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revision 1.3, Thu May 28 18:08:56 2009 UTC revision 1.19, Tue Sep 13 21:07:59 2011 UTC
# Line 27  Line 27 
27      use HyperLink;      use HyperLink;
28      use AliasAnalysis;      use AliasAnalysis;
29      use LoaderUtils;      use LoaderUtils;
30        use SeedUtils;
31        use gjoseqlib;
32        use MD5Computer;
33      use base 'BaseSaplingLoader';      use base 'BaseSaplingLoader';
34    
35  =head1 Sapling Feature Load Group Class  =head1 Sapling Feature Load Group Class
# Line 45  Line 48 
48    
49  =item erdb  =item erdb
50    
51  [[SaplingPm]] object for the database being loaded.  L<Sapling> object for the database being loaded.
52    
53  =item options  =item options
54    
# Line 64  Line 67 
67      my ($class, $erdb, $options) = @_;      my ($class, $erdb, $options) = @_;
68      # Create the table list.      # Create the table list.
69      my @tables = sort qw(Feature FeatureEssential FeatureEvidence FeatureLink      my @tables = sort qw(Feature FeatureEssential FeatureEvidence FeatureLink
70                           FeatureVirulent IsOwnerOf IsLocatedIn Identifies                           FeatureVirulent IsOwnerOf IsLocatedIn IsIdentifiedBy
71                           Identifier IsNamedBy ProteinSequence Concerns                           Identifier IsNamedBy ProteinSequence Concerns
72                           IsAttachmentSiteFor Publication IsProteinFor);                           IsAttachmentSiteFor Publication IsProteinFor
73                             Role RoleIndex IsFunctionalIn);
74      # Create the BaseSaplingLoader object.      # Create the BaseSaplingLoader object.
75      my $retVal = BaseSaplingLoader::new($class, $erdb, $options, @tables);      my $retVal = BaseSaplingLoader::new($class, $erdb, $options, @tables);
76      # Return it.      # Return it.
# Line 88  Line 92 
92      my ($self) = @_;      my ($self) = @_;
93      # Get the database object.      # Get the database object.
94      my $erdb = $self->db();      my $erdb = $self->db();
95      # Only proceed if this is a normal section. There's no global feature data.      # Check for local or global.
96      if (! $self->global()) {      if (! $self->global()) {
97          # Get the section ID.          # Here we are generating data for a genome.
98          my $genomeID = $self->section();          my $genomeID = $self->section();
99          # Load this genome's features.          # Load this genome's features.
100          $self->LoadGenomeFeatures($genomeID);          $self->LoadGenomeFeatures($genomeID);
101        } else {
102            # The global data is the roles from subsystems and the publications.
103            my $fig = $self->source();
104            # We need the master map of roles to IDs.
105            my %roleHash;
106            my $lastRoleIndex = -1;
107            my $roleMapFile = $erdb->LoadDirectory() . "/roleMap.tbl";
108            if (-f $roleMapFile) {
109                for my $mapLine (Tracer::GetFile($roleMapFile)) {
110                    my ($role, $idx) = split /\t/, $mapLine;
111                    $roleHash{$role} = $idx;
112                    if ($idx > $lastRoleIndex) {
113                        $lastRoleIndex = $idx;
114                    }
115                }
116            }
117            # We'll track duplicate roles in here.
118            my %roleList;
119            # Now we get the subsystem list.
120            my $subHash = $erdb->SubsystemHash();
121            for my $sub (sort keys %$subHash) {
122                $self->Add(subsystems => 1);
123                Trace("Processing roles for $sub.") if T(3);
124                # Get this subsystem's roles and write them out.
125                my @roles = $fig->subsystem_to_roles($sub);
126                for my $role (@roles) {
127                    $self->Add(subsystemRoles => 1);
128                    # Check to see if this role is hypothetical.
129                    my $hypo = hypo($role);
130                    if (! $hypo) {
131                        # Is this role in the role index hash?
132                        my $roleIndex = $roleHash{$role};
133                        if (! defined $roleIndex) {
134                            # No, compute a new index for it.
