--- Sprout.pm 2005/01/26 22:26:09 1.7 +++ Sprout.pm 2006/06/14 19:47:19 1.60 @@ -1,16 +1,18 @@ package Sprout; - use Data::Dumper; - use strict; - use Carp; - use DBKernel; - use XML::Simple; - use DBQuery; - use DBObject; - use ERDB; - use Tracer; - use FIGRules; - use Stats; + require Exporter; + use ERDB; + @ISA = qw(Exporter ERDB); + use Data::Dumper; + use strict; + use Carp; + use DBKernel; + use XML::Simple; + use DBQuery; + use DBObject; + use Tracer; + use FIGRules; + use Stats; use POSIX qw(strftime); @@ -32,6 +34,8 @@ query tasks. For example, L lists the IDs of all the genomes in the database and L returns the DNA sequence for a specified genome location. +The Sprout object is a subclass of the ERDB object and inherits all its properties and methods. + =cut #: Constructor SFXlate->new_sprout_only(); @@ -62,14 +66,18 @@ * B name of the XML file containing the database definition (default C) -* B user name and password, delimited by a slash (default C) +* B user name and password, delimited by a slash (default same as SEED) * B connection port (default C<0>) +* B connection socket (default same as SEED) + * B maximum number of residues per feature segment, (default C<4500>) * B maximum number of residues per sequence, (default C<8000>) +* B suppresses the connection to the database if TRUE, else FALSE + =back For example, the following constructor call specifies a database named I and a user name of @@ -81,34 +89,45 @@ =cut sub new { - # Get the parameters. - my ($class, $dbName, $options) = @_; - # Compute the options. We do this by starting with a table of defaults and overwriting with - # the incoming data. - my $optionTable = Tracer::GetOptions({ - dbType => 'mysql', # database type - dataDir => 'Data', # data file directory - xmlFileName => 'SproutDBD.xml', # database definition file name - userData => 'root/', # user name and password - port => 0, # database connection port - maxSegmentLength => 4500, # maximum feature segment length - maxSequenceLength => 8000, # maximum contig sequence length - }, $options); - # Get the data directory. - my $dataDir = $optionTable->{dataDir}; - # Extract the user ID and password. - $optionTable->{userData} =~ m!([^/]*)/(.*)$!; - my ($userName, $password) = ($1, $2); - # Connect to the database. - my $dbh = DBKernel->new($optionTable->{dbType}, $dbName, $userName, $password, $optionTable->{port}); - # Create the ERDB object. - my $xmlFileName = "$optionTable->{xmlFileName}"; - my $erdb = ERDB->new($dbh, $xmlFileName); - # Create this object. - my $self = { _erdb => $erdb, _options => $optionTable, _xmlName => $xmlFileName }; - # Bless and return it. - bless $self; - return $self; + # Get the parameters. + my ($class, $dbName, $options) = @_; + # Compute the options. We do this by starting with a table of defaults and overwriting with + # the incoming data. + my $optionTable = Tracer::GetOptions({ + dbType => $FIG_Config::dbms, + # database type + dataDir => $FIG_Config::sproutData, + # data file directory + xmlFileName => "$FIG_Config::fig/SproutDBD.xml", + # database definition file name + userData => "$FIG_Config::dbuser/$FIG_Config::dbpass", + # user name and password + port => $FIG_Config::dbport, + # database connection port + sock => $FIG_Config::dbsock, + maxSegmentLength => 4500, # maximum feature segment length + maxSequenceLength => 8000, # maximum contig sequence length + noDBOpen => 0, # 1 to suppress the database open + }, $options); + # Get the data directory. + my $dataDir = $optionTable->{dataDir}; + # Extract the user ID and password. + $optionTable->{userData} =~ m!([^/]*)/(.*)$!; + my ($userName, $password) = ($1, $2); + # Connect to the database. + my $dbh; + if (! $optionTable->{noDBOpen}) { + $dbh = DBKernel->new($optionTable->{dbType}, $dbName, $userName, + $password, $optionTable->{port}, undef, $optionTable->{sock}); + } + # Create the ERDB object. + my $xmlFileName = "$optionTable->{xmlFileName}"; + my $retVal = ERDB::new($class, $dbh, $xmlFileName); + # Add the option table and XML file name. + $retVal->{_options} = $optionTable; + $retVal->{_xmlName} = $xmlFileName; + # Return it. + return $retVal; } =head3 MaxSegment @@ -124,8 +143,8 @@ =cut #: Return Type $; sub MaxSegment { - my $self = shift @_; - return $self->{_options}->{maxSegmentLength}; + my ($self) = @_; + return $self->{_options}->{maxSegmentLength}; } =head3 MaxSequence @@ -139,318 +158,241 @@ =cut #: Return Type $; sub MaxSequence { - my $self = shift @_; - return $self->{_options}->{maxSequenceLength}; + my ($self) = @_; + return $self->{_options}->{maxSequenceLength}; } -=head3 Get - -C<< my $query = $sprout->Get(\@objectNames, $filterClause, \@parameterList); >> - -This method allows a general query against the Sprout data using a specified filter clause. - -The filter is a standard WHERE/ORDER BY clause with question marks as parameter markers and each -field name represented in the form B(I)>. For example, the -following call requests all B objects for the genus specified in the variable -$genus. - -C<< $query = $sprout->Get(['Genome'], "Genome(genus) = ?", [$genus]); >> - -The WHERE clause