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revision 1.75, Sun Oct 22 05:17:10 2006 UTC revision 1.76, Fri Nov 3 00:43:22 2006 UTC
# Line 80  Line 80 
80  Either the name of the file containing the list of trusted subsystems or a reference  Either the name of the file containing the list of trusted subsystems or a reference
81  to a list of subsystem names. If nothing is specified, all NMPDR subsystems will be  to a list of subsystem names. If nothing is specified, all NMPDR subsystems will be
82  considered trusted. (A subsystem is considered NMPDR if it has a file named C<NMPDR>  considered trusted. (A subsystem is considered NMPDR if it has a file named C<NMPDR>
83  in its data directory.) Only subsystem data related to the trusted subsystems is loaded.  in its data directory.) Only subsystem data related to the NMPDR subsystems is loaded.
84    
85  =item options  =item options
86    
# Line 138  Line 138 
138          if (! defined $subsysFile || $subsysFile eq '') {          if (! defined $subsysFile || $subsysFile eq '') {
139              # Here we want all the usable subsystems. First we get the whole list.              # Here we want all the usable subsystems. First we get the whole list.
140              my @subs = $fig->all_subsystems();              my @subs = $fig->all_subsystems();
141              # Loop through, checking for usability.              # Loop through, checking for the NMPDR file.
142              for my $sub (@subs) {              for my $sub (@subs) {
143                  if ($fig->usable_subsystem($sub)) {                  if ($fig->nmpdr_subsystem($sub)) {
144                      $subsystems{$sub} = 1;                      $subsystems{$sub} = 1;
145                  }                  }
146              }              }
# Line 168  Line 168 
168              my $name = $subsystem;              my $name = $subsystem;
169              $name =~ s/_/ /g;              $name =~ s/_/ /g;
170              my $classes = $fig->subsystem_classification($subsystem);              my $classes = $fig->subsystem_classification($subsystem);
171              my @classList = map { " $_" } @{$classes};              $name .= " " . join(" ", @{$classes});
             $name .= join("", @classList);  
172              $subsystems{$subsystem} = $name;              $subsystems{$subsystem} = $name;
173          }          }
174      }      }
# Line 470  Line 469 
469      IsLocatedIn      IsLocatedIn
470      HasFeature      HasFeature
471      HasRoleInSubsystem      HasRoleInSubsystem
472        FeatureEssential
473        FeatureVirulent
474        FeatureIEDB
475    
476  =over 4  =over 4
477    
# Line 498  Line 500 
500      my $loadFeatureUpstream = $self->_TableLoader('FeatureUpstream');      my $loadFeatureUpstream = $self->_TableLoader('FeatureUpstream');
501      my $loadHasFeature = $self->_TableLoader('HasFeature', $self->PrimaryOnly);      my $loadHasFeature = $self->_TableLoader('HasFeature', $self->PrimaryOnly);
502      my $loadHasRoleInSubsystem = $self->_TableLoader('HasRoleInSubsystem', $self->PrimaryOnly);      my $loadHasRoleInSubsystem = $self->_TableLoader('HasRoleInSubsystem', $self->PrimaryOnly);
503        my $loadFeatureEssential = $self->_TableLoader('FeatureEssential');
504        my $loadFeatureVirulent = $self->_TableLoader('FeatureVirulent');
505        my $loadFeatureIEDB = $self->_TableLoader('FeatureIEDB');
506      # Get the subsystem hash.      # Get the subsystem hash.
507      my $subHash = $self->{subsystems};      my $subHash = $self->{subsystems};
508      # Get the maximum sequence size. We need this later for splitting up the      # Get the maximum sequence size. We need this later for splitting up the
# Line 530  Line 535 
535                      $oldFeatureID = $featureID;                      $oldFeatureID = $featureID;
536                      # Count this feature.                      # Count this feature.
537                      $loadFeature->Add("featureIn");                      $loadFeature->Add("featureIn");
538                      # Begin building the keywords.                      # Begin building the keywords. We start with the genome ID, the
539                      my @keywords = ($genomeID);                      # feature ID, and the organism name.
