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revision 1.7, Wed Nov 25 21:00:45 2009 UTC revision 1.18, Wed Aug 24 17:58:54 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 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        # Compute the MD5 identifiers for the genome and its contigs.
210        my $genomeMD5Data = MD5Computer->new_from_fasta("$FIG_Config::organisms/$genomeID/contigs");
211      # Loop through them.      # Loop through them.
212      for my $feature (@$featureList) {      for my $feature (@$featureList) {
213          # Get this feature's data.          # Get this feature's data.
# Line 184  Line 260 
260              if ($assignment =~ /att([LR])\s+for\s+(fig\|.+)/) {              if ($assignment =~ /att([LR])\s+for\s+(fig\|.+)/) {
261                  $self->PutR(IsAttachmentSiteFor => $fid, $2, edge => $1);                  $self->PutR(IsAttachmentSiteFor => $fid, $2, edge => $1);
262              } else {              } else {
263                  Trace("Invalid attachment function for $fid: $assignment") if T(1);                  Trace("Invalid attachment function for $fid: $assignment") if T(ERDBLoadGroup => 1);
264                  $self->Add(badAttachment => 1);                  $self->Add(badAttachment => 1);
265              }              }
266          }          }
267            # Compute the MD5 identifier. This may fail if there is an error in the
268            # feature definition.
269            my $md5Alias;
270            eval {
271                $md5Alias = $genomeMD5Data->ComputeFeatureMD5($type, map { $_->String() } @locs);
272            };
273            if ($@) {
274                Trace("Error in $fid MD5 computation: $@") if T(0);
275                $self->Add(md5ComputeError => 1);
276            }
277          # Emit the feature record.          # Emit the feature record.
278          $self->PutE(Feature => $fid, feature_type => $type,          $self->PutE(Feature => $fid, feature_type => $type,
279                      sequence_length => $seqLen, function => $assignment,                      sequence_length => $seqLen, function => $assignment,
280                      locked => $fig->is_locked_fid($fid));                      locked => $fig->is_locked_fid($fid));
281          # Connect the feature to its genome.          # Connect the feature to its genome.
282          $self->PutR(IsOwnerOf => $genomeID, $fid);          $self->PutR(IsOwnerOf => $genomeID, $fid);
283            # Connect the feature to its roles.
284            my ($roles, $errors) = SeedUtils::roles_for_loading($assignment);
285            if (! defined $roles) {
286                # Here the functional assignment was suspicious.
287                $self->Add(suspiciousFunction => 1);
288                Trace("$fid has a suspicious function: $assignment") if T(ERDBLoadGroup => 1);
289            } else {
290                # Here we have a good assignment.
291                for my $role (@$roles) {
292                    $self->Add(featureRole => 1);
293                    $self->PutR(IsFunctionalIn => $role, $fid);
294                    $self->PutE(Role => $role, hypothetical => hypo($role));
295                }
296                $self->Add(badFeatureRoles => $errors);
297            }
298          # 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
299          # secondary Feature tables. First is the evidence codes.          # secondary Feature tables. First is the evidence codes. This is special
300            # because we have to save the DLIT numbers.
301            my @dlits;
302          my @evidenceTuples = $fig->get_attributes($fid, 'evidence_code');          my @evidenceTuples = $fig->get_attributes($fid, 'evidence_code');
303          for my $evidenceTuple (@evidenceTuples) {          for my $evidenceTuple (@evidenceTuples) {
304              my (undef, undef, $code) = @$evidenceTuple;              my (undef, undef, $code) = @$evidenceTuple;
305              $self->PutE(FeatureEvidence => $fid, 'evidence-code' => $code);              $self->PutE(FeatureEvidence => $fid, 'evidence-code' => $code);
306                # If this is a direct literature reference, save it.
307                if ($code =~ /dlit\((\d+)/) {
308                    push @dlits, $1;
309                    $self->Add(dlits => 1);
310                }
311          }          }
312          # Now we have the external links. These are stored using hyperlink objects.          # Now we have the external links. These are stored using hyperlink objects.
313          my @links = $fig->fid_links($fid);          my @links = $fig->fid_links($fid);
# Line 231  Line 339 
339          my $proteinID;          my $proteinID;
340          if ($type eq 'peg') {          if ($type eq 'peg') {
341              # Get the translation.              # Get the translation.