contains a single question mark, so there is a single additional -parameter representing the parameter value. It would also be possible to code - -C<< $query = $sprout->Get(['Genome'], "Genome(genus) = \'$genus\'"); >> - -however, this version of the call would generate a syntax error if there were any quote -characters inside the variable C<$genus>. - -The use of the strange parenthesized notation for field names enables us to distinguish -hyphens contained within field names from minus signs that participate in the computation -of the WHERE clause. All of the methods that manipulate fields will use this same notation. - -It is possible to specify multiple entity and relationship names in order to retrieve more than -one object's data at the same time, which allows highly complex joined queries. For example, - -C<< $query = $sprout->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", [$genus]); >> - -This query returns all the genomes for a particular genus and allows access to the -sources from which they came. The join clauses to go from Genome to Source are generated -automatically. - -Finally, the filter clause can contain sort information. To do this, simply put an C -clause at the end of the filter. Field references in the ORDER BY section follow the same rules -as they do in the filter itself; in other words, each one must be of the form B(I)>. -For example, the following filter string gets all genomes for a particular genus and sorts -them by species name. - -C<< $query = $sprout->Get(['Genome'], "Genome(genus) = ? ORDER BY Genome(species)", [$genus]); >> +=head3 Load -It is also permissible to specify I an ORDER BY clause. For example, the following invocation gets -all genomes ordered by genus and species. +C<< $sprout->Load($rebuild); >>; -C<< $query = $sprout->Get(['Genome'], "ORDER BY Genome(genus), Genome(species)"); >> +Load the database from files in the data directory, optionally re-creating the tables. -Odd things may happen if one of the ORDER BY fields is in a secondary relation. So, for example, an -attempt to order Bs by alias may (depending on the underlying database engine used) cause -a single feature to appear more than once. +This method always deletes the data from the database before loading, even if the tables are not +re-created. The data is loaded into the relations from files in the data directory either having the +same name as the target relation with no extension or with an extension of C<.dtx>. Files without an +extension are used in preference to the files with an extension. -If multiple names are specified, then the query processor will automatically determine a -join path between the entities and relationships. The algorithm used is very simplistic. -In particular, you can't specify any entity or relationship more than once, and if a -relationship is recursive, the path is determined by the order in which the entity -and the relationship appear. For example, consider a recursive relationship B -which relates B objects to other B objects. If the join path is -coded as C<['People', 'IsParentOf']>, then the people returned will be parents. If, however, -the join path is C<['IsParentOf', 'People']>, then the people returned will be children. +The files are loaded based on the presumption that each line of the file is a record in the +relation, and the individual fields are delimited by tabs. Tab and new-line characters inside +fields must be represented by the escape sequences C<\t> and C<\n>, respectively. The fields must +be presented in the order given in the relation tables produced by the L method. =over 4 -=item objectNames - -List containing the names of the entity and relationship objects to be retrieved. - -=item filterClause - -WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can -be parameterized with parameter markers (C). Each field used must be specified in the standard form -B(I)>. Any parameters specified in the filter clause should be added to the -parameter list as additional parameters. The fields in a filter clause can come from primary -entity relations, relationship relations, or secondary entity relations; however, all of the -entities and relationships involved must be included in the list of object names. - -=item parameterList +=item rebuild -List of the parameters to be substituted in for the parameters marks in the filter clause. +TRUE if the data tables need to be created or re-created, else FALSE =item RETURN -Returns a B that can be used to iterate through all of the results. +Returns a statistical object containing the number of records read, the number of duplicates found, +the number of errors, and a list of the error messages. =back =cut - -sub Get { - # Get the parameters. - my $self = shift @_; - my ($objectNames, $filterClause, $parameterList) = @_; - # We differ from the ERDB Get method in that the parameter list is passed in as a list reference - # rather than a list of parameters. The next step is to convert the parameters from a reference - # to a real list. We can only do this if the parameters have been specified. - my @parameters; - if ($parameterList) { @parameters = @{$parameterList}; } - return $self->{_erdb}->Get($objectNames, $filterClause, @parameters); +#: Return Type %; +sub Load { + # Get the parameters. + my ($self, $rebuild) = @_; + # Load the tables from the data directory. + my $retVal = $self->LoadTables($self->{_options}->{dataDir}, $rebuild); + # Return the statistics. + return $retVal; } -=head3 GetEntity +=head3 LoadUpdate -C<< my $entityObject = $sprout->GetEntity($entityType, $ID); >> +C<< my $stats = $sprout->LoadUpdate($truncateFlag, \@tableList); >> -Return an object describing the entity instance with a specified ID. +Load updates to one or more database tables. This method enables the client to make changes to one +or two tables without reloading the whole database. For each table, there must be a corresponding +file in the data directory, either with the same name as the table, or with a C<.dtx> suffix. So, +for example, to make updates to the B relation, there must be a +C file in the data directory. Unlike a full load, files without an extension +are not examined. This allows update files to co-exist with files from an original load. =over 4 -=item entityType +=item truncateFlag -Entity type name. +TRUE if the tables should be rebuilt before loading, else FALSE. A value of TRUE therefore causes +current data and schema of the tables to be replaced, while a value of FALSE means the new data +is added to the existing data in the various relations. -=item ID +=item tableList -ID of the desired entity. +List of the tables to be updated. =item RETURN -Returns a B representing the desired entity instance, or an undefined value if no -instance is found with the specified key. +Returns a statistical object containing the number of records read, the number of duplicates found, +the number of errors encountered, and a list of error messages. =back =cut - -sub GetEntity { - # Get the parameters. - my $self = shift @_; - my ($entityType, $ID) = @_; - # Create a query. - my $query = $self->Get([$entityType], "$entityType(id) = ?", [$ID]); - # Get the first (and only) object. - my $retVal = $query->Fetch(); - # Return the result. - return $retVal; +#: Return Type $%; +sub LoadUpdate { + # Get the parameters. + my ($self, $truncateFlag, $tableList) = @_; + # Declare the return value. + my $retVal = Stats->new(); + # Get the data directory. + my $optionTable = $self->{_options}; + my $dataDir = $optionTable->{dataDir}; + # Loop through the incoming table names. + for my $tableName (@{$tableList}) { + # Find the table's file. + my $fileName = LoadFileName($dataDir, $tableName); + if (! $fileName) { + Trace("No load file found for $tableName in $dataDir.") if T(0); + } else { + # Attempt to load this table. + my $result = $self->LoadTable($fileName, $tableName, $truncateFlag); + # Accumulate the resulting statistics. + $retVal->Accumulate($result); + } + } + # Return the statistics. + return $retVal; } -=head3 GetEntityValues +=head3 GenomeCounts -C<< my @values = GetEntityValues($entityType, $ID, \@fields); >> +C<< my ($arch, $bact, $euk, $vir, $env, $unk) = $sprout->GenomeCounts($complete); >> -Return a list of values from a specified entity instance. +Count the number of genomes in each domain. If I<$complete> is TRUE, only complete +genomes will be included in the counts. =over 4 -=item entityType +=item complete -Entity type name. - -=item ID - -ID of the desired entity. - -=item fields - -List of field names, each of the form IC<(>IC<)>. +TRUE if only complete genomes are to be counted, FALSE if all genomes are to be +counted =item RETURN -Returns a flattened list of the values of the specified fields for the specified entity. - -=back - -=cut -#: Return Type @; -sub GetEntityValues { - # Get the parameters. - my $self = shift @_; - my ($entityType, $ID, $fields) = @_; - # Get the specified entity. - my $entity = $self->GetEntity($entityType, $ID); - # Declare the return list. - my @retVal = (); - # If we found the entity, push the values into the return list. - if ($entity) { - push @retVal, $entity->Values($fields); - } - # Return the result. - return @retVal; -} - -=head3 ShowMetaData - -C<< $sprout->ShowMetaData($fileName); >> - -This method outputs a description of the database to an HTML file in the data directory. - -=over 4 - -=item fileName - -Fully-qualified name to give to the output file. +A six-element list containing the number of genomes in each of six categories-- +Archaea, Bacteria, Eukaryota, Viral, Environmental, and Unknown, respectively. =back =cut -sub ShowMetaData { - # Get the parameters. - my $self = shift @_; - my ($fileName) = @_; - # Compute the file name. - my $options = $self->{_options}; - # Call the show method on the underlying ERDB object. - $self->{_erdb}->ShowMetaData($fileName); +sub GenomeCounts { + # Get the parameters. + my ($self, $complete) = @_; + # Set the filter based on the completeness flag. + my $filter = ($complete ? "Genome(complete) = 1" : ""); + # Get all the genomes and the related taxonomy information. + my @genomes = $self->GetAll(['Genome'], $filter, [], ['Genome(id)', 'Genome(taxonomy)']); + # Clear the