540                        my @keywords = ($genomeID, $featureID, $fig->genus_species($genomeID));
541                      # Get the functional assignment and aliases. This                      # Get the functional assignment and aliases. This
542                      # depends on the feature type.                      # depends on the feature type.
543                      my $assignment;                      my $assignment;
# Line 593  Line 599 
599                              }                              }
600                          }                          }
601                      }                      }
602                      # The final task is to add virulence and essentiality attributes.                      # There are three special attributes computed from property
603                      if ($fig->virulent($featureID)) {                      # data that we build next. If the special attribute is non-empty,
604                          push @keywords, "virulent";                      # its name will be added to the keyword list. First, we get all
605                      }                      # the attributes for this feature. They will come back as
606                      if ($fig->essential($featureID)) {                      # 4-tuples: [peg, name, value, URL]. We use a 3-tuple instead:
607                          push @keywords, "essential";                      # [name, value, value with URL]. (We don't need the PEG, since
608                        # we already know it.)
609                        my @attributes = map { [$_->[1], $_->[2], Tracer::CombineURL($_->[2], $_->[3])] }
610                                             $fig->get_attributes($featureID);
611                        # Now we process each of the special attributes.
612                        if (SpecialAttribute($featureID, \@attributes,
613                                             1, 2, '^(essential|potential_essential)$',
614                                             $loadFeatureEssential)) {
615                            push @keywords, 'essential';
616                            $loadFeature->Add('essential');
617                        }
618                        if (SpecialAttribute($featureID, \@attributes,
619                                             0, 2, '^virulen',
620                                             $loadFeatureVirulent)) {
621                            push @keywords, 'virulent';
622                            $loadFeature->Add('virulent');
623                        }
624                        if (SpecialAttribute($featureID, \@attributes,
625                                             0, 2, '^iedb_',
626                                             $loadFeatureIEDB)) {
627                            push @keywords, 'iedb';
628                            $loadFeature->Add('iedb');
629                      }                      }
630                      # Now we need to bust up hyphenated words in the keyword                      # Now we need to bust up hyphenated words in the keyword
631                      # list.                      # list.
# Line 1578  Line 1605 
1605      return $retVal;      return $retVal;
1606  }  }
1607    
1608    =head3 LoadDrugData
1609    
1610    C<< my $stats = $spl->LoadDrugData(); >>
1611    
1612    Load the drug target data into Sprout.
1613    
1614    The following relations are loaded by this method.
1615    
1616        DrugProject
1617        ContainsTopic
1618        DrugTopic
1619        ContainsAnalysisOf
1620        PDB
1621        IncludesBound
1622        IsBoundIn
1623        BindsWith
1624        Ligand
1625        DescribesProteinForFeature
1626        FeatureConservation
1627    
1628    The source information for these relations is taken from flat files in the
1629    C<$FIG_Config::drug_directory>. The file C<master_tables.list> contains
1630    a list of drug project names paired with file names. The named file (in the
1631    same directory) contains all the data for the project.
1632    
1633    =over 4
1634    
1635    =item RETURNS
1636    
1637    Returns a statistics object for the loads.
1638    
1639    =back
1640    
1641    =cut
1642    #: Return Type $%;
1643    sub LoadDrugData {
1644        # Get this object instance.
1645        my ($self) = @_;
1646        # Get the FIG object.
1647        my $fig = $self->{fig};
1648        # Get the genome hash.
1649        my $genomeHash = $self->{genomes};
1650        # Create load objects for the tables we're loading.
1651        my $loadDrugProject = $self->_TableLoader('DrugProject');
1652        my $loadContainsTopic = $self->_TableLoader('ContainsTopic');
1653        my $loadDrugTopic = $self->_TableLoader('DrugTopic');
1654        my $loadContainsAnalysisOf = $self->_TableLoader('ContainsAnalysisOf');
1655        my $loadPDB = $self->_TableLoader('PDB');
1656        my $loadIncludesBound = $self->_TableLoader('IncludesBound');
1657        my $loadIsBoundIn = $self->_TableLoader('IsBoundIn');
1658        my $loadBindsWith = $self->_TableLoader('BindsWith');
1659        my $loadLigand = $self->_TableLoader('Ligand');
1660        my $loadDescribesProteinForFeature = $self->_TableLoader('DescribesProteinForFeature');
1661        my $loadFeatureConservation = $self->_TableLoader('FeatureConservation');
1662        if ($self->{options}->{loadOnly}) {
1663            Trace("Loading from existing files.") if T(2);
1664        } else {
1665            Trace("Generating drug target data.") if T(2);
1666            # Load the project list. The file comes in as a list of chomped lines,
1667            # and we split them on the TAB character to make the project name the
1668            # key and the file name the value of the resulting hash.
1669            my %projects = map { split /\t/, $_ } Tracer::GetFile("$FIG_Config::drug_directory/master_tables.list");
1670            # Create hashes for the derived objects: PDBs, Features, and Ligands. These objects
1671            # may occur multiple times in a single project file or even in multiple project
1672            # files.
1673            my %ligands = ();
1674            my %pdbs = ();
1675            my %features = ();
1676            my %bindings = ();
1677            # Set up a counter for drug topics. This will be used as the key.
1678            my $topicCounter = 0;
1679            # Loop through the projects. We sort the keys not because we need them sorted, but
1680            # because it makes it easier to infer our progress from trace messages.
1681            for my $project (sort keys %projects) {
1682                Trace("Processing project $project.") if T(3);
1683                # Only proceed if the download file exists.
1684                my $projectFile = "$FIG_Config::drug_directory/$projects{$project}";
1685                if (! -f $projectFile) {
1686                    Trace("Project file $projectFile not found.") if T(0);
1687                } else {
1688                    # Create the project record.
1689                    $loadDrugProject->Put($project);
1690                    # Create a hash for the topics. Each project has one or more topics. The
1691                    # topic is identified by a URL, a category, and an identifier.
1692                    my %topics = ();
1693                    # Now we can open the project file.
1694                    Trace("Reading project file $projectFile.") if T(3);
1695                    Open(\*PROJECT, "<$projectFile");
1696                    # Get the first record, which is a list of column headers. We don't use this
1697                    # for anything, but it may be useful for debugging.
1698                    my $headerLine = <PROJECT>;
1699                    # Loop through the rest of the records.
1700                    while (! eof PROJECT) {
1701                        # Get the current line of data. Note that not all lines will have all
1702                        # the fields. In particular, the CLIBE data is fairly rare.
1703                        my ($authorOrganism, $category, $tag, $refURL, $peg, $conservation,
1704                            $pdbBound, $pdbBoundEval, $pdbFree, $pdbFreeEval, $pdbFreeTitle,
1705                            $protDistInfo, $passAspInfo, $passAspFile, $passWeightInfo,
1706                            $passWeightFile, $clibeInfo, $clibeURL, $clibeTotalEnergy,
1707                            $clibeVanderwaals, $clibeHBonds, $clibeEI, $clibeSolvationE)
1708                           = Tracer::GetLine(\*PROJECT);
1709                        # The tag contains an identifier for the current line of data followed
1710                        # by a text statement that generally matches a property name in the
1711                        # main database. We split it up, since the identifier goes with
1712                        # the PDB data and the text statement is part of the topic.
1713                        my ($lineID, $topicTag) = split /\s*,\s*/, $tag;
1714                        $loadDrugProject->Add("data line");
1715                        # Check for a new topic.
1716                        my $topicData = "$category\t$topicTag\t$refURL";
1717                        if (! exists $topics{$topicData}) {
1718                            # Here we have a new topic. Compute its ID.
1719                            $topicCounter++;
1720                            $topics{$topicData} = $topicCounter;
1721                            # Create its database record.
1722                            $loadDrugTopic->Put($topicCounter, $refURL, $category, $authorOrganism,
1723                                                $topicTag);
1724                            # Connect it to the project.