135                            $roleIndex = ++$lastRoleIndex;
136                            $roleHash{$role} = $roleIndex;
137                        }
138                        if (! $roleList{$role}) {
139                            $roleList{$role} = 1;
140                            $self->PutE(RoleIndex => $role, role_index => $roleIndex);
141                        }
142                    }
143                    $self->PutE(Role => $role, hypothetical => $hypo);
144                }
145            }
146            Trace("Subsystem roles generated.") if T(2);
147            # Write out the role master file.
148            Tracer::PutFile($roleMapFile, [map { "$_\t$roleHash{$_}" } keys %roleHash]);
149            Trace("Role master file written to $roleMapFile.") if T(2);
150            # Now, we get the publications.
151            my $pubs = $fig->all_titles();
152            for my $pub (@$pubs) {
153                # Get the ID and title.
154                my ($pubmedID, $title) = @$pub;
155                # Only proceed if the ID is valid.
156                if ($pubmedID) {
157                    # Create a hyperlink from the title and the pubmed ID.
158                    my $link;
159                    if (! $title) {
160                        $link = HyperLink->new("<unknown>");
161                    } else {
162                        $link = HyperLink->new($title, "http://www.ncbi.nlm.nih.gov/pubmed/$pubmedID");
163                    }
164                    # Create the publication record.
165                    $self->PutE(Publication => $pubmedID, citation => $link);
166                }
167            }
168            Trace("Publications generated.") if T(2);
169      }      }
170  }  }
171    
# Line 126  Line 198 
198      my $aliasDir = $sapling->LoadDirectory() . "/AliasData";      my $aliasDir = $sapling->LoadDirectory() . "/AliasData";
199      my $aliasHash = LoaderUtils::ReadAliasFile($aliasDir, $genomeID);      my $aliasHash = LoaderUtils::ReadAliasFile($aliasDir, $genomeID);
200      if (! defined $aliasHash) {      if (! defined $aliasHash) {
201          Trace("No aliases found for $genomeID.") if T(1);          Trace("No aliases found for $genomeID.") if T(ERDBLoadGroup => 1);
202          $self->Add(missingAliasFile => 1);          $self->Add(missingAliasFile => 1);
203          $aliasHash = {};          $aliasHash = {};
204      }      }
205        # Get all of this genome's protein sequences.
206        my %seqs = map { $_->[0] => $_->[2] } gjoseqlib::read_fasta("$FIG_Config::organisms/$genomeID/Features/peg/fasta");
207      # Get all of this genome's features.      # Get all of this genome's features.
208      my $featureList = $fig->all_features_detailed_fast($genomeID);      my $featureList = $fig->all_features_detailed_fast($genomeID);
209      # Loop through them.      # Loop through them.
# Line 138  Line 212 
212          my ($fid, $locationString, $aliases, $type, undef, undef, $assignment,          my ($fid, $locationString, $aliases, $type, undef, undef, $assignment,
213              $assignmentMaker, $quality) = @$feature;              $assignmentMaker, $quality) = @$feature;
214          $self->Track(Features => $fid, 1000);          $self->Track(Features => $fid, 1000);
215          # Fix the assignment for non-PEG features.          # Fix missing assignments. For RNAs, the assignment may be in the alias list.
216          if (! defined $assignment) {          if (! defined $assignment) {
217                if ($type eq 'rna') {
218              $assignment = $aliases;              $assignment = $aliases;
219              $assignmentMaker ||= 'master';              $assignmentMaker ||= 'master';
220                } else {
221                    $assignment = '';
222                }
223          }          }
224          # Convert the location string to a list of location objects.          # Convert the location string to a list of location objects.
225          my @locs = map { BasicLocation->new($_) } split /\s*,\s*/, $locationString;          my @locs = map { BasicLocation->new($_) } split /\s*,\s*/, $locationString;
# Line 180  Line 258 
258              if ($assignment =~ /att([LR])\s+for\s+(fig\|.+)/) {              if ($assignment =~ /att([LR])\s+for\s+(fig\|.+)/) {
259                  $self->PutR(IsAttachmentSiteFor => $fid, $2, edge => $1);                  $self->PutR(IsAttachmentSiteFor => $fid, $2, edge => $1);
260              } else {              } else {
261                  Trace("Invalid attachment function for $fid: $assignment") if T(1);                  Trace("Invalid attachment function for $fid: $assignment") if T(ERDBLoadGroup => 1);
262                  $self->Add(badAttachment => 1);                  $self->Add(badAttachment => 1);
263              }              }
264          }          }
# Line 190  Line 268 
268                      locked => $fig->is_locked_fid($fid));                      locked => $fig->is_locked_fid($fid));
269          # Connect the feature to its genome.          # Connect the feature to its genome.