counters. + my ($arch, $bact, $euk, $vir, $env, $unk) = (0, 0, 0, 0, 0, 0); + # Loop through, counting the domains. + for my $genome (@genomes) { + if ($genome->[1] =~ /^archaea/i) { ++$arch } + elsif ($genome->[1] =~ /^bacter/i) { ++$bact } + elsif ($genome->[1] =~ /^eukar/i) { ++$euk } + elsif ($genome->[1] =~ /^vir/i) { ++$vir } + elsif ($genome->[1] =~ /^env/i) { ++$env } + else { ++$unk } + } + # Return the counts. + return ($arch, $bact, $euk, $vir, $env, $unk); } -=head3 Load - -C<< $sprout->Load($rebuild); >>; +=head3 ContigCount -Load the database from files in the data directory, optionally re-creating the tables. - -This method always deletes the data from the database before loading, even if the tables are not -re-created. The data is loaded into the relations from files in the data directory either having the -same name as the target relation with no extension or with an extension of C<.dtx>. Files without an -extension are used in preference to the files with an extension. +C<< my $count = $sprout->ContigCount($genomeID); >> -The files are loaded based on the presumption that each line of the file is a record in the -relation, and the individual fields are delimited by tabs. Tab and new-line characters inside -fields must be represented by the escape sequences C<\t> and C<\n>, respectively. The fields must -be presented in the order given in the relation tables produced by the L method. +Return the number of contigs for the specified genome ID. =over 4 -=item rebuild +=item genomeID -TRUE if the data tables need to be created or re-created, else FALSE +ID of the genome whose contig count is desired. =item RETURN -Returns a statistical object containing the number of records read, the number of duplicates found, -the number of errors, and a list of the error messages. +Returns the number of contigs for the specified genome. =back =cut -#: Return Type %; -sub Load { - # Get the parameters. - my $self = shift @_; - my ($rebuild) = @_; - # Get the database object. - my $erdb = $self->{_erdb}; - # Load the tables from the data directory. - my $retVal = $erdb->LoadTables($self->{_options}->{dataDir}, $rebuild); - # Return the statistics. - return $retVal; + +sub ContigCount { + # Get the parameters. + my ($self, $genomeID) = @_; + # Get the contig count. + my $retVal = $self->GetCount(['Contig', 'HasContig'], "HasContig(from-link) = ?", [$genomeID]); + # Return the result. + return $retVal; } -=head3 LoadUpdate +=head3 GeneMenu -C<< my %stats = $sprout->LoadUpdate($truncateFlag, \@tableList); >> +C<< my $selectHtml = $sprout->GeneMenu(\%attributes, $filterString, \@params); >> -Load updates to one or more database tables. This method enables the client to make changes to one -or two tables without reloading the whole database. For each table, there must be a corresponding -file in the data directory, either with the same name as the table, or with a C<.dtx> suffix. So, -for example, to make updates to the B relation, there must be a -C file in the data directory. Unlike a full load, files without an extension -are not examined. This allows update files to co-exist with files from an original load. +Return an HTML select menu of genomes. Each genome will be an option in the menu, +and will be displayed by name with the ID and a contig count attached. The selection +value will be the genome ID. The genomes will be sorted by genus/species name. =over 4 -=item truncateFlag +=item attributes -TRUE if the tables should be rebuilt before loading, else FALSE. A value of TRUE therefore causes -current data and schema of the tables to be replaced, while a value of FALSE means the new data -is added to the existing data in the various relations. +Reference to a hash mapping attributes to values for the SELECT tag generated. -=item tableList +=item filterString -List of the tables to be updated. +A filter string for use in selecting the genomes. The filter string must conform +to the rules for the C<< ERDB->Get >> method. + +=item params + +Reference to a list of values to be substituted in for the parameter marks in +the filter string. =item RETURN -Returns a statistical object containing the number of records read, the number of duplicates found, -the number of errors encountered, and a list of error messages. +Returns an HTML select menu with the specified genomes as selectable options. =back =cut -#: Return Type $%; -sub LoadUpdate { - # Get the parameters. - my $self = shift @_; - my ($truncateFlag, $tableList) = @_; - # Get the database object. - my $erdb = $self->{_erdb}; - # Declare the return value. - my $retVal = Stats->new(); - # Get the data directory. - my $optionTable = $self->{_options}; - my $dataDir = $optionTable->{dataDir}; - # Loop through the incoming table names. - for my $tableName (@{$tableList}) { - # Find the table's file. - my $fileName = "$dataDir/$tableName"; - if (! -e $fileName) { - $fileName = "$fileName.dtx"; - } - # Attempt to load this table. - my $result = $erdb->LoadTable($fileName, $tableName, $truncateFlag); - # Accumulate the resulting statistics. - $retVal->Accumulate($result); - } - # Return the statistics. - return $retVal; -} +sub GeneMenu { + # Get the parameters. + my ($self, $attributes, $filterString, $params) = @_; + # Start the menu. + my $retVal = "\n"; + # Return the result. + return $retVal; +} =head3 Build C<< $sprout->Build(); >> @@ -462,10 +404,10 @@ =cut #: Return Type ; sub Build { - # Get the parameters. - my $self = shift @_; - # Create the tables. - $self->{_erdb}->CreateTables; + # Get the parameters. + my ($self) = @_; + # Create the tables. + $self->CreateTables(); } =head3 Genomes @@ -477,12 +419,12 @@ =cut #: Return Type @; sub Genomes { - # Get the parameters. - my $self = shift @_; - # Get all the genomes. - my @retVal = $self->GetFlat(['Genome'], "", [], 'Genome(id)'); - # Return the list of IDs. - return @retVal; + # Get the parameters. + my ($self) = @_; + # Get all the genomes. + my @retVal = $self->GetFlat(['Genome'], "", [], 'Genome(id)'); + # Return the list of IDs. + return @retVal; } =head3 GenusSpecies @@ -507,15 +449,14 @@ =cut #: Return Type $; sub GenusSpecies { - # Get the parameters. - my $self = shift @_; - my ($genomeID) = @_; - # Get the data for the specified genome. - my @values = $self->GetEntityValues('Genome', $genomeID, ['Genome(genus)', 'Genome(species)', - 'Genome(unique-characterization)']); - # Format the result and return it. - my $retVal = join(' ', @values); - return $retVal; + # Get the parameters. + my ($self, $genomeID) = @_; + # Get the data for the specified genome. + my @values = $self->GetEntityValues('Genome', $genomeID, ['Genome(genus)', 'Genome(species)', + 'Genome(unique-characterization)']); + # Format the result and return it. + my $retVal = join(' ', @values); + return $retVal; } =head3 FeaturesOf @@ -544,24 +485,23 @@ =cut #: Return Type @; sub FeaturesOf { - # Get the parameters. - my $self = shift @_; - my ($genomeID,$ftype) = @_; - # Get the features we want. - my @features; - if (!$ftype) { - @features = $self->GetFlat(['HasContig', 'IsLocatedIn'], "HasContig(from-link) = ?", - [$genomeID], 'IsLocatedIn(from-link)'); - } else { - @features = $self->GetFlat(['HasContig', 'IsLocatedIn', 'Feature'], - "HasContig(from-link) = ? AND Feature(feature-type) = ?", - [$genomeID, $ftype], 'IsLocatedIn(from-link)'); - } - # Return the list with duplicates merged out. We need to merge out duplicates because - # a feature will appear twice if it spans more than one contig. - my @retVal = Tracer::Merge(@features); - # Return the list of feature IDs. - return @retVal; + # Get the parameters. + my ($self, $genomeID,$ftype) = @_; + # Get the features we want. + my @features; + if (!$ftype) { + @features = $self->GetFlat(['HasContig', 'IsLocatedIn'], "HasContig(from-link) = ?", + [$genomeID], 'IsLocatedIn(from-link)'); + } else { + @features = $self->GetFlat(['HasContig', 'IsLocatedIn', 'Feature'], + "HasContig(from-link) = ? AND Feature(feature-type) = ?", + [$genomeID, $ftype], 'IsLocatedIn(from-link)'); + } + # Return the list with duplicates merged out. We need to merge out duplicates because + # a feature will appear twice if it spans more than one contig. + my @retVal = Tracer::Merge(@features); + # Return the list of feature IDs. + return @retVal; } =head3 FeatureLocation @@ -590,7 +530,7 @@ =item RETURN Returns a list of the feature's contig segments. The locations are returned as a list in a list -context and as a space-delimited string in a scalar context. +context and as a comma-delimited string in a scalar context. =back @@ -598,43 +538,49 @@ #: Return Type @; #: Return Type $; sub FeatureLocation { - # Get the parameters. - my $self = shift @_; - my ($featureID) = @_; - # Create a query for the feature locations. - my $query = $self->Get(['IsLocatedIn'], "IsLocatedIn(from-link) = ? ORDER BY IsLocatedIn(locN)", - [$featureID]); - # Create the return list. - my @retVal = (); - # Set up the variables used to determine if we have adjacent segments. This initial setup will - # not match anything. - my ($prevContig, $prevBeg, $prevDir, $prevLen) = ("", 0, "0", 0); - # Loop through the query results, creating location specifiers. - while (my $location = $query->Fetch()) { - # Get the location parameters. - my ($contigID, $beg, $dir, $len) = $location->Values(['IsLocatedIn(to-link)', - 'IsLocatedIn(beg)', 'IsLocatedIn(dir)', 'IsLocatedIn(len)']); - # Check to see if we are adjacent to the previous segment. - if ($prevContig eq $contigID && $dir eq $prevDir) { - # Here the new segment is in the same direction on the same contig. Insure the - # new segment's beginning is next to the old segment's end. - if (($dir eq "-" && $beg == $prevBeg - $prevLen) || - ($dir eq "+" && $beg == $prevBeg + $prevLen)) { - # Here we need to merge two segments. Adjust the beginning and length values - # to include both segments. - $beg = $prevBeg; - $len += $prevLen; - # Pop the old segment off. The new one will replace it later. - pop @retVal; - } - } - # Remember this specifier for the adjacent-segment test the next time through. - ($prevContig, $prevBeg, $prevDir, $prevLen) = ($contigID, $beg, $dir, $len); - # Add the specifier to the list. - push @retVal, "${contigID}_$beg$dir$len"; - } - # Return