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revision 1.4, Tue Aug 16 20:35:03 2005 UTC revision 1.74, Sat Oct 21 06:44:17 2006 UTC
# Line 10  Line 10 
10      use Sprout;      use Sprout;
11      use Stats;      use Stats;
12      use BasicLocation;      use BasicLocation;
13        use HTML;
14    
15  =head1 Sprout Load Methods  =head1 Sprout Load Methods
16    
# Line 29  Line 30 
30      $stats->Accumulate($spl->LoadFeatureData());      $stats->Accumulate($spl->LoadFeatureData());
31      print $stats->Show();      print $stats->Show();
32    
 This module makes use of the internal Sprout property C<_erdb>.  
   
33  It is worth noting that the FIG object does not need to be a real one. Any object  It is worth noting that the FIG object does not need to be a real one. Any object
34  that implements the FIG methods for data retrieval could be used. So, for example,  that implements the FIG methods for data retrieval could be used. So, for example,
35  this object could be used to copy data from one Sprout database to another, or  this object could be used to copy data from one Sprout database to another, or
# Line 40  Line 39 
39  a variable called C<$fig>. This makes it fairly straightforward to determine which  a variable called C<$fig>. This makes it fairly straightforward to determine which
40  FIG methods are required to load the Sprout database.  FIG methods are required to load the Sprout database.
41    
42    This object creates the load files; however, the tables are not created until it
43    is time to actually do the load from the files into the target database.
44    
45  =cut  =cut
46    
47  #: Constructor SproutLoad->new();  #: Constructor SproutLoad->new();
# Line 48  Line 50 
50    
51  =head3 new  =head3 new
52    
53  C<< my $spl = SproutLoad->new($sprout, $fig, $genomeFile, $subsysFile); >>  C<< my $spl = SproutLoad->new($sprout, $fig, $genomeFile, $subsysFile, $options); >>
54    
55  Construct a new Sprout Loader object, specifying the two participating databases and  Construct a new Sprout Loader object, specifying the two participating databases and
56  the name of the files containing the list of genomes and subsystems to use.  the name of the files containing the list of genomes and subsystems to use.
# Line 76  Line 78 
78  =item subsysFile  =item subsysFile
79    
80  Either the name of the file containing the list of trusted subsystems or a reference  Either the name of the file containing the list of trusted subsystems or a reference
81  to a list of subsystem names. If nothing is specified, all known subsystems will be  to a list of subsystem names. If nothing is specified, all NMPDR subsystems will be
82  considered trusted. Only subsystem data related to the trusted subsystems is loaded.  considered trusted. (A subsystem is considered NMPDR if it has a file named C<NMPDR>
83    in its data directory.) Only subsystem data related to the trusted subsystems is loaded.
84    
85    =item options
86    
87    Reference to a hash of command-line options.
88    
89  =back  =back
90    
# Line 85  Line 92 
92    
93  sub new {  sub new {
94      # Get the parameters.      # Get the parameters.
95      my ($class, $sprout, $fig, $genomeFile, $subsysFile) = @_;      my ($class, $sprout, $fig, $genomeFile, $subsysFile, $options) = @_;
96      # Load the list of genomes into a hash.      # Create the genome hash.
97      my %genomes;      my %genomes = ();
98        # We only need it if load-only is NOT specified.
99        if (! $options->{loadOnly}) {
100      if (! defined($genomeFile) || $genomeFile eq '') {      if (! defined($genomeFile) || $genomeFile eq '') {
101          # Here we want all the complete genomes and an access code of 1.          # Here we want all the complete genomes and an access code of 1.
102          my @genomeList = $fig->genomes(1);          my @genomeList = $fig->genomes(1);
# Line 111  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} = $accessCode;
# Line 121  Line 130 
130              Confess("Invalid genome parameter ($type) in SproutLoad constructor.");              Confess("Invalid genome parameter ($type) in SproutLoad constructor.");
131          }          }
132      }      }
133        }
134      # Load the list of trusted subsystems.      # Load the list of trusted subsystems.
135      my %subsystems = ();      my %subsystems = ();
136        # We only need it if load-only is NOT specified.
137        if (! $options->{loadOnly}) {
138      if (! defined $subsysFile || $subsysFile eq '') {      if (! defined $subsysFile || $subsysFile eq '') {
139          # Here we want all the subsystems.              # Here we want all the usable subsystems. First we get the whole list.
140          %subsystems = map { $_ => 1 } $fig->all_subsystems();              my @subs = $fig->all_subsystems();
141                # Loop through, checking for usability.
142                for my $sub (@subs) {
143                    if ($fig->usable_subsystem($sub)) {
144                        $subsystems{$sub} = 1;
145                    }
146                }
147      } else {      } else {
148          my $type = ref $subsysFile;          my $type = ref $subsysFile;
149          if ($type eq 'ARRAY') {          if ($type eq 'ARRAY') {
# Line 145  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();
178      # Create the Sprout load object.      # Create the Sprout load object.
# Line 154  Line 182 
182                    subsystems => \%subsystems,                    subsystems => \%subsystems,
183                    sprout => $sprout,                    sprout => $sprout,
184                    loadDirectory => $directory,                    loadDirectory => $directory,
185                    erdb => $sprout->{_erdb},                    erdb => $sprout,
186                    loaders => []                    loaders => [],
187                      options => $options
188                   };                   };
189      # Bless and return it.      # Bless and return it.
190      bless $retVal, $class;      bless $retVal, $class;
191      return $retVal;      return $retVal;
192  }  }
193    
194    =head3 LoadOnly
195    
196    C<< my $flag = $spl->LoadOnly; >>
197    
198    Return TRUE if we are in load-only mode, else FALSE.
199    
200    =cut
201    
202    sub LoadOnly {
203        my ($self) = @_;
204        return $self->{options}->{loadOnly};
205    }
206    
207    =head3 PrimaryOnly
208    
209    C<< my $flag = $spl->PrimaryOnly; >>
210    
211    Return TRUE if only the main entity is to be loaded, else FALSE.
212    
213    =cut
214    
215    sub PrimaryOnly {
216        my ($self) = @_;
217        return $self->{options}->{primaryOnly};
218    }
219    
220  =head3 LoadGenomeData  =head3 LoadGenomeData
221    
222  C<< my $stats = $spl->LoadGenomeData(); >>  C<< my $stats = $spl->LoadGenomeData(); >>
# Line 189  Line 244 
244    
245  =back  =back
246    
 B<TO DO>  
   
 Real quality vectors instead of C<unknown> for everything.  
   
 GenomeGroup relation. (The original script took group information from the C<NMPDR> file  
 in each genome's main directory, but no such file exists anywhere in my version of the  
 data store.)  
   
247  =cut  =cut
248  #: Return Type $%;  #: Return Type $%;
249  sub LoadGenomeData {  sub LoadGenomeData {
# Line 207  Line 254 
254      # Get the genome count.      # Get the genome count.
255      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
256      my $genomeCount = (keys %{$genomeHash});      my $genomeCount = (keys %{$genomeHash});
     Trace("Beginning genome data load.") if T(2);  
257      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
258      my $loadGenome = $self->_TableLoader('Genome', $genomeCount);      my $loadGenome = $self->_TableLoader('Genome');
259      my $loadHasContig = $self->_TableLoader('HasContig', $genomeCount * 300);      my $loadHasContig = $self->_TableLoader('HasContig', $self->PrimaryOnly);
260      my $loadContig = $self->_TableLoader('Contig', $genomeCount * 300);      my $loadContig = $self->_TableLoader('Contig', $self->PrimaryOnly);
261      my $loadIsMadeUpOf = $self->_TableLoader('IsMadeUpOf', $genomeCount * 60000);      my $loadIsMadeUpOf = $self->_TableLoader('IsMadeUpOf', $self->PrimaryOnly);
262      my $loadSequence = $self->_TableLoader('Sequence', $genomeCount * 60000);      my $loadSequence = $self->_TableLoader('Sequence', $self->PrimaryOnly);
263        if ($self->{options}->{loadOnly}) {
264            Trace("Loading from existing files.") if T(2);
265        } else {
266            Trace("Generating genome data.") if T(2);
267      # Now we loop through the genomes, generating the data for each one.      # Now we loop through the genomes, generating the data for each one.
268      for my $genomeID (sort keys %{$genomeHash}) {      for my $genomeID (sort keys %{$genomeHash}) {
269          Trace("Loading data for genome $genomeID.") if T(3);              Trace("Generating data for genome $genomeID.") if T(3);
270                $loadGenome->Add("genomeIn");
271          # The access code comes in via the genome hash.          # The access code comes in via the genome hash.
272          my $accessCode = $genomeHash->{$genomeID};          my $accessCode = $genomeHash->{$genomeID};
273          # Get the genus, species, and strain from the scientific name. Note that we append              # Get the genus, species, and strain from the scientific name.
         # the genome ID to the strain. In some cases this is the totality of the strain name.  
274          my ($genus, $species, @extraData) = split / /, $self->{fig}->genus_species($genomeID);          my ($genus, $species, @extraData) = split / /, $self->{fig}->genus_species($genomeID);
275          my $extra = join " ", @extraData, "[$genomeID]";              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) {
295              Trace("Processing contig $contigID for $genomeID.") if T(4);              Trace("Processing contig $contigID for $genomeID.") if T(4);
296                    $loadContig->Add("contigIn");
297                    $loadSequence->Add("contigIn");
298              # Create the contig ID.              # Create the contig ID.