270          $self->PutR(IsOwnerOf => $genomeID, $fid);          $self->PutR(IsOwnerOf => $genomeID, $fid);
271            # Connect the feature to its roles.
272            my ($roles, $errors) = SeedUtils::roles_for_loading($assignment);
273            if (! defined $roles) {
274                # Here the functional assignment was suspicious.
275                $self->Add(suspiciousFunction => 1);
276                Trace("$fid has a suspicious function: $assignment") if T(ERDBLoadGroup => 1);
277            } else {
278                # Here we have a good assignment.
279                for my $role (@$roles) {
280                    $self->Add(featureRole => 1);
281                    $self->PutR(IsFunctionalIn => $role, $fid);
282                    $self->PutE(Role => $role, hypothetical => hypo($role));
283                }
284                $self->Add(badFeatureRoles => $errors);
285            }
286          # Now we have a whole bunch of attribute-related stuff to store in          # Now we have a whole bunch of attribute-related stuff to store in
287          # secondary Feature tables. First is the evidence codes.          # secondary Feature tables. First is the evidence codes. This is special
288            # because we have to save the DLIT numbers.
289            my @dlits;
290          my @evidenceTuples = $fig->get_attributes($fid, 'evidence_code');          my @evidenceTuples = $fig->get_attributes($fid, 'evidence_code');
291          for my $evidenceTuple (@evidenceTuples) {          for my $evidenceTuple (@evidenceTuples) {
292              my (undef, undef, $code) = @$evidenceTuple;              my (undef, undef, $code) = @$evidenceTuple;
293              $self->PutE(FeatureEvidence => $fid, 'evidence-code' => $code);              $self->PutE(FeatureEvidence => $fid, 'evidence-code' => $code);
294                # If this is a direct literature reference, save it.
295                if ($code =~ /dlit\((\d+)/) {
296                    push @dlits, $1;
297                    $self->Add(dlits => 1);
298                }
299          }          }
300          # Now we have the external links. These are stored using hyperlink objects.          # Now we have the external links. These are stored using hyperlink objects.
301          my @links = $fig->fid_links($fid);          my @links = $fig->fid_links($fid);
# Line 214  Line 314 
314          my @essentials = $fig->get_attributes($fid, undef, ['essential', 'potential-essential']);          my @essentials = $fig->get_attributes($fid, undef, ['essential', 'potential-essential']);
315          for my $essentialTuple (@essentials) {          for my $essentialTuple (@essentials) {
316              my (undef, undef, $essentialityType, $url) = @$essentialTuple;              my (undef, undef, $essentialityType, $url) = @$essentialTuple;
317                # Only keep this datum if it has a URL. The ones without URLs are
318                # all duplicates.
319                if ($url) {
320              # Form a hyperlink from this essentiality tuple.              # Form a hyperlink from this essentiality tuple.
321              my $link = HyperLink->new($essentialityType, $url);              my $link = HyperLink->new($essentialityType, $url);
322              # Store it as essentiality data for this feature.              # Store it as essentiality data for this feature.
323              $self->PutE(FeatureEssential => $fid, essential => $link);              $self->PutE(FeatureEssential => $fid, essential => $link);
324          }          }
325            }
326          # If this is a PEG, we have a protein sequence.          # If this is a PEG, we have a protein sequence.
327          my $proteinID;          my $proteinID;
328          if ($type eq 'peg') {          if ($type eq 'peg') {
329              # Get the translation.              # Get the translation.
330              my $proteinSequence = $fig->get_translation($fid);              my $proteinSequence = $seqs{$fid};
331                if (! $proteinSequence) {
332                    Trace("No protein sequence found for $fid.") if T(ERDBLoadGroup => 2);
333                    $self->Add(missingProtein => 1);
334                    # Here there was some sort of error and the protein sequence did
335                    # not come back. Ask for the DNA and translate it instead.
336                    my $dna = $fig->get_dna_seq($fid);
337                    $proteinSequence = FIG::translate($dna, undef, 1);
338                }
339              # Compute the ID.              # Compute the ID.
340              $proteinID = ERDB::DigestKey($proteinSequence);              $proteinID = $sapling->ProteinID($proteinSequence);
341              # Create the protein record.              # Create the protein record.
342              $self->PutE(ProteinSequence => $proteinID, sequence => $proteinSequence);              $self->PutE(ProteinSequence => $proteinID, sequence => $proteinSequence);
343              $self->PutR(IsProteinFor => $proteinID, $fid);              $self->PutR(IsProteinFor => $proteinID, $fid);
344              # Get the publications for this PEG.              # Connect this protein to the feature's publications (if any).
345              my @pubs = $fig->get_attributes($fid, 'PUBMED_CURATED_RELEVANT');              for my $pub (@dlits) {
346              for my $pub (@pubs) {                  $self->PutR(Concerns => $pub, $proteinID);
                 # Parse out the article title from the data.  
                 my (undef, undef, $data, $url) = @$pub;  
                 my @pieces = split /,/, $data, 3;  
                 if (defined $pieces[2]) {  
                     # Create the publication record.  
                     my $hl = HyperLink->new($pieces[2], $url);  
                     my $key = ERDB::DigestKey($url);  
                     $self->PutE(Publication => $key, citation => $hl);  
                     # Connect it to the protein.  
                     $self->PutR(Concerns => $key, $proteinID);  
                 }  
347              }              }
348          }          }
349          # Now we need to compute the identifiers. We start with the aliases.          # Now we need to compute the identifiers. We start with the aliases.
# Line 253  Line 354 
354          for my $aliasTuple (@$aliasList) {          for my $aliasTuple (@$aliasList) {
355              my ($aliasID, $aliasType, $aliasConf) = @$aliasTuple;              my ($aliasID, $aliasType, $aliasConf) = @$aliasTuple;
356              # Get the natural form. If there is none, then the canonical              # Get the natural form. If there is none, then the canonical
357              # form IS the natural form.              # form IS the natural form. Note we have to make a special check
358              my $natural = AliasAnalysis::Type($aliasType => $aliasID) || $aliasID;              # for locus tags, which have an insane number of variants.
359                my $natural;
360                if ($aliasID =~ /LocusTag:(.+)/) {
361                    $natural = $1;
362                } else {
363                    $natural = AliasAnalysis::Type($aliasType => $aliasID) || $aliasID;
364                }
365              # Create the identifier record.              # Create the identifier record.
366              $self->PutE(Identifier => $aliasID, natural_form => $natural,              $self->PutE(Identifier => $aliasID, natural_form => $natural,
367                          source => $type);                          source => $aliasType);
368              # Is this a protein alias?              # Is this a protein alias?
369              if ($aliasConf eq 'C' && $proteinID) {              if ($aliasConf eq 'C' && $proteinID) {
370                  # Yes. Connect it using IsNamedBy.                  # Yes. Connect it using IsNamedBy.
371                  $self->PutR(IsNamedBy => $proteinID, $aliasID);                  $self->PutR(IsNamedBy => $proteinID, $aliasID);
372              } else {              } else {
373                  # No. Connect it to the feature.                  # No. Connect it to the feature.
374                  $self->PutR(Identifies => $aliasID, $fid, conf => $aliasConf);                  $self->PutR(IsIdentifiedBy => $fid, $aliasID, conf => $aliasConf);
375              }              }
376          }          }
377          # Finally, this feature is an alias of itself.          # Finally, this feature is an alias of itself.
378          $self->PutE(Identifier => $fid, natural_form => $fid,          $self->PutE(Identifier => $fid, natural_form => $fid,
379                      source => 'SEED');                      source => 'SEED');
380          $self->PutR(Identifies => $fid, $fid, conf => 'A');          $self->PutR(IsIdentifiedBy => $fid, $fid, conf => 'A');
         if ($proteinID) {  
             $self->PutR(IsNamedBy => $proteinID, $fid);  
         }  
381      }      }
382  }  }
383    

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