the list in the format indicated by the context. - return (wantarray ? @retVal : join(' ', @retVal)); + # Get the parameters. + my ($self, $featureID) = @_; + # Create a query for the feature locations. + my $query = $self->Get(['IsLocatedIn'], "IsLocatedIn(from-link) = ? ORDER BY IsLocatedIn(locN)", + [$featureID]); + # Create the return list. + my @retVal = (); + # Set up the variables used to determine if we have adjacent segments. This initial setup will + # not match anything. + my ($prevContig, $prevBeg, $prevDir, $prevLen) = ("", 0, "0", 0); + # Loop through the query results, creating location specifiers. + while (my $location = $query->Fetch()) { + # Get the location parameters. + my ($contigID, $beg, $dir, $len) = $location->Values(['IsLocatedIn(to-link)', + 'IsLocatedIn(beg)', 'IsLocatedIn(dir)', 'IsLocatedIn(len)']); + # Check to see if we are adjacent to the previous segment. + if ($prevContig eq $contigID && $dir eq $prevDir) { + # Here the new segment is in the same direction on the same contig. Insure the + # new segment's beginning is next to the old segment's end. + if ($dir eq "-" && $beg + $len == $prevBeg) { + # Here we're merging two backward blocks, so we keep the new begin point + # and adjust the length. + $len += $prevLen; + # Pop the old segment off. The new one will replace it later. + pop @retVal; + } elsif ($dir eq "+" && $beg == $prevBeg + $prevLen) { + # Here we need to merge two forward blocks. Adjust the beginning and + # length values to include both segments. + $beg = $prevBeg; + $len += $prevLen; + # Pop the old segment off. The new one will replace it later. + pop @retVal; + } + } + # Remember this specifier for the adjacent-segment test the next time through. + ($prevContig, $prevBeg, $prevDir, $prevLen) = ($contigID, $beg, $dir, $len); + # Compute the initial base pair. + my $start = ($dir eq "+" ? $beg : $beg + $len - 1); + # Add the specifier to the list. + push @retVal, "${contigID}_$start$dir$len"; + } + # Return the list in the format indicated by the context. + return (wantarray ? @retVal : join(',', @retVal)); } =head3 ParseLocation @@ -660,23 +606,77 @@ =cut #: Return Type @; sub ParseLocation { - # Get the parameter. - my ($location) = @_; - # Parse it into segments. - $location =~ /^(.*)_(\d*)([+-_])(\d*)$/; - my ($contigID, $start, $dir, $len) = ($1, $2, $3, $4); - # If the direction is an underscore, convert it to a + or -. - if ($dir eq "_") { - if ($start < $len) { - $dir = "+"; - $len = $len - $start + 1; - } else { - $dir = "-"; - $len = $start - $len + 1; - } - } - # Return the result. - return ($contigID, $start, $dir, $len); + # Get the parameter. Note that if we're called as an instance method, we ignore + # the first parameter. + shift if UNIVERSAL::isa($_[0],__PACKAGE__); + my ($location) = @_; + # Parse it into segments. + $location =~ /^(.+)_(\d+)([+\-_])(\d+)$/; + my ($contigID, $start, $dir, $len) = ($1, $2, $3, $4); + # If the direction is an underscore, convert it to a + or -. + if ($dir eq "_") { + if ($start < $len) { + $dir = "+"; + $len = $len - $start + 1; + } else { + $dir = "-"; + $len = $start - $len + 1; + } + } + # Return the result. + return ($contigID, $start, $dir, $len); +} + +=head3 PointLocation + +C<< my $found = Sprout::PointLocation($location, $point); >> + +Return the offset into the specified location of the specified point on the contig. If +the specified point is before the location, a negative value will be returned. If it is +beyond the location, an undefined value will be returned. It is assumed that the offset +is for the location's contig. The location can either be new-style (using a C<+> or C<-> +and a length) or old-style (using C<_> and start and end positions. + +=over 4 + +=item location + +A location specifier (see L for a description). + +=item point + +The offset into the contig of the point in which we're interested. + +=item RETURN + +Returns the offset inside the specified location of the specified point, a negative +number if the point is before the location, or an undefined value if the point is past +the location. If the length of the location is 0, this method will B denote +that it is outside the location. The offset will always be relative to the left-most +position in the location. + +=back + +=cut +#: Return Type $; +sub PointLocation { + # Get the parameter. Note that if we're called as an instance method, we ignore + # the first parameter. + shift if UNIVERSAL::isa($_[0],__PACKAGE__); + my ($location, $point) = @_; + # Parse out the location elements. Note that this works on both old-style and new-style + # locations. + my ($contigID, $start, $dir, $len) = ParseLocation($location); + # Declare the return variable. + my $retVal; + # Compute the offset. The computation is dependent on the direction of the location. + my $offset = (($dir == '+') ? $point - $start : $point - ($start - $len + 1)); + # Return the offset if it's valid. + if ($offset < $len) { + $retVal = $offset; + } + # Return the offset found. + return $retVal; } =head3 DNASeq @@ -687,12 +687,17 @@ should be of the form returned by L when in a list context. In