299              my $sproutContigID = "$genomeID:$contigID";              my $sproutContigID = "$genomeID:$contigID";
300              # Create the contig record and relate it to the genome.              # Create the contig record and relate it to the genome.
# Line 243  Line 306 
306              # Now we get the sequence a chunk at a time.              # Now we get the sequence a chunk at a time.
307              my $contigLen = $fig->contig_ln($genomeID, $contigID);              my $contigLen = $fig->contig_ln($genomeID, $contigID);
308              for (my $i = 1; $i <= $contigLen; $i += $chunkSize) {              for (my $i = 1; $i <= $contigLen; $i += $chunkSize) {
309                        $loadSequence->Add("chunkIn");
310                  # Compute the endpoint of this chunk.                  # Compute the endpoint of this chunk.
311                  my $end = FIG::min($i + $chunkSize - 1, $contigLen);                  my $end = FIG::min($i + $chunkSize - 1, $contigLen);
312                  # Get the actual DNA.                  # Get the actual DNA.
# Line 255  Line 319 
319              }              }
320          }          }
321      }      }
322        }
323      # Finish the loads.      # Finish the loads.
324      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
325      # Return the result.      # Return the result.
# Line 295  Line 360 
360      my $fig = $self->{fig};      my $fig = $self->{fig};
361      # Get the genome hash.      # Get the genome hash.
362      my $genomeFilter = $self->{genomes};      my $genomeFilter = $self->{genomes};
363      my $genomeCount = (keys %{$genomeFilter});      # Set up an ID counter for the PCHs.
364      my $featureCount = $genomeCount * 4000;      my $pchID = 0;
365      # Start the loads.      # Start the loads.
366      my $loadCoupling = $self->_TableLoader('Coupling', $featureCount * $genomeCount);      my $loadCoupling = $self->_TableLoader('Coupling');
367      my $loadIsEvidencedBy = $self->_TableLoader('IsEvidencedBy', $featureCount * 8000);      my $loadIsEvidencedBy = $self->_TableLoader('IsEvidencedBy', $self->PrimaryOnly);
368      my $loadPCH = $self->_TableLoader('PCH', $featureCount * 2000);      my $loadPCH = $self->_TableLoader('PCH', $self->PrimaryOnly);
369      my $loadParticipatesInCoupling = $self->_TableLoader('ParticipatesInCoupling', $featureCount * 2000);      my $loadParticipatesInCoupling = $self->_TableLoader('ParticipatesInCoupling', $self->PrimaryOnly);
370      my $loadUsesAsEvidence = $self->_TableLoader('UsesAsEvidence', $featureCount * 8000);      my $loadUsesAsEvidence = $self->_TableLoader('UsesAsEvidence', $self->PrimaryOnly);
371      Trace("Beginning coupling data load.") if T(2);      if ($self->{options}->{loadOnly}) {
372            Trace("Loading from existing files.") if T(2);
373        } else {
374            Trace("Generating coupling data.") if T(2);
375      # Loop through the genomes found.      # Loop through the genomes found.
376      for my $genome (sort keys %{$genomeFilter}) {      for my $genome (sort keys %{$genomeFilter}) {
377          Trace("Generating coupling data for $genome.") if T(3);          Trace("Generating coupling data for $genome.") if T(3);
378                $loadCoupling->Add("genomeIn");
379          # Create a hash table for holding coupled pairs. We use this to prevent          # Create a hash table for holding coupled pairs. We use this to prevent
380          # duplicates. For example, if A is coupled to B, we don't want to also          # duplicates. For example, if A is coupled to B, we don't want to also
381          # assert that B is coupled to A, because we already know it. Fortunately,          # assert that B is coupled to A, because we already know it. Fortunately,
# Line 317  Line 386 
386          my @pegs = $fig->pegs_of($genome);          my @pegs = $fig->pegs_of($genome);
387          # Loop through the PEGs.          # Loop through the PEGs.
388          for my $peg1 (@pegs) {          for my $peg1 (@pegs) {
389                    $loadCoupling->Add("pegIn");
390              Trace("Processing PEG $peg1 for $genome.") if T(4);              Trace("Processing PEG $peg1 for $genome.") if T(4);
391              # Get a list of the coupled PEGs.              # Get a list of the coupled PEGs.
392              my @couplings = $fig->coupled_to($peg1);              my @couplings = $fig->coupled_to($peg1);
# Line 325  Line 395 
395              for my $coupleData (@couplings) {              for my $coupleData (@couplings) {
396                  my ($peg2, $score) = @{$coupleData};                  my ($peg2, $score) = @{$coupleData};
397                  # Compute the coupling ID.                  # Compute the coupling ID.
398                  my $coupleID = Sprout::CouplingID($peg1, $peg2);                      my $coupleID = $self->{erdb}->CouplingID($peg1, $peg2);
399                  if (! exists $dupHash{$coupleID}) {                  if (! exists $dupHash{$coupleID}) {
400                            $loadCoupling->Add("couplingIn");
401                      # Here we have a new coupling to store in the load files.                      # Here we have a new coupling to store in the load files.
402                      Trace("Storing coupling ($coupleID) with score $score.") if T(4);                      Trace("Storing coupling ($coupleID) with score $score.") if T(4);
403                      # Ensure we don't do this again.                      # Ensure we don't do this again.
# Line 342  Line 413 
413                      my %evidenceMap = ();                      my %evidenceMap = ();
414                      # Process each evidence item.                      # Process each evidence item.
415                      for my $evidenceData (@evidence) {                      for my $evidenceData (@evidence) {
416                                $loadPCH->Add("evidenceIn");
417                          my ($peg3, $peg4, $usage) = @{$evidenceData};                          my ($peg3, $peg4, $usage) = @{$evidenceData};
418                          # Only proceed if the evidence is from a Sprout                          # Only proceed if the evidence is from a Sprout
419                          # genome.                          # genome.
420                          if ($genomeFilter->{$fig->genome_of($peg3)}) {                          if ($genomeFilter->{$fig->genome_of($peg3)}) {
421                                    $loadUsesAsEvidence->Add("evidenceChosen");
422                              my $evidenceKey = "$coupleID $peg3 $peg4";                              my $evidenceKey = "$coupleID $peg3 $peg4";
423                              # We store this evidence in the hash if the usage                              # We store this evidence in the hash if the usage
424                              # is nonzero or no prior evidence has been found. This                              # is nonzero or no prior evidence has been found. This
425                              # insures that if there is duplicate evidence, we                              # insures that if there is duplicate evidence, we
426                              # at least keep the meaningful ones. Only evidence is                                  # at least keep the meaningful ones. Only evidence in
427                              # the hash makes it to the output.                              # the hash makes it to the output.
428                              if ($usage || ! exists $evidenceMap{$evidenceKey}) {                              if ($usage || ! exists $evidenceMap{$evidenceKey}) {
429                                  $evidenceMap{$evidenceKey} = $evidenceData;                                  $evidenceMap{$evidenceKey} = $evidenceData;
# Line 358  Line 431 
431                          }                          }
432                      }                      }
433                      for my $evidenceID (keys %evidenceMap) {                      for my $evidenceID (keys %evidenceMap) {
434                                # Get the ID for this evidence.
435                                $pchID++;
436                          # Create the evidence record.                          # Create the evidence record.
437                          my ($peg3, $peg4, $usage) = @{$evidenceMap{$evidenceID}};                          my ($peg3, $peg4, $usage) = @{$evidenceMap{$evidenceID}};
438                          $loadPCH->Put($evidenceID, $usage);                              $loadPCH->Put($pchID, $usage);
439                          # Connect it to the coupling.                          # Connect it to the coupling.
440                          $loadIsEvidencedBy->Put($coupleID, $evidenceID);                              $loadIsEvidencedBy->Put($coupleID, $pchID);
441                          # Connect it to the features.                          # Connect it to the features.
442                          $loadUsesAsEvidence->Put($evidenceID, $peg3, 1);                              $loadUsesAsEvidence->Put($pchID, $peg3, 1);
443                          $loadUsesAsEvidence->Put($evidenceID, $peg4, 1);                              $loadUsesAsEvidence->Put($pchID, $peg4, 2);
444                            }
445                      }                      }
446                  }                  }
447              }              }
# Line 392  Line 468 
468      FeatureTranslation      FeatureTranslation
469      FeatureUpstream      FeatureUpstream
470      IsLocatedIn      IsLocatedIn
471        HasFeature
472        HasRoleInSubsystem
473    
474  =over 4  =over 4
475    
# Line 406  Line 484 
484  sub LoadFeatureData {  sub LoadFeatureData {
485      # Get this object instance.      # Get this object instance.