342              my $proteinSequence = $fig->get_translation($fid);              my $proteinSequence = $seqs{$fid};
343              if (! $proteinSequence) {              if (! $proteinSequence) {
344                  Trace("No protein sequence found for $fid.") if T(2);                  Trace("No protein sequence found for $fid.") if T(ERDBLoadGroup => 2);
345                  $self->Add(missingProtein => 1);                  $self->Add(missingProtein => 1);
346                  # Here there was some sort of error and the protein sequence did                  # Here there was some sort of error and the protein sequence did
347                  # not come back. Ask for the DNA and translate it instead.                  # not come back. Ask for the DNA and translate it instead.
# Line 241  Line 349 
349                  $proteinSequence = FIG::translate($dna, undef, 1);                  $proteinSequence = FIG::translate($dna, undef, 1);
350              }              }
351              # Compute the ID.              # Compute the ID.
352              $proteinID = ERDB::DigestKey($proteinSequence);              $proteinID = $sapling->ProteinID($proteinSequence);
353              # Create the protein record.              # Create the protein record.
354              $self->PutE(ProteinSequence => $proteinID, sequence => $proteinSequence);              $self->PutE(ProteinSequence => $proteinID, sequence => $proteinSequence);
355              $self->PutR(IsProteinFor => $proteinID, $fid);              $self->PutR(IsProteinFor => $proteinID, $fid);
356              # Get the publications for this PEG.              # Connect this protein to the feature's publications (if any).
357              my @pubs = $fig->get_attributes($fid, 'PUBMED_CURATED_RELEVANT');              for my $pub (@dlits) {
358              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);  
                 }  
359              }              }
360          }          }
361          # 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 269  Line 366 
366          for my $aliasTuple (@$aliasList) {          for my $aliasTuple (@$aliasList) {
367              my ($aliasID, $aliasType, $aliasConf) = @$aliasTuple;              my ($aliasID, $aliasType, $aliasConf) = @$aliasTuple;
368              # Get the natural form. If there is none, then the canonical              # Get the natural form. If there is none, then the canonical
369              # form IS the natural form.              # form IS the natural form. Note we have to make a special check
370              my $natural = AliasAnalysis::Type($aliasType => $aliasID) || $aliasID;              # for locus tags, which have an insane number of variants.
371                my $natural;
372                if ($aliasID =~ /LocusTag:(.+)/) {
373                    $natural = $1;
374                } else {
375                    $natural = AliasAnalysis::Type($aliasType => $aliasID) || $aliasID;
376                }
377              # Create the identifier record.              # Create the identifier record.
378              $self->PutE(Identifier => $aliasID, natural_form => $natural,              $self->PutE(Identifier => $aliasID, natural_form => $natural,
379                          source => $aliasType);                          source => $aliasType);
# Line 280  Line 383 
383                  $self->PutR(IsNamedBy => $proteinID, $aliasID);                  $self->PutR(IsNamedBy => $proteinID, $aliasID);
384              } else {              } else {
385                  # No. Connect it to the feature.                  # No. Connect it to the feature.
386                  $self->PutR(Identifies => $aliasID, $fid, conf => $aliasConf);                  $self->PutR(IsIdentifiedBy => $fid, $aliasID, conf => $aliasConf);
387                }
388              }              }
389            # Make the MD5 identifier an alias.
390            if (defined $md5Alias) {
391                $self->PutE(Identifier => "ubi|$md5Alias", natural_form => $md5Alias,
392                            source => 'UBI');
393                $self->PutR(IsIdentifiedBy => $fid, "ubi|$md5Alias", conf => 'A');
394          }          }
395          # Finally, this feature is an alias of itself.          # Finally, this feature is an alias of itself.
396          $self->PutE(Identifier => $fid, natural_form => $fid,          $self->PutE(Identifier => $fid, natural_form => $fid,
397                      source => 'SEED');                      source => 'SEED');
398          $self->PutR(Identifies => $fid, $fid, conf => 'A');          $self->PutR(IsIdentifiedBy => $fid, $fid, conf => 'A');
399      }      }
400  }  }
401    

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