other words, each location is of the form IC<_>III. +For example, the following would return the DNA sequence for contig C<83333.1:NC_000913> +between positions 1401 and 1532, inclusive. + + my $sequence = $sprout->DNASeq('83333.1:NC_000913_1401_1532'); + =over 4 =item locationList -List of location specifiers, each in the form IC<_>III (see -L for more about this format). +List of location specifiers, each in the form IC<_>III or +IC<_>IC<_>I (see L for more about this format). =item RETURN @@ -703,57 +708,59 @@ =cut #: Return Type $; sub DNASeq { - # Get the parameters. - my $self = shift @_; - my ($locationList) = @_; - # Create the return string. - my $retVal = ""; - # Loop through the locations. - for my $location (@{$locationList}) { - # Set up a variable to contain the DNA at this location. - my $locationDNA = ""; - # Parse out the contig ID, the beginning point, the direction, and the end point. - my ($contigID, $beg, $dir, $len) = ParseLocation($location); - # Now we must create a query to return all the sequences in the contig relevant to the region - # specified. First, we compute the start and stop points when reading through the sequences. - # For a forward transcription, the start point is the beginning; for a backward transcription, - # the start point is the ending. Note that in the latter case we must reverse the DNA string - # before putting it in the return value. - my ($start, $stop); - if ($dir eq "+") { - $start = $beg; - $stop = $beg + $len - 1; - } else { - $start = $beg + $len + 1; - $stop = $beg; - } - my $query = $self->Get(['IsMadeUpOf','Sequence'], - "IsMadeUpOf(from-link) = ? AND IsMadeUpOf(start-position) + IsMadeUpOf(len) > ? AND " . - " IsMadeUpOf(start-position) <= ? ORDER BY IsMadeUpOf(start-position)", - [$contigID, $start, $stop]); - # Loop through the sequences. - while (my $sequence = $query->Fetch()) { - # Determine whether the location starts, stops, or continues through this sequence. - my ($startPosition, $sequenceData, $sequenceLength) = - $sequence->Values(['IsMadeUpOf(start-position)', 'Sequence(sequence)', - 'IsMadeUpOf(len)']); - my $stopPosition = $startPosition + $sequenceLength; - # Figure out the start point and length of the relevant section. - my $pos1 = ($start < $startPosition ? 0 : $start - $startPosition); - my $len = ($stopPosition <= $stop ? $stopPosition : $stop) - $startPosition - $pos1; - # Add the relevant data to the location data. - $locationDNA .= substr($sequenceData, $pos1, $len); - } - # Add this location's data to the return string. Note that we may need to reverse it. - if ($dir eq '+') { - $retVal .= $locationDNA; - } else { - $locationDNA = join('', reverse split //, $locationDNA); - $retVal .= $locationDNA; - } - } - # Return the result. - return $retVal; + # Get the parameters. + my ($self, $locationList) = @_; + # Create the return string. + my $retVal = ""; + # Loop through the locations. + for my $location (@{$locationList}) { + # Set up a variable to contain the DNA at this location. + my $locationDNA = ""; + # Parse out the contig ID, the beginning point, the direction, and the end point. + my ($contigID, $beg, $dir, $len) = ParseLocation($location); + # Now we must create a query to return all the sequences in the contig relevant to the region + # specified. First, we compute the start and stop points when reading through the sequences. + # For a forward transcription, the start point is the beginning; for a backward transcription, + # the start point is the ending. Note that in the latter case we must reverse the DNA string + # before putting it in the return value. + my ($start, $stop); + Trace("Parse of \"$location\" is $beg$dir$len.") if T(SDNA => 4); + if ($dir eq "+") { + $start = $beg; + $stop = $beg + $len - 1; + } else { + $start = $beg - $len + 1; + $stop = $beg; + } + Trace("Looking for sequences containing $start through $stop.") if T(SDNA => 4); + my $query = $self->Get(['IsMadeUpOf','Sequence'], + "IsMadeUpOf(from-link) = ? AND IsMadeUpOf(start-position) + IsMadeUpOf(len) > ? AND " . + " IsMadeUpOf(start-position) <= ? ORDER BY IsMadeUpOf(start-position)", + [$contigID, $start, $stop]); + # Loop through the sequences. + while (my $sequence = $query->Fetch()) { + # Determine whether the location starts, stops, or continues through this sequence. + my ($startPosition, $sequenceData, $sequenceLength) = + $sequence->Values(['IsMadeUpOf(start-position)', 'Sequence(sequence)', + 'IsMadeUpOf(len)']); + my $stopPosition = $startPosition + $sequenceLength; + Trace("Sequence is from $startPosition to $stopPosition.") if T(SDNA => 4); + # Figure out the start point and length of the relevant section. + my $pos1 = ($start < $startPosition ? 0 : $start - $startPosition); + my $len1 = ($stopPosition < $stop ? $stopPosition : $stop) + 1 - $startPosition - $pos1; + Trace("Position is $pos1 for length $len1.") if T(SDNA => 4); + # Add the relevant data to the location data. + $locationDNA .= substr($sequenceData, $pos1, $len1); + } + # Add this location's data to the return string. Note that we may need to reverse it. + if ($dir eq '+') { + $retVal .