1725                            $loadContainsTopic->Put($project, $topicCounter);
1726                            $loadDrugTopic->Add("topic");
1727                        }
1728                        # Now we know the topic ID exists in the hash and the topic will
1729                        # appear in the database, so we get this topic's ID.
1730                        my $topicID = $topics{$topicData};
1731                        # If the feature in this line is new, we need to save its conservation
1732                        # number.
1733                        if (! exists $features{$peg}) {
1734                            $loadFeatureConservation->Put($peg, $conservation);
1735                            $features{$peg} = 1;
1736                        }
1737                        # Now we have two PDBs to deal with-- a bound PDB and a free PDB.
1738                        # The free PDB will have data about docking points; the bound PDB
1739                        # will have data about docking. We store both types as PDBs, and
1740                        # the special data comes from relationships. First we process the
1741                        # bound PDB.
1742                        if ($pdbBound) {
1743                            $loadPDB->Add("bound line");
1744                            # Insure this PDB is in the database.
1745                            $self->CreatePDB($pdbBound, lc "$pdbFreeTitle (bound)", "bound", \%pdbs, $loadPDB);
1746                            # Connect it to this topic.
1747                            $loadIncludesBound->Put($topicID, $pdbBound);
1748                            # Check for CLIBE data.
1749                            if ($clibeInfo) {
1750                                $loadLigand->Add("clibes");
1751                                # We have CLIBE data, so we create a ligand and relate it to the PDB.
1752                                if (! exists $ligands{$clibeInfo}) {
1753                                    # This is a new ligand, so create its record.
1754                                    $loadLigand->Put($clibeInfo);
1755                                    $loadLigand->Add("ligand");
1756                                    # Make sure we know this ligand already exists.
1757                                    $ligands{$clibeInfo} = 1;
1758                                }
1759                                # Now connect the PDB to the ligand using the CLIBE data.
1760                                $loadBindsWith->Put($pdbBound, $clibeInfo, $clibeURL, $clibeHBonds, $clibeEI,
1761                                                    $clibeSolvationE, $clibeVanderwaals);
1762                            }
1763                            # Connect this PDB to the feature.
1764                            $loadDescribesProteinForFeature->Put($pdbBound, $peg, $protDistInfo, $pdbBoundEval);
1765                        }
1766                        # Next is the free PDB.
1767                        if ($pdbFree) {
1768                            $loadPDB->Add("free line");
1769                            # Insure this PDB is in the database.
1770                            $self->CreatePDB($pdbFree, lc $pdbFreeTitle, "free", \%pdbs, $loadPDB);
1771                            # Connect it to this topic.
1772                            $loadContainsAnalysisOf->Put($topicID, $pdbFree, $passAspInfo,
1773                                                         $passWeightFile, $passWeightInfo, $passAspFile);
1774                            # Connect this PDB to the feature.
1775                            $loadDescribesProteinForFeature->Put($pdbFree, $peg, $protDistInfo, $pdbFreeEval);
1776                        }
1777                        # If we have both PDBs, we may need to link them.
1778                        if ($pdbFree && $pdbBound) {
1779                            $loadIsBoundIn->Add("connection");
1780                            # Insure we only link them once.
1781                            my $bindingKey =  "$pdbFree\t$pdbBound";
1782                            if (! exists $bindings{$bindingKey}) {
1783                                $loadIsBoundIn->Add("newConnection");
1784                                $loadIsBoundIn->Put($pdbFree, $pdbBound);
1785                                $bindings{$bindingKey} = 1;
1786                            }
1787                        }
1788                    }
1789                    # Close off this project.
1790                    close PROJECT;
1791                }
1792            }
1793        }
1794        # Finish the load.
1795        my $retVal = $self->_FinishAll();
1796        return $retVal;
1797    }
1798    
1799    
1800  =head2 Internal Utility Methods  =head2 Internal Utility Methods
1801    
1802    =head3 SpecialAttribute
1803    
1804    C<< my $count = SproutLoad::SpecialAttribute($id, \@attributes, $idxMatch, $idxValue, $pattern, $loader); >>
1805    
1806    Look for special attributes of a given type. A special attribute is found by comparing one of
1807    the columns of the incoming attribute list to a search pattern. If a match is found, then
1808    another column is put into an output table connected to the specified ID.
1809    
1810    For example, when processing features, the attribute list we look at has three columns: attribute
1811    name, attribute value, and attribute value HTML. The IEDB attribute exists if the attribute name
1812    begins with C<iedb_>. The call signature is therefore
1813    
1814        my $found = SpecialAttribute($fid, \@attributeList, 0, 2, '^iedb_', $loadFeatureIEDB);
1815    
1816    The pattern is matched against column 0, and if we have a match, then column 2's value is put
1817    to the output along with the specified feature ID.
1818    
1819    =over 4
1820    
1821    =item id
1822    
1823    ID of the object whose special attributes are being loaded. This forms the first column of the
1824    output.
1825    
1826    =item attributes
1827    
1828    Reference to a list of tuples.
1829    
1830    =item idxMatch
1831    
1832    Index in each tuple of the column to be matched against the pattern. If the match is
1833    successful, an output record will be generated.
1834    
1835    =item idxValue
1836    
1837    Index in each tuple of the column to be put as the second column of the output.
1838    
1839    =item pattern
1840    
1841    Pattern to be matched against the specified column. The match will be case-insensitive.
1842    
1843    =item loader
1844    
1845    An object to which each output record will be put. Usually this is an B<ERDBLoad> object,
1846    but technically it could be anything with a C<Put> method.
1847    
1848    =item RETURN
1849    
1850    Returns a count of the matches found.
1851    
1852    =item
1853    
1854    =back
1855    
1856    =cut
1857    
1858    sub SpecialAttribute {
1859        # Get the parameters.
1860        my ($id, $attributes, $idxMatch, $idxValue, $pattern, $loader) = @_;
1861        # Declare the return variable.
1862        my $retVal = 0;
1863        # Loop through the attribute rows.
1864        for my $row (@{$attributes}) {
1865            # Check for a match.
1866            if ($row->[$idxMatch] =~ m/$pattern/i) {
1867                # We have a match, so output a row.
1868                $loader->Put($id, $row->[$idxValue]);
1869                $retVal++;
1870            }
1871        }
1872        Trace("$retVal special attributes found for $id and loader " . $loader->RelName() . ".") if T(4) && $retVal;
1873        # Return the number of matches.
1874        return $retVal;
1875    }
1876    
1877    =head3 CreatePDB
1878    
1879    C<< $loader->CreatePDB($pdbID, $title, $type, \%pdbHash); >>
1880    
1881    Insure that a PDB record exists for the identified PDB. If one does not exist, it will be
1882    created.
1883    
1884    =over 4
1885    
1886    =item pdbID
1887    
1888    ID string (usually an unqualified file name) for the desired PDB.
1889    
1890    =item title
1891    
1892    Title to use if the PDB must be created.
1893    
1894    =item type
1895    
1896    Type of PDB: C<free> or C<bound>
1897    
1898    =item pdbHash
1899    
1900    Hash containing the IDs of PDBs that have already been created.
1901    
1902    =item pdbLoader
1903    
1904    Load object for the PDB table.
1905    
1906    =back
1907    
1908    =cut
1909    
1910    sub CreatePDB {
1911        # Get the parameters.
1912        my ($self, $pdbID, $title, $type, $pdbHash, $pdbLoader) = @_;
1913        $pdbLoader->Add("PDB check");
1914        # Check to see if this is a new PDB.
1915        if (! exists $pdbHash->{$pdbID}) {
1916            # It is, so we create it.
1917            $pdbLoader->Put($pdbID, $title, $type);
1918            $pdbHash->{$pdbID} = 1;
1919            # Count it.
1920            $pdbLoader->Add("PDB-$type");
1921        }
1922    }
1923    
1924  =head3 TableLoader  =head3 TableLoader
1925    
1926  Create an ERDBLoad object for the specified table. The object is also added to  Create an ERDBLoad object for the specified table. The object is also added to
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