486      my ($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};
     my $genomeCount = (keys %{$genomeHash});  
     my $featureCount = $genomeCount * 4000;  
492      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
493      my $loadFeature = $self->_TableLoader('Feature', $featureCount);      my $loadFeature = $self->_TableLoader('Feature');
494      my $loadFeatureAlias = $self->_TableLoader('FeatureAlias', $featureCount * 6);      my $loadIsLocatedIn = $self->_TableLoader('IsLocatedIn', $self->PrimaryOnly);
495      my $loadFeatureLink = $self->_TableLoader('FeatureLink', $featureCount * 10);      my $loadFeatureAlias = $self->_TableLoader('FeatureAlias');
496      my $loadFeatureTranslation = $self->_TableLoader('FeatureTranslation', $featureCount);      my $loadFeatureLink = $self->_TableLoader('FeatureLink');
497      my $loadFeatureUpstream = $self->_TableLoader('FeatureUpstream', $featureCount);      my $loadFeatureTranslation = $self->_TableLoader('FeatureTranslation');
498      my $loadIsLocatedIn = $self->_TableLoader('IsLocatedIn', $featureCount);      my $loadFeatureUpstream = $self->_TableLoader('FeatureUpstream');
499        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 = $self->{sprout}->MaxSegment();
506      Trace("Beginning feature data load.") if T(2);      if ($self->{options}->{loadOnly}) {
507            Trace("Loading from existing files.") if T(2);
508        } else {
509            Trace("Generating feature data.") if T(2);
510      # Now we loop through the genomes, generating the data for each one.      # Now we loop through the genomes, generating the data for each one.
511      for my $genomeID (sort keys %{$genomeHash}) {      for my $genomeID (sort keys %{$genomeHash}) {
512          Trace("Loading features for genome $genomeID.") if T(3);          Trace("Loading features for genome $genomeID.") if T(3);
513                $loadFeature->Add("genomeIn");
514          # Get the feature list for this genome.          # Get the feature list for this genome.
515          my $features = $fig->all_features_detailed($genomeID);          my $features = $fig->all_features_detailed($genomeID);
516                # Sort and count the list.
517                my @featureTuples = sort { $a->[0] cmp $b->[0] } @{$features};
518                my $count = scalar @featureTuples;
519                Trace("$count features found for genome $genomeID.") if T(3);
520                # Set up for our duplicate-feature check.
521                my $oldFeatureID = "";
522          # Loop through the features.          # Loop through the features.
523          for my $featureData (@{$features}) {              for my $featureTuple (@featureTuples) {
524              # Split the tuple.              # Split the tuple.
525              my ($featureID, $locations, $aliases, $type) = @{$featureData};                  my ($featureID, $locations, undef, $type) = @{$featureTuple};
526              # Create the feature record.                  # Check for duplicates.
527              $loadFeature->Put("$genomeID:$featureID", 1, $type);                  if ($featureID eq $oldFeatureID) {
528                        Trace("Duplicate feature $featureID found.") if T(1);
529                    } else {
530                        $oldFeatureID = $featureID;
531                        # Count this feature.
532                        $loadFeature->Add("featureIn");
533                        # Get the functional assignment.
534                        my $assignment = $fig->function_of($featureID);
535                        # Begin building the keywords.
536                        my $keywords = "$assignment $genomeID";
537                        # Link this feature to the parent genome.
538                        $loadHasFeature->Put($genomeID, $featureID, $type);
539              # Create the aliases.              # Create the aliases.
540              for my $alias (split /\s*,\s*/, $aliases) {                      for my $alias ($fig->feature_aliases($featureID)) {
541                  $loadFeatureAlias->Put($featureID, $alias);                  $loadFeatureAlias->Put($featureID, $alias);
542                            $keywords .= " $alias";
543              }              }
544              # Get the links.              # Get the links.
545              my @links = $fig->fid_links($featureID);              my @links = $fig->fid_links($featureID);
# Line 445  Line 548 
548              }              }
549              # If this is a peg, generate the translation and the upstream.              # If this is a peg, generate the translation and the upstream.
550              if ($type eq 'peg') {              if ($type eq 'peg') {
551                            $loadFeatureTranslation->Add("pegIn");
552                  my $translation = $fig->get_translation($featureID);                  my $translation = $fig->get_translation($featureID);
553                  if ($translation) {                  if ($translation) {
554                      $loadFeatureTranslation->Put($featureID, $translation);                      $loadFeatureTranslation->Put($featureID, $translation);
# Line 455  Line 559 
559                      $loadFeatureUpstream->Put($featureID, $upstream);                      $loadFeatureUpstream->Put($featureID, $upstream);
560                  }                  }
561              }              }
562                        # Now we need to find the subsystems this feature participates in.
563                        # We also add the subsystems to the keyword list. Before we do that,
564                        # we must convert underscores to spaces and tack on the classifications.
565                        my @subsystems = $fig->peg_to_subsystems($featureID);
566                        for my $subsystem (@subsystems) {
567                            # Only proceed if we like this subsystem.
568                            if (exists $subHash->{$subsystem}) {
569                                # Store the has-role link.
570                                $loadHasRoleInSubsystem->Put($featureID, $subsystem, $genomeID, $type);
571                                # Save the subsystem's keyword data.
572                                my $subKeywords = $subHash->{$subsystem};
573                                $keywords .= " $subKeywords";
574                            }
575                        }
576                        # The final task is to add virulence and essentiality attributes.
577                        if ($fig->virulent($featureID)) {
578                            $keywords .= " virulent";
579                        }
580                        if ($fig->essential($featureID)) {
581                            $keywords .= " essential";
582                        }
583                        # Clean the keyword list.
584                        my $cleanWords = $sprout->CleanKeywords($keywords);
585                        # Create the feature record.
586                        $loadFeature->Put($featureID, 1, $type, $assignment, $cleanWords);
587              # 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
588              # 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
589              # the maximum segment size. This simplifies the genes_in_region processing              # the maximum segment size. This simplifies the genes_in_region processing
590              # for Sprout.              # for Sprout.
591              my @locationList = split /\s*,\s*/, $locations;              my @locationList = split /\s*,\s*/, $locations;
592                        # Create the location position indicator.
593                        my $i = 1;
594              # Loop through the locations.              # Loop through the locations.
595              for my $location (@locationList) {              for my $location (@locationList) {
596                  # Parse the location.                  # Parse the location.
597                  my $locObject = BasicLocation->new($location);                          my $locObject = BasicLocation->new("$genomeID:$location");
598                  # Split it into a list of chunks.                  # Split it into a list of chunks.
599                  my @locOList = ();                  my @locOList = ();
600                  while (my $peeling = $locObject->Peel($chunkSize)) {                  while (my $peeling = $locObject->Peel($chunkSize)) {
601                                $loadIsLocatedIn->Add("peeling");
602                      push @locOList, $peeling;                      push @locOList, $peeling;
603                  }                  }
604                  push @locOList, $locObject;                  push @locOList, $locObject;
605                  # Loop through the chunks, creating IsLocatedIn records. The variable                  # Loop through the chunks, creating IsLocatedIn records. The variable
606                  # "$i" will be used to keep the location index.                  # "$i" will be used to keep the location index.
                 my $i = 1;  
607                  for my $locChunk (@locOList) {                  for my $locChunk (@locOList) {
608                      $loadIsLocatedIn->Put($featureID, $locChunk->Contig, $locChunk->Left,                      $loadIsLocatedIn->Put($featureID, $locChunk->Contig, $locChunk->Left,
609                                            $locChunk->Dir, $locChunk->Length, $i);                                            $locChunk->Dir, $locChunk->Length, $i);
# Line 481  Line 612 
612              }              }
613          }          }
614      }      }
     # Finish the loads.  
     my $retVal = $self->_FinishAll();  
     return $retVal;  
 }  
   
 =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};  
     my $genomeCount = (keys %{$genomeHash});  
     my $featureCount = $genomeCount * 4000;  
     # Create load objects for each of the tables we're loading.  
     my $loadIsBidirectionalBestHitOf = $self->_TableLoader('IsBidirectionalBestHitOf',  
                                                            $featureCount * $genomeCount);  
     Trace("Beginning BBH load.") if T(2);  
     # Now we loop through the genomes, generating the data for each one.  
     for my $genomeID (sort keys %{$genomeHash}) {  
         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);  
                 }  
             }  
615          }          }
616      }      }
617      # Finish the loads.      # Finish the loads.
# Line 567  Line 634 
634  The following relations are loaded by this method.  The following relations are loaded by this method.
635    
636      Subsystem      Subsystem
637        SubsystemClass
638      Role      Role
639        RoleEC
640      SSCell      SSCell
641      ContainsFeature      ContainsFeature
642      IsGenomeOf      IsGenomeOf
# Line 575  Line 644 
644      OccursInSubsystem      OccursInSubsystem
645      ParticipatesIn      ParticipatesIn
646      HasSSCell      HasSSCell
647        ConsistsOfRoles
648        RoleSubset
649        HasRoleSubset
650        ConsistsOfGenomes
651        GenomeSubset
652        HasGenomeSubset
653        Catalyzes
654        Diagram
655        RoleOccursIn
656    
657  =over 4  =over 4
658    
# Line 584  Line 662 
662    
663  =back  =back
664    
 B<TO DO>  
   
 Generate RoleName table?  
   
665  =cut  =cut
666  #: Return Type $%;  #: Return Type $%;
667  sub LoadSubsystemData {  sub LoadSubsystemData {
# Line 601  Line 675 
675      # Get the subsystem hash. This lists the subsystems we'll process.      # Get the subsystem hash. This lists the subsystems we'll process.
676      my $subsysHash = $self->{subsystems};      my $subsysHash = $self->{subsystems};
677      my @subsysIDs = sort keys %{$subsysHash};      my @subsysIDs = sort keys %{$subsysHash};
678      my $subsysCount = @subsysIDs;      # Get the map list.
679      my $genomeCount = (keys %{$genomeHash});      my @maps = $fig->all_maps;
     my $featureCount = $genomeCount * 4000;  
680      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
681      my $loadSubsystem = $self->_TableLoader('Subsystem', $subsysCount);      my $loadDiagram = $self->_TableLoader('Diagram', $self->PrimaryOnly);
682      my $loadRole = $self->_TableLoader('Role', $featureCount * 6);      my $loadRoleOccursIn = $self->_TableLoader('RoleOccursIn', $self->PrimaryOnly);
683      my $loadSSCell = $self->_TableLoader('SSCell', $featureCount * $genomeCount);      my $loadSubsystem = $self->_TableLoader('Subsystem');
684      my $loadContainsFeature = $self->_TableLoader('ContainsFeature', $featureCount * $subsysCount);      my $loadRole = $self->_TableLoader('Role', $self->PrimaryOnly);
685      my $loadIsGenomeOf = $self->_TableLoader('IsGenomeOf', $featureCount * $genomeCount);      my $loadRoleEC = $self->_TableLoader('RoleEC', $self->PrimaryOnly);
686      my $loadIsRoleOf = $self->_TableLoader('IsRoleOf', $featureCount * $genomeCount);      my $loadCatalyzes = $self->_TableLoader('Catalyzes', $self->PrimaryOnly);
687      my $loadOccursInSubsystem = $self->_TableLoader('OccursInSubsystem', $featureCount * 6);      my $loadSSCell = $self->_TableLoader('SSCell', $self->PrimaryOnly);
688      my $loadParticipatesIn = $self->_TableLoader('ParticipatesIn', $subsysCount * $genomeCount);      my $loadContainsFeature = $self->_TableLoader('ContainsFeature', $self->PrimaryOnly);
689      my $loadHasSSCell = $self->_TableLoader('HasSSCell', $featureCount * $genomeCount);      my $loadIsGenomeOf = $self->_TableLoader('IsGenomeOf', $self->PrimaryOnly);
690      Trace("Beginning subsystem data load.") if T(2);      my $loadIsRoleOf = $self->_TableLoader('IsRoleOf', $self->PrimaryOnly);
691        my $loadOccursInSubsystem = $self->_TableLoader('OccursInSubsystem', $self->PrimaryOnly);
692        my $loadParticipatesIn = $self->_TableLoader('ParticipatesIn', $self->PrimaryOnly);
693        my $loadHasSSCell = $self->_TableLoader('HasSSCell', $self->PrimaryOnly);
694        my $loadRoleSubset = $self->_TableLoader('RoleSubset', $self->PrimaryOnly);
695        my $loadGenomeSubset = $self->_TableLoader('GenomeSubset', $self->PrimaryOnly);
696        my $loadConsistsOfRoles = $self->_TableLoader('ConsistsOfRoles', $self->PrimaryOnly);
697        my $loadConsistsOfGenomes = $self->_TableLoader('ConsistsOfGenomes', $self->PrimaryOnly);
698        my $loadHasRoleSubset = $self->_TableLoader('HasRoleSubset', $self->PrimaryOnly);
699        my $loadHasGenomeSubset = $self->_TableLoader('HasGenomeSubset', $self->PrimaryOnly);
700        my $loadSubsystemClass = $self->_TableLoader('SubsystemClass', $self->PrimaryOnly);
701        if ($self->{options}->{loadOnly}) {
702            Trace("Loading from existing files.") if T(2);
703        } else {
704            Trace("Generating subsystem data.") if T(2);
705            # This hash will contain the role for each EC. When we're done, this
706            # information will be used to generate the Catalyzes table.
707            my %ecToRoles = ();
708      # Loop through the subsystems. Our first task will be to create the      # Loop through the subsystems. Our first task will be to create the
709      # roles. We do this by looping through the subsystems and creating a      # roles. We do this by looping through the subsystems and creating a
710      # role hash. The hash tracks each role ID so that we don't create      # role hash. The hash tracks each role ID so that we don't create
711      # duplicates. As we move along, we'll connect the roles and subsystems.          # duplicates. As we move along, we'll connect the roles and subsystems
712            # and memorize up the reactions.
713            my ($genomeID, $roleID);
714      my %roleData = ();      my %roleData = ();
715      for my $subsysID (@subsysIDs) {      for my $subsysID (@subsysIDs) {
716                # Get the subsystem object.
717                my $sub = $fig->get_subsystem($subsysID);
718                # Only proceed if the subsystem has a spreadsheet.
719                if (! $sub->{empty_ss}) {
720          Trace("Creating subsystem $subsysID.") if T(3);          Trace("Creating subsystem $subsysID.") if T(3);
721                    $loadSubsystem->Add("subsystemIn");
722          # Create the subsystem record.          # Create the subsystem record.
723          $loadSubsystem->Put($subsysID);                  my $curator = $sub->get_curator();
724          # Get the subsystem's roles.                  my $notes = $sub->get_notes();
725          my @roles = $fig->subsys_to_roles($subsysID);                  $loadSubsystem->Put($subsysID, $curator, $notes);
726          # Connect the roles to the subsystem. If a role is new, we create                  # Now for the classification string. This comes back as a list
727          # a role record for it.                  # reference and we convert it to a space-delimited string.
728          for my $roleID (@roles) {                  my $classList = $fig->subsystem_classification($subsysID);
729              $loadOccursInSubsystem->Put($roleID, $subsysID);                  my $classString = join(" : ", grep { $_ } @$classList);
730                    $loadSubsystemClass->Put($subsysID, $classString);
731                    # Connect it to its roles. Each role is a column in the subsystem spreadsheet.
732                    for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {
733                        # Connect to this role.
734                        $loadOccursInSubsystem->Add("roleIn");
735                        $loadOccursInSubsystem->Put($roleID, $subsysID, $col);
736                        # If it's a new role, add it to the role table.
737              if (! exists $roleData{$roleID}) {              if (! exists $roleData{$roleID}) {
738                  $loadRole->Put($roleID);                          # Get the role's abbreviation.
739                            my $abbr = $sub->get_role_abbr($col);
740                            # Add the role.
741                            $loadRole->Put($roleID, $abbr);
742                  $roleData{$roleID} = 1;                  $roleData{$roleID} = 1;
743                            # Check for an EC number.
744                            if ($roleID =~ /\(EC ([^.]+\.[^.]+\.[^.]+\.[^)]+)\)\s*$/) {
745                                my $ec = $1;
746                                $loadRoleEC->Put($roleID, $ec);
747                                $ecToRoles{$ec} = $roleID;
748                            }
749              }              }
750          }          }
751          # Now all roles for this subsystem have been filled in. We create the                  # Now we create the spreadsheet for the subsystem by matching roles to
752          # spreadsheet by matches roles to genomes. To do this, we need to                  # genomes. Each genome is a row and each role is a column. We may need
753          # get the genomes on the sheet.                  # to actually create the roles as we find them.
754          Trace("Creating subsystem $subsysID spreadsheet.") if T(3);          Trace("Creating subsystem $subsysID spreadsheet.") if T(3);
755          my @genomes = map { $_->[0] } @{$fig->subsystem_genomes($subsysID)};                  for (my $row = 0; defined($genomeID = $sub->get_genome($row)); $row++) {
756          for my $genomeID (@genomes) {                      # Only proceed if this is one of our genomes.
             # Only process this genome if it's one of ours.  
757              if (exists $genomeHash->{$genomeID}) {              if (exists $genomeHash->{$genomeID}) {
758                  # Connect the genome to the subsystem.                          # Count the PEGs and cells found for verification purposes.
759                  $loadParticipatesIn->Put($genomeID, $subsysID);                          my $pegCount = 0;
760                            my $cellCount = 0;
761                            # Create a list for the PEGs we find. This list will be used
762                            # to generate cluster numbers.
763                            my @pegsFound = ();
764                            # Create a hash that maps spreadsheet IDs to PEGs. We will
765                            # use this to generate the ContainsFeature data after we have
766                            # the cluster numbers.
767                            my %cellPegs = ();
768                            # Get the genome's variant code for this subsystem.
769                            my $variantCode = $sub->get_variant_code($row);
770                  # Loop through the subsystem's roles. We use an index because it is                  # Loop through the subsystem's roles. We use an index because it is
771                  # part of the spreadsheet cell ID.                  # part of the spreadsheet cell ID.
772                  for (my $i = 0; $i <= $#roles; $i++) {                          for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {
                     my $role = $roles[$i];  
773                      # Get the features in the spreadsheet cell for this genome and role.                      # Get the features in the spreadsheet cell for this genome and role.
774                      my @pegs = $fig->pegs_in_subsystem_coll($subsysID, $genomeID, $i);                              my @pegs = grep { !$fig->is_deleted_fid($_) } $sub->get_pegs_from_cell($row, $col);
775                      # Only proceed if features exist.                      # Only proceed if features exist.
776                      if (@pegs > 0) {                      if (@pegs > 0) {
777                          # Create the spreadsheet cell.                          # Create the spreadsheet cell.
778                          my $cellID = "$subsysID:$genomeID:$i";                                  $cellCount++;
779                                    my $cellID = "$subsysID:$genomeID:$col";
780                          $loadSSCell->Put($cellID);                          $loadSSCell->Put($cellID);
781                          $loadIsGenomeOf->Put($genomeID, $cellID);                          $loadIsGenomeOf->Put($genomeID, $cellID);
782                          $loadIsRoleOf->Put($role, $cellID);                                  $loadIsRoleOf->Put($roleID, $cellID);
783                          $loadHasSSCell->Put($subsysID, $cellID);                          $loadHasSSCell->Put($subsysID, $cellID);
784                          # Attach the features to it.                                  # Remember its features.
785                          for my $pegID (@pegs) {                                  push @pegsFound, @pegs;
786                              $loadContainsFeature->Put($cellID, $pegID);                                  $cellPegs{$cellID} = \@pegs;
787                                    $pegCount += @pegs;
788                                }
789                            }
790                            # If we found some cells for this genome, we need to compute clusters and
791                            # denote it participates in the subsystem.
792                            if ($pegCount > 0) {
793                                Trace("$pegCount PEGs in $cellCount cells for $genomeID.") if T(3);
794                                $loadParticipatesIn->Put($genomeID, $subsysID, $variantCode);
795                                # Create a hash mapping PEG IDs to cluster numbers.
796                                # We default to -1 for all of them.
797                                my %clusterOf = map { $_ => -1 } @pegsFound;
798                                # Partition the PEGs found into clusters.
799                                my @clusters = $fig->compute_clusters([keys %clusterOf], $sub);
800                                for (my $i = 0; $i <= $#clusters; $i++) {
801                                    my $subList = $clusters[$i];
802                                    for my $peg (@{$subList}) {
803                                        $clusterOf{$peg} = $i;
804                                    }
805                                }
806                                # Create the ContainsFeature data.
807                                for my $cellID (keys %cellPegs) {
808                                    my $cellList = $cellPegs{$cellID};
809                                    for my $cellPeg (@$cellList) {
810                                        $loadContainsFeature->Put($cellID, $cellPeg, $clusterOf{$cellPeg});
811                          }                          }
812                      }                      }
813                  }                  }
814              }              }
815          }          }
816                    # Now we need to generate the subsets. The subset names must be concatenated to
817                    # the subsystem name to make them unique keys. There are two types of subsets:
818                    # genome subsets and role subsets. We do the role subsets first.
819                    my @subsetNames = $sub->get_subset_names();
820                    for my $subsetID (@subsetNames) {
821                        # Create the subset record.
822                        my $actualID = "$subsysID:$subsetID";
823                        $loadRoleSubset->Put($actualID);
824                        # Connect the subset to the subsystem.
825                        $loadHasRoleSubset->Put($subsysID, $actualID);
826                        # Connect the subset to its roles.
827                        my @roles = $sub->get_subsetC_roles($subsetID);
828                        for my $roleID (@roles) {
829                            $loadConsistsOfRoles->Put($actualID, $roleID);
830      }      }
     # Finish the load.  
     my $retVal = $self->_FinishAll();  
     return $retVal;  
831  }  }
832                    # Next the genome subsets.
833  =head3 LoadDiagramData                  @subsetNames = $sub->get_subset_namesR();
834                    for my $subsetID (@subsetNames) {
835  C<< my $stats = $spl->LoadDiagramData(); >>                      # Create the subset record.
836                        my $actualID = "$subsysID:$subsetID";
837  Load the diagram data from FIG into Sprout.                      $loadGenomeSubset->Put($actualID);
838                        # Connect the subset to the subsystem.
839  Diagrams are used to organize functional roles. The diagram shows the                      $loadHasGenomeSubset->Put($subsysID, $actualID);
840  connections between chemicals that interact with a subsystem.                      # Connect the subset to its genomes.
841                        my @genomes = $sub->get_subsetR($subsetID);
842  The following relations are loaded by this method.                      for my $genomeID (@genomes) {
843                            $loadConsistsOfGenomes->Put($actualID, $genomeID);
844      Diagram                      }
845      RoleOccursIn                  }
846                }
847  =over 4          }
848            # Now we loop through the diagrams. We need to create the diagram records
849  =item RETURNS          # and link each diagram to its roles. Note that only roles which occur
850            # in subsystems (and therefore appear in the %ecToRoles hash) are
851  Returns a statistics object for the loads.          # included.
852            for my $map (@maps) {
 =back  
   
 =cut  
 #: Return Type $%;  
 sub LoadDiagramData {  
     # Get this object instance.  
     my ($self) = @_;  
     # Get the FIG object.  
     my $fig = $self->{fig};  
     # Get the map list.  
     my @maps = $fig->all_maps;  
     my $mapCount = @maps;  
     my $genomeCount = (keys %{$self->{genomes}});  
     my $featureCount = $genomeCount * 4000;  
     # Create load objects for each of the tables we're loading.  
     my $loadDiagram = $self->_TableLoader('Diagram', $mapCount);  
     my $loadRoleOccursIn = $self->_TableLoader('RoleOccursIn', $featureCount * 6);  
     Trace("Beginning diagram data load.") if T(2);  
     # Loop through the diagrams.  
     for my $map ($fig->all_maps) {  
853          Trace("Loading diagram $map.") if T(3);          Trace("Loading diagram $map.") if T(3);
854          # Get the diagram's descriptive name.          # Get the diagram's descriptive name.
855          my $name = $fig->map_name($map);          my $name = $fig->map_name($map);
# Line 721  Line 858 
858          # A hash is used to prevent duplicates.          # A hash is used to prevent duplicates.
859          my %roleHash = ();          my %roleHash = ();
860          for my $role ($fig->map_to_ecs($map)) {          for my $role ($fig->map_to_ecs($map)) {
861              if (! $roleHash{$role}) {                  if (exists $ecToRoles{$role} && ! $roleHash{$role}) {
862                  $loadRoleOccursIn->Put($role, $map);                      $loadRoleOccursIn->Put($ecToRoles{$role}, $map);
863                  $roleHash{$role} = 1;                  $roleHash{$role} = 1;
864              }              }
865          }          }
866      }      }
867            # Before we leave, we must create the Catalyzes table. We start with the reactions,
868            # then use the "ecToRoles" table to convert EC numbers to role IDs.
869            my @reactions = $fig->all_reactions();
870            for my $reactionID (@reactions) {
871                # Get this reaction's list of roles. The results will be EC numbers.
872                my @roles = $fig->catalyzed_by($reactionID);
873                # Loop through the roles, creating catalyzation records.
874                for my $thisRole (@roles) {
875                    if (exists $ecToRoles{$thisRole}) {
876                        $loadCatalyzes->Put($ecToRoles{$thisRole}, $reactionID);
877                    }
878                }
879            }
880        }
881      # Finish the load.      # Finish the load.
882      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
883      return $retVal;      return $retVal;
# Line 768  Line 919 
919      my $fig = $self->{fig};      my $fig = $self->{fig};
920      # Get the genome hash.      # Get the genome hash.
921      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
922      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
923      my $loadProperty = $self->_TableLoader('Property', $genomeCount * 1500);      my $loadProperty = $self->_TableLoader('Property');
924      my $loadHasProperty = $self->_TableLoader('HasProperty', $genomeCount * 1500);      my $loadHasProperty = $self->_TableLoader('HasProperty', $self->PrimaryOnly);
925      Trace("Beginning property data load.") if T(2);      if ($self->{options}->{loadOnly}) {
926            Trace("Loading from existing files.") if T(2);
927        } else {
928            Trace("Generating property data.") if T(2);
929      # Create a hash for storing property IDs.      # Create a hash for storing property IDs.
930      my %propertyKeys = ();      my %propertyKeys = ();
931      my $nextID = 1;      my $nextID = 1;
932      # Loop through the genomes.      # Loop through the genomes.
933      for my $genomeID (keys %{$genomeHash}) {          for my $genomeID (sort keys %{$genomeHash}) {
934                $loadProperty->Add("genomeIn");
935                Trace("Generating properties for $genomeID.") if T(3);
936          # 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
937          # tuples returned by "all_features_detailed". We use "all_features_detailed"          # tuples returned by "all_features_detailed". We use "all_features_detailed"
938          # rather than "all_features" because we want all features regardless of type.          # rather than "all_features" because we want all features regardless of type.
939          my @features = map { $_->[0] } @{$fig->all_features_detailed($genomeID)};          my @features = map { $_->[0] } @{$fig->all_features_detailed($genomeID)};
940                my $featureCount = 0;
941                my $propertyCount = 0;
942          # Loop through the features, creating HasProperty records.          # Loop through the features, creating HasProperty records.
943          for my $fid (@features) {          for my $fid (@features) {
944              # 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
945              # to insure we do not get any genome attributes.              # to insure we do not get any genome attributes.
946              my @attributeList = $fig->get_attributes($fid, '', '', '');              my @attributeList = $fig->get_attributes($fid, '', '', '');
947                    # Add essentiality and virulence attributes.
948                    if ($fig->essential($fid)) {
949                        push @attributeList, [$fid, 'essential', 1, ''];
950                    }
951                    if ($fig->virulent($fid)) {
952                        push @attributeList, [$fid, 'virulent', 1, ''];
953                    }
954                    if (scalar @attributeList) {
955                        $featureCount++;
956                    }
957              # Loop through the attributes.              # Loop through the attributes.
958              for my $tuple (@attributeList) {              for my $tuple (@attributeList) {
959                        $propertyCount++;
960                  # Get this attribute value's data. Note that we throw away the FID,                  # Get this attribute value's data. Note that we throw away the FID,
961                  # since it will always be the same as the value if "$fid".                  # since it will always be the same as the value if "$fid".
962                  my (undef, $key, $value, $url) = @{$tuple};                  my (undef, $key, $value, $url) = @{$tuple};
# Line 810  Line 978 
978                  $loadHasProperty->Put($fid, $propertyID, $url);                  $loadHasProperty->Put($fid, $propertyID, $url);
979              }              }
980          }          }
981                # Update the statistics.
982                Trace("$propertyCount attributes processed for $featureCount features.") if T(3);
983                $loadHasProperty->Add("featuresIn", $featureCount);
984                $loadHasProperty->Add("propertiesIn", $propertyCount);
985            }
986      }      }
987      # Finish the load.      # Finish the load.
988      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
# Line 850  Line 1023 
1023      my $fig = $self->{fig};      my $fig = $self->{fig};
1024      # Get the genome hash.      # Get the genome hash.
1025      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
1026      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
1027      my $loadAnnotation = $self->_TableLoader('Annotation', $genomeCount * 4000);      my $loadAnnotation = $self->_TableLoader('Annotation');
1028      my $loadIsTargetOfAnnotation = $self->_TableLoader('IsTargetOfAnnotation', $genomeCount * 4000);      my $loadIsTargetOfAnnotation = $self->_TableLoader('IsTargetOfAnnotation', $self->PrimaryOnly);
1029      my $loadSproutUser = $self->_TableLoader('SproutUser', 100);      my $loadSproutUser = $self->_TableLoader('SproutUser', $self->PrimaryOnly);
1030      my $loadUserAccess = $self->_TableLoader('UserAccess', 1000);      my $loadUserAccess = $self->_TableLoader('UserAccess', $self->PrimaryOnly);
1031      my $loadMadeAnnotation = $self->_TableLoader('MadeAnnotation', $genomeCount * 4000);      my $loadMadeAnnotation = $self->_TableLoader('MadeAnnotation', $self->PrimaryOnly);
1032      Trace("Beginning annotation data load.") if T(2);      if ($self->{options}->{loadOnly}) {
1033            Trace("Loading from existing files.") if T(2);
1034        } else {
1035            Trace("Generating annotation data.") if T(2);
1036      # Create a hash of user names. We'll use this to prevent us from generating duplicate      # Create a hash of user names. We'll use this to prevent us from generating duplicate
1037      # user records.      # user records.
1038      my %users = ( FIG => 1, master => 1 );      my %users = ( FIG => 1, master => 1 );
# Line 869  Line 1044 
1044      # Get the current time.      # Get the current time.
1045      my $time = time();      my $time = time();
1046      # Loop through the genomes.      # Loop through the genomes.
1047      for my $genomeID (%{$genomeHash}) {          for my $genomeID (sort keys %{$genomeHash}) {
1048          Trace("Processing $genomeID.") if T(3);          Trace("Processing $genomeID.") if T(3);
         # Get the genome's PEGs.  
         my @pegs = $fig->pegs_of($genomeID);  
         for my $peg (@pegs) {  
             Trace("Processing $peg.") if T(4);  
1049              # Create a hash of timestamps. We use this to prevent duplicate time stamps              # Create a hash of timestamps. We use this to prevent duplicate time stamps
1050              # from showing up for a single PEG's annotations.              # from showing up for a single PEG's annotations.
1051              my %seenTimestamps = ();              my %seenTimestamps = ();
1052              # Check for a functional assignment.              # Get the genome's annotations.
1053              my $func = $fig->function_of($peg);              my @annotations = $fig->read_all_annotations($genomeID);
1054              if ($func) {              Trace("Processing annotations.") if T(2);
1055                  # If this is NOT a hypothetical assignment, we create an              for my $tuple (@annotations) {
1056                  # assignment annotation for it.                  # Get the annotation tuple.
1057                  if (! FIG::hypo($peg)) {                  my ($peg, $timestamp, $user, $text) = @{$tuple};
                     # Note that we double the slashes so that what goes into the database is  
                     # a new-line escape sequence rather than an actual new-line.  
                     $loadAnnotation->Put("$peg:$time", $time, "FIG\\nSet function to\\n$func");  
                     $loadIsTargetOfAnnotation->Put($peg, "$peg:$time");  
                     $loadMadeAnnotation->Put("FIG", "$peg:$time");  
                     # Denote we've seen this timestamp.  
                     $seenTimestamps{$time} = 1;  
                 }  
                 # Now loop through the real annotations.  
                 for my $tuple ($fig->feature_annotations($peg, "raw")) {  
                     my ($fid, $timestamp, $user, $text) = $tuple;  
1058                      # Here we fix up the annotation text. "\r" is removed,                      # Here we fix up the annotation text. "\r" is removed,
1059                      # and "\t" and "\n" are escaped. Note we use the "s"                  # and "\t" and "\n" are escaped. Note we use the "gs"
1060                      # modifier so that new-lines inside the text do not                      # modifier so that new-lines inside the text do not
1061                      # stop the substitution search.                      # stop the substitution search.
1062                      $text =~ s/\r//gs;                      $text =~ s/\r//gs;
# Line 906  Line 1066 
1066                      $text =~ s/Set master function/Set FIG function/s;                      $text =~ s/Set master function/Set FIG function/s;
1067                      # Insure the time stamp is valid.                      # Insure the time stamp is valid.
1068                      if ($timestamp =~ /^\d+$/) {                      if ($timestamp =~ /^\d+$/) {
1069                          # Here it's a number. We need to insure it's unique.                      # Here it's a number. We need to insure the one we use to form
1070                          while ($seenTimestamps{$timestamp}) {                      # the key is unique.
1071                              $timestamp++;                      my $keyStamp = $timestamp;
1072                        while ($seenTimestamps{"$peg:$keyStamp"}) {
1073                            $keyStamp++;
1074                          }                          }
1075                          $seenTimestamps{$timestamp} = 1;                      my $annotationID = "$peg:$keyStamp";
1076                          my $annotationID = "$peg:$timestamp";                      $seenTimestamps{$annotationID} = 1;
1077                          # Insure the user exists.                          # Insure the user exists.
1078                          if (! $users{$user}) {                          if (! $users{$user}) {
1079                              $loadSproutUser->Put($user, "SEED user");                              $loadSproutUser->Put($user, "SEED user");
# Line 919  Line 1081 
1081                              $users{$user} = 1;                              $users{$user} = 1;
1082                          }                          }
1083                          # Generate the annotation.                          # Generate the annotation.
1084                          $loadAnnotation->Put($annotationID, $timestamp, "$user\\n$text");                      $loadAnnotation->Put($annotationID, $timestamp, $text);
1085                          $loadIsTargetOfAnnotation->Put($peg, $annotationID);                          $loadIsTargetOfAnnotation->Put($peg, $annotationID);
1086                          $loadMadeAnnotation->Put($user, $annotationID);                          $loadMadeAnnotation->Put($user, $annotationID);
1087                      } else {                      } else {
# Line 929  Line 1091 
1091                  }                  }
1092              }              }
1093          }          }
1094        # Finish the load.
1095        my $retVal = $self->_FinishAll();
1096        return $retVal;
1097    }
1098    
1099    =head3 LoadSourceData
1100    
1101    C<< my $stats = $spl->LoadSourceData(); >>
1102    
1103    Load the source data from FIG into Sprout.
1104    
1105    Source data links genomes to information about the organizations that
1106    mapped it.
1107    
1108    The following relations are loaded by this method.
1109    
1110        ComesFrom
1111        Source
1112        SourceURL
1113    
1114    There is no direct support for source attribution in FIG, so we access the SEED
1115    files directly.
1116    
1117    =over 4
1118    
1119    =item RETURNS
1120    
1121    Returns a statistics object for the loads.
1122    
1123    =back
1124    
1125    =cut
1126    #: Return Type $%;
1127    sub LoadSourceData {
1128        # Get this object instance.
1129        my ($self) = @_;
1130        # Get the FIG object.
1131        my $fig = $self->{fig};
1132        # Get the genome hash.
1133        my $genomeHash = $self->{genomes};
1134        # Create load objects for each of the tables we're loading.
1135        my $loadComesFrom = $self->_TableLoader('ComesFrom', $self->PrimaryOnly);
1136        my $loadSource = $self->_TableLoader('Source');
1137        my $loadSourceURL = $self->_TableLoader('SourceURL');
1138        if ($self->{options}->{loadOnly}) {
1139            Trace("Loading from existing files.") if T(2);
1140        } else {
1141            Trace("Generating annotation data.") if T(2);
1142            # Create hashes to collect the Source information.
1143            my %sourceURL = ();
1144            my %sourceDesc = ();
1145            # Loop through the genomes.
1146            my $line;
1147            for my $genomeID (sort keys %{$genomeHash}) {
1148                Trace("Processing $genomeID.") if T(3);
1149                # Open the project file.
1150                if ((open(TMP, "<$FIG_Config::organisms/$genomeID/PROJECT")) &&
1151                    defined($line = <TMP>)) {
1152                    chomp $line;
1153                    my($sourceID, $desc, $url) = split(/\t/,$line);
1154                    $loadComesFrom->Put($genomeID, $sourceID);
1155                    if ($url && ! exists $sourceURL{$sourceID}) {
1156                        $loadSourceURL->Put($sourceID, $url);
1157                        $sourceURL{$sourceID} = 1;
1158                    }
1159                    if ($desc) {
1160                        $sourceDesc{$sourceID} = $desc;
1161                    } elsif (! exists $sourceDesc{$sourceID}) {
1162                        $sourceDesc{$sourceID} = $sourceID;
1163                    }
1164                }
1165                close TMP;
1166            }
1167            # Write the source descriptions.
1168            for my $sourceID (keys %sourceDesc) {
1169                $loadSource->Put($sourceID, $sourceDesc{$sourceID});
1170            }
1171      }      }
1172      # Finish the load.      # Finish the load.
1173      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
1174      return $retVal;      return $retVal;
1175  }  }
1176    
1177    =head3 LoadExternalData
1178    
1179    C<< my $stats = $spl->LoadExternalData(); >>
1180    
1181    Load the external data from FIG into Sprout.
1182    
1183    External data contains information about external feature IDs.
1184    
1185    The following relations are loaded by this method.
1186    
1187        ExternalAliasFunc
1188        ExternalAliasOrg
1189    
1190    The support for external IDs in FIG is hidden beneath layers of other data, so
1191    we access the SEED files directly to create these tables. This is also one of
1192    the few load methods that does not proceed genome by genome.
1193    
1194    =over 4
1195    
1196    =item RETURNS
1197    
1198    Returns a statistics object for the loads.
1199    
1200    =back
1201    
1202    =cut
1203    #: Return Type $%;
1204    sub LoadExternalData {
1205        # Get this object instance.
1206        my ($self) = @_;
1207        # Get the FIG object.
1208        my $fig = $self->{fig};
1209        # Get the genome hash.
1210        my $genomeHash = $self->{genomes};
1211        # Convert the genome hash. We'll get the genus and species for each genome and make
1212        # it the key.
1213        my %speciesHash = map { $fig->genus_species($_) => $_ } (keys %{$genomeHash});
1214        # Create load objects for each of the tables we're loading.
1215        my $loadExternalAliasFunc = $self->_TableLoader('ExternalAliasFunc');
1216        my $loadExternalAliasOrg = $self->_TableLoader('ExternalAliasOrg');
1217        if ($self->{options}->{loadOnly}) {
1218            Trace("Loading from existing files.") if T(2);
1219        } else {
1220            Trace("Generating external data.") if T(2);
1221            # We loop through the files one at a time. First, the organism file.
1222            Open(\*ORGS, "sort +0 -1 -u -t\"\t\" $FIG_Config::global/ext_org.table |");
1223            my $orgLine;
1224            while (defined($orgLine = <ORGS>)) {
1225                # Clean the input line.
1226                chomp $orgLine;
1227                # Parse the organism name.
1228                my ($protID, $name) = split /\s*\t\s*/, $orgLine;
1229                $loadExternalAliasOrg->Put($protID, $name);
1230            }
1231            close ORGS;
1232            # Now the function file.
1233            my $funcLine;
1234            Open(\*FUNCS, "sort +0 -1 -u -t\"\t\" $FIG_Config::global/ext_func.table |");
1235            while (defined($funcLine = <FUNCS>)) {
1236                # Clean the line ending.
1237                chomp $funcLine;
1238                # Only proceed if the line is non-blank.
1239                if ($funcLine) {
1240                    # Split it into fields.
1241                    my @funcFields = split /\s*\t\s*/, $funcLine;
1242                    # If there's an EC number, append it to the description.
1243                    if ($#funcFields >= 2 && $funcFields[2] =~ /^(EC .*\S)/) {
1244                        $funcFields[1] .= " $1";
1245                    }
1246                    # Output the function line.
1247                    $loadExternalAliasFunc->Put(@funcFields[0,1]);
1248                }
1249            }
1250        }
1251        # Finish the load.
1252        my $retVal = $self->_FinishAll();
1253        return $retVal;
1254    }
1255    
1256    
1257    =head3 LoadReactionData
1258    
1259    C<< my $stats = $spl->LoadReactionData(); >>
1260    
1261    Load the reaction data from FIG into Sprout.
1262    
1263    Reaction data connects reactions to the compounds that participate in them.
1264    
1265    The following relations are loaded by this method.
1266    
1267        Reaction
1268        ReactionURL
1269        Compound
1270        CompoundName
1271        CompoundCAS
1272        IsAComponentOf
1273    
1274    This method proceeds reaction by reaction rather than genome by genome.
1275    
1276    =over 4
1277    
1278    =item RETURNS
1279    
1280    Returns a statistics object for the loads.
1281    
1282    =back
1283    
1284    =cut
1285    #: Return Type $%;
1286    sub LoadReactionData {
1287        # Get this object instance.
1288        my ($self) = @_;
1289        # Get the FIG object.
1290        my $fig = $self->{fig};
1291        # Create load objects for each of the tables we're loading.
1292        my $loadReaction = $self->_TableLoader('Reaction');
1293        my $loadReactionURL = $self->_TableLoader('ReactionURL', $self->PrimaryOnly);
1294        my $loadCompound = $self->_TableLoader('Compound', $self->PrimaryOnly);
1295        my $loadCompoundName = $self->_TableLoader('CompoundName', $self->PrimaryOnly);
1296        my $loadCompoundCAS = $self->_TableLoader('CompoundCAS', $self->PrimaryOnly);
1297        my $loadIsAComponentOf = $self->_TableLoader('IsAComponentOf', $self->PrimaryOnly);
1298        if ($self->{options}->{loadOnly}) {
1299            Trace("Loading from existing files.") if T(2);
1300        } else {
1301            Trace("Generating annotation data.") if T(2);
1302            # First we create the compounds.
1303            my @compounds = $fig->all_compounds();
1304            for my $cid (@compounds) {
1305                # Check for names.
1306                my @names = $fig->names_of_compound($cid);
1307                # Each name will be given a priority number, starting with 1.
1308                my $prio = 1;
1309                for my $name (@names) {
1310                    $loadCompoundName->Put($cid, $name, $prio++);
1311                }
1312                # Create the main compound record. Note that the first name
1313                # becomes the label.
1314                my $label = (@names > 0 ? $names[0] : $cid);
1315                $loadCompound->Put($cid, $label);
1316                # Check for a CAS ID.
1317                my $cas = $fig->cas($cid);
1318                if ($cas) {
1319                    $loadCompoundCAS->Put($cid, $cas);
1320                }
1321            }
1322            # All the compounds are set up, so we need to loop through the reactions next. First,
1323            # we initialize the discriminator index. This is a single integer used to insure
1324            # duplicate elements in a reaction are not accidentally collapsed.
1325            my $discrim = 0;
1326            my @reactions = $fig->all_reactions();
1327            for my $reactionID (@reactions) {
1328                # Create the reaction record.
1329                $loadReaction->Put($reactionID, $fig->reversible($reactionID));
1330                # Compute the reaction's URL.
1331                my $url = HTML::reaction_link($reactionID);
1332                # Put it in the ReactionURL table.
1333                $loadReactionURL->Put($reactionID, $url);
1334                # Now we need all of the reaction's compounds. We get these in two phases,
1335                # substrates first and then products.
1336                for my $product (0, 1) {
1337                    # Get the compounds of the current type for the current reaction. FIG will
1338                    # give us 3-tuples: [ID, stoichiometry, main-flag]. At this time we do not
1339                    # have location data in SEED, so it defaults to the empty string.
1340                    my @compounds = $fig->reaction2comp($reactionID, $product);
1341                    for my $compData (@compounds) {
1342                        # Extract the compound data from the current tuple.
1343                        my ($cid, $stoich, $main) = @{$compData};
1344                        # Link the compound to the reaction.
1345                        $loadIsAComponentOf->Put($cid, $reactionID, $discrim++, "", $main,
1346                                                 $product, $stoich);
1347                    }
1348                }
1349            }
1350        }
1351        # Finish the load.
1352        my $retVal = $self->_FinishAll();
1353        return $retVal;
1354    }
1355    
1356    =head3 LoadGroupData
1357    
1358    C<< my $stats = $spl->LoadGroupData(); >>
1359    
1360    Load the genome Groups into Sprout.
1361    
1362    The following relations are loaded by this method.
1363    
1364        GenomeGroups
1365    
1366    Currently, we do not use groups. We used to use them for NMPDR groups,
1367    butThere is no direct support for genome groups in FIG, so we access the SEED
1368    files directly.
1369    
1370    =over 4
1371    
1372    =item RETURNS
1373    
1374    Returns a statistics object for the loads.
1375    
1376    =back
1377    
1378    =cut
1379    #: Return Type $%;
1380    sub LoadGroupData {
1381        # Get this object instance.
1382        my ($self) = @_;
1383        # Get the FIG object.
1384        my $fig = $self->{fig};
1385        # Get the genome hash.
1386        my $genomeHash = $self->{genomes};
1387        # Create a load object for the table we're loading.
1388        my $loadGenomeGroups = $self->_TableLoader('GenomeGroups');
1389        if ($self->{options}->{loadOnly}) {
1390            Trace("Loading from existing files.") if T(2);
1391        } else {
1392            Trace("Generating group data.") if T(2);
1393            # Currently there are no groups.