= $locationDNA; + } else { + $retVal .= FIG::reverse_comp($locationDNA); + } + } + # Return the result. + return $retVal; } =head3 AllContigs @@ -777,14 +784,13 @@ =cut #: Return Type @; sub AllContigs { - # Get the parameters. - my $self = shift @_; - my ($genomeID) = @_; - # Ask for the genome's Contigs. - my @retVal = $self->GetFlat(['HasContig'], "HasContig(from-link) = ?", [$genomeID], - 'HasContig(to-link)'); - # Return the list of Contigs. - return @retVal; + # Get the parameters. + my ($self, $genomeID) = @_; + # Ask for the genome's Contigs. + my @retVal = $self->GetFlat(['HasContig'], "HasContig(from-link) = ?", [$genomeID], + 'HasContig(to-link)'); + # Return the list of Contigs. + return @retVal; } =head3 ContigLength @@ -808,23 +814,70 @@ =cut #: Return Type $; sub ContigLength { - # Get the parameters. - my $self = shift @_; - my ($contigID) = @_; - # Get the contig's last sequence. - my $query = $self->Get(['IsMadeUpOf'], - "IsMadeUpOf(from-link) = ? ORDER BY IsMadeUpOf(start-position) DESC", - [$contigID]); - my $sequence = $query->Fetch(); - # Declare the return value. - my $retVal = 0; - # Set it from the sequence data, if any. - if ($sequence) { - my ($start, $len) = $sequence->Values(['IsMadeUpOf(start-position)', 'IsMadeUpOf(len)']); - $retVal = $start + $len; - } - # Return the result. - return $retVal; + # Get the parameters. + my ($self, $contigID) = @_; + # Get the contig's last sequence. + my $query = $self->Get(['IsMadeUpOf'], + "IsMadeUpOf(from-link) = ? ORDER BY IsMadeUpOf(start-position) DESC", + [$contigID]); + my $sequence = $query->Fetch(); + # Declare the return value. + my $retVal = 0; + # Set it from the sequence data, if any. + if ($sequence) { + my ($start, $len) = $sequence->Values(['IsMadeUpOf(start-position)', 'IsMadeUpOf(len)']); + $retVal = $start + $len - 1; + } + # Return the result. + return $retVal; +} + +=head3 ClusterPEGs + +C<< my $clusteredList = $sprout->ClusterPEGs($sub, \@pegs); >> + +Cluster the PEGs in a list according to the cluster coding scheme of the specified +subsystem. In order for this to work properly, the subsystem object must have +been used recently to retrieve the PEGs using the B method. +This causes the cluster numbers to be pulled into the subsystem's color hash. +If a PEG is not found in the color hash, it will not appear in the output +sequence. + +=over 4 + +=item sub + +Sprout subsystem object for the relevant subsystem, from the L +method. + +=item pegs + +Reference to the list of PEGs to be clustered. + +=item RETURN + +Returns a list of the PEGs, grouped into smaller lists by cluster number. + +=back + +=cut +#: Return Type $@@; +sub ClusterPEGs { + # Get the parameters. + my ($self, $sub, $pegs) = @_; + # Declare the return variable. + my $retVal = []; + # Loop through the PEGs, creating arrays for each cluster. + for my $pegID (@{$pegs}) { + my $clusterNumber = $sub->get_cluster_number($pegID); + # Only proceed if the PEG is in a cluster. + if ($clusterNumber >= 0) { + # Push this PEG onto the sub-list for the specified cluster number. + push @{$retVal->[$clusterNumber]}, $pegID; + } + } + # Return the result. + return $retVal; } =head3 GenesInRegion @@ -852,72 +905,91 @@ Returns a three-element list. The first element is a list of feature IDs for the features that overlap the region of interest. The second and third elements are the minimum and maximum locations of the features provided on the specified contig. These may extend outside -the start and stop values. +the start and stop values. The first element (that is, the list of features) is sorted +roughly by location. =back =cut -#: Return Type @; +#: Return Type @@; sub GenesInRegion { - # Get the parameters. - my $self = shift @_; - my ($contigID, $start, $stop) = @_; - # Get the maximum segment length. - my $maximumSegmentLength = $self->MaxSegment; - # Create a hash to receive the feature list. We use a hash so that we can eliminate - # duplicates easily. - my %featuresFound = (); - # Prime the values we'll use for the returned beginning and end. - my ($min, $max) = ($self->ContigLength($contigID), 0); - # Create a table of parameters for each query. Each query looks for features travelling in - # a particular direction. The query parameters include the contig ID, the feature direction, - # the lowest possible start position, and the highest possible start position. This works - # because each feature segment length must be no greater than the maximum segment length. - my %queryParms = (forward => [$contigID, '+', $start - $maximumSegmentLength + 1, $stop], - reverse => [$contigID, '-', $start, $stop + $maximumSegmentLength - 1]); - # Loop through the query parameters. - for my $parms (values %queryParms) { - # Create the query. - my $query = $self->Get(['IsLocatedIn'], - "IsLocatedIn(to-link)= ? AND IsLocatedIn(dir) = ? AND IsLocatedIn(beg) >= ? AND IsLocatedIn(beg) <= ?", - $parms); - # Loop through the feature segments found. - while (my $segment = $query->Fetch) { - # Get the data about this segment. - my ($featureID, $dir, $beg, $len) = $segment->Values(['IsLocatedIn(from-link)', - 'IsLocatedIn(dir)', 'IsