special attributes are being loaded. This forms the first column of the
1824    output.
1825    
1826    =item attributes
1827    
1828    Reference to a list of tuples.
1829    
1830    =item idxMatch
1831    
1832    Index in each tuple of the column to be matched against the pattern. If the match is
1833    successful, an output record will be generated.
1834    
1835    =item idxValues
1836    
1837    Reference to a list containing the indexes in each tuple of the columns to be put as
1838    the second column of the output.
1839    
1840    =item pattern
1841    
1842    Pattern to be matched against the specified column. The match will be case-insensitive.
1843    
1844    =item loader
1845    
1846    An object to which each output record will be put. Usually this is an B<ERDBLoad> object,
1847    but technically it could be anything with a C<Put> method.
1848    
1849    =item RETURN
1850    
1851    Returns a count of the matches found.
1852    
1853    =item
1854    
1855    =back
1856    
1857    =cut
1858    
1859    sub SpecialAttribute {
1860        # Get the parameters.
1861        my ($id, $attributes, $idxMatch, $idxValues, $pattern, $loader) = @_;
1862        # Declare the return variable.
1863        my $retVal = 0;
1864        # Loop through the attribute rows.
1865        for my $row (@{$attributes}) {
1866            # Check for a match.
1867            if ($row->[$idxMatch] =~ m/$pattern/i) {
1868                # We have a match, so output a row. This is a bit tricky, since we may
1869                # be putting out multiple columns of data from the input.
1870                my $value = join(" ", map { $row->[$_] } @{$idxValues});
1871                $loader->Put($id, $value);
1872                $retVal++;
1873            }
1874        }
1875        Trace("$retVal special attributes found for $id and loader " . $loader->RelName() . ".") if T(4) && $retVal;
1876        # Return the number of matches.
1877        return $retVal;
1878    }
1879    
1880    =head3 CreatePDB
1881    
1882    C<< $loader->CreatePDB($pdbID, $title, $type, \%pdbHash); >>
1883    
1884    Insure that a PDB record exists for the identified PDB. If one does not exist, it will be
1885    created.
1886    
1887    =over 4
1888    
1889    =item pdbID
1890    
1891    ID string (usually an unqualified file name) for the desired PDB.
1892    
1893    =item title
1894    
1895    Title to use if the PDB must be created.
1896    
1897    =item type
1898    
1899    Type of PDB: C<free> or C<bound>
1900    
1901    =item pdbHash
1902    
1903    Hash containing the IDs of PDBs that have already been created.
1904    
1905    =item pdbLoader
1906    
1907    Load object for the PDB table.
1908    
1909    =back
1910    
1911    =cut
1912    
1913    sub CreatePDB {
1914        # Get the parameters.
1915        my ($self, $pdbID, $title, $type, $pdbHash, $pdbLoader) = @_;
1916        $pdbLoader->Add("PDB check");
1917        # Check to see if this is a new PDB.
1918        if (! exists $pdbHash->{$pdbID}) {
1919            # It is, so we create it.
1920            $pdbLoader->Put($pdbID, $title, $type);
1921            $pdbHash->{$pdbID} = 1;
1922            # Count it.
1923            $pdbLoader->Add("PDB-$type");
1924        }
1925    }
1926    
1927  =head3 TableLoader  =head3 TableLoader
1928    
1929  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

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