1394        }
1395        # Finish the load.
1396        my $retVal = $self->_FinishAll();
1397        return $retVal;
1398    }
1399    
1400    =head3 LoadSynonymData
1401    
1402    C<< my $stats = $spl->LoadSynonymData(); >>
1403    
1404    Load the synonym groups into Sprout.
1405    
1406    The following relations are loaded by this method.
1407    
1408        SynonymGroup
1409        IsSynonymGroupFor
1410    
1411    The source information for these relations is taken from the C<maps_to_id> method
1412    of the B<FIG> object. Unfortunately, to make this work, we need to use direct
1413    SQL against the FIG database.
1414    
1415    =over 4
1416    
1417    =item RETURNS
1418    
1419    Returns a statistics object for the loads.
1420    
1421    =back
1422    
1423    =cut
1424    #: Return Type $%;
1425    sub LoadSynonymData {
1426        # Get this object instance.
1427        my ($self) = @_;
1428        # Get the FIG object.
1429        my $fig = $self->{fig};
1430        # Get the genome hash.
1431        my $genomeHash = $self->{genomes};
1432        # Create a load object for the table we're loading.
1433        my $loadSynonymGroup = $self->_TableLoader('SynonymGroup');
1434        my $loadIsSynonymGroupFor = $self->_TableLoader('IsSynonymGroupFor');
1435        if ($self->{options}->{loadOnly}) {
1436            Trace("Loading from existing files.") if T(2);
1437        } else {
1438            Trace("Generating synonym group data.") if T(2);
1439            # Get the database handle.
1440            my $dbh = $fig->db_handle();
1441            # Ask for the synonyms.
1442            my $sth = $dbh->prepare_command("SELECT maps_to, syn_id FROM peg_synonyms ORDER BY maps_to");
1443            my $result = $sth->execute();
1444            if (! defined($result)) {
1445                Confess("Database error in Synonym load: " . $sth->errstr());
1446            } else {
1447                # Remember the current synonym.
1448                my $current_syn = "";
1449                # Count the features.
1450                my $featureCount = 0;
1451                # Loop through the synonym/peg pairs.
1452                while (my @row = $sth->fetchrow()) {
1453                    # Get the synonym ID and feature ID.
1454                    my ($syn_id, $peg) = @row;
1455                    # Insure it's for one of our genomes.
1456                    my $genomeID = FIG::genome_of($peg);
1457                    if (exists $genomeHash->{$genomeID}) {
1458                        # Verify the synonym.
1459                        if ($syn_id ne $current_syn) {
1460                            # It's new, so put it in the group table.
1461                            $loadSynonymGroup->Put($syn_id);
1462                            $current_syn = $syn_id;
1463                        }
1464                        # Connect the synonym to the peg.
1465                        $loadIsSynonymGroupFor->Put($syn_id, $peg);
1466                        # Count this feature.
1467                        $featureCount++;
1468                        if ($featureCount % 1000 == 0) {
1469                            Trace("$featureCount features processed.") if T(3);
1470                        }
1471                    }
1472                }
1473            }
1474        }
1475        # Finish the load.
1476        my $retVal = $self->_FinishAll();
1477        return $retVal;
1478    }
1479    
1480    =head3 LoadFamilyData
1481    
1482    C<< my $stats = $spl->LoadFamilyData(); >>
1483    
1484    Load the protein families into Sprout.
1485    
1486    The following relations are loaded by this method.
1487    
1488        Family
1489        IsFamilyForFeature
1490    
1491    The source information for these relations is taken from the C<families_for_protein>,
1492    C<family_function>, and C<sz_family> methods of the B<FIG> object.
1493    
1494    =over 4
1495    
1496    =item RETURNS
1497    
1498    Returns a statistics object for the loads.
1499    
1500    =back
1501    
1502    =cut
1503    #: Return Type $%;
1504    sub LoadFamilyData {
1505        # Get this object instance.
1506        my ($self) = @_;
1507        # Get the FIG object.
1508        my $fig = $self->{fig};
1509        # Get the genome hash.
1510        my $genomeHash = $self->{genomes};
1511        # Create load objects for the tables we're loading.
1512        my $loadFamily = $self->_TableLoader('Family');
1513        my $loadIsFamilyForFeature = $self->_TableLoader('IsFamilyForFeature');
1514        if ($self->{options}->{loadOnly}) {
1515            Trace("Loading from existing files.") if T(2);
1516        } else {
1517            Trace("Generating family data.") if T(2);
1518            # Create a hash for the family IDs.
1519            my %familyHash = ();
1520            # Loop through the genomes.
1521            for my $genomeID (sort keys %{$genomeHash}) {
1522                Trace("Processing features for $genomeID.") if T(2);
1523                # Loop through this genome's PEGs.
1524                for my $fid ($fig->all_features($genomeID, "peg")) {
1525                    $loadIsFamilyForFeature->Add("features", 1);
1526                    # Get this feature's families.
1527                    my @families = $fig->families_for_protein($fid);
1528                    # Loop through the families, connecting them to the feature.
1529                    for my $family (@families) {
1530                        $loadIsFamilyForFeature->Put($family, $fid);
1531                        # If this is a new family, create a record for it.
1532                        if (! exists $familyHash{$family}) {
1533                            $familyHash{$family} = 1;
1534                            $loadFamily->Add("families", 1);
1535                            my $size = $fig->sz_family($family);
1536                            my $func = $fig->family_function($family);
1537                            $loadFamily->Put($family, $size, $func);
1538                        }
1539                    }
1540                }
1541            }
1542        }
1543        # Finish the load.
1544        my $retVal = $self->_FinishAll();
1545        return $retVal;
1546    }
1547    
1548    
1549    
1550  =head2 Internal Utility Methods  =head2 Internal Utility Methods
1551    
1552  =head3 TableLoader  =head3 TableLoader
# Line 951  Line 1563 
1563    
1564  Name of the table (relation) being loaded.  Name of the table (relation) being loaded.
1565    
1566  =item rowCount (optional)  =item ignore
1567    
1568  Estimated maximum number of rows in the table.  TRUE if the table should be ignored entirely, else FALSE.
1569    
1570  =item RETURN  =item RETURN
1571    
# Line 965  Line 1577 
1577    
1578  sub _TableLoader {  sub _TableLoader {
1579      # Get the parameters.      # Get the parameters.
1580      my ($self, $tableName, $rowCount) = @_;      my ($self, $tableName, $ignore) = @_;
1581      # Create the load object.      # Create the load object.
1582      my $retVal = ERDBLoad->new($self->{erdb}, $tableName, $self->{loadDirectory}, $rowCount);      my $retVal = ERDBLoad->new($self->{erdb}, $tableName, $self->{loadDirectory}, $self->LoadOnly,
1583                                   $ignore);
1584      # Cache it in the loader list.      # Cache it in the loader list.
1585      push @{$self->{loaders}}, $retVal;      push @{$self->{loaders}}, $retVal;
1586      # Return it to the caller.      # Return it to the caller.
# Line 1001  Line 1614 
1614      my $retVal = Stats->new();      my $retVal = Stats->new();
1615      # Get the loader list.      # Get the loader list.
1616      my $loadList = $self->{loaders};      my $loadList = $self->{loaders};
1617        # Create a hash to hold the statistics objects, keyed on relation name.
1618        my %loaderHash = ();
1619      # Loop through the list, finishing the loads. Note that if the finish fails, we die      # Loop through the list, finishing the loads. Note that if the finish fails, we die
1620      # ignominiously. At some future point, we want to make the loads restartable.      # ignominiously. At some future point, we want to make the loads more restartable.
1621      while (my $loader = pop @{$loadList}) {      while (my $loader = pop @{$loadList}) {
1622            # Get the relation name.
1623            my $relName = $loader->RelName;
1624            # Check the ignore flag.
1625            if ($loader->Ignore) {
1626                Trace("Relation $relName not loaded.") if T(2);
1627            } else {
1628                # Here we really need to finish.
1629                Trace("Finishing $relName.") if T(2);
1630          my $stats = $loader->Finish();          my $stats = $loader->Finish();
1631                $loaderHash{$relName} = $stats;
1632            }
1633        }
1634        # Now we loop through again, actually loading the tables. We want to finish before
1635        # loading so that if something goes wrong at this point, all the load files are usable
1636        # and we don't have to redo all that work.
1637        for my $relName (sort keys %loaderHash) {
1638            # Get the statistics for this relation.
1639            my $stats = $loaderHash{$relName};
1640            # Check for a database load.
1641            if ($self->{options}->{dbLoad}) {
1642                # Here we want to use the load file just created to load the database.
1643                Trace("Loading relation $relName.") if T(2);
1644                my $newStats = $self->{sprout}->LoadUpdate(1, [$relName]);
1645                # Accumulate the statistics from the DB load.
1646                $stats->Accumulate($newStats);
1647            }
1648          $retVal->Accumulate($stats);          $retVal->Accumulate($stats);
         my $relName = $loader->RelName;  
1649          Trace("Statistics for $relName:\n" . $stats->Show()) if T(2);          Trace("Statistics for $relName:\n" . $stats->Show()) if T(2);
1650      }      }
1651      # Return the load statistics.      # Return the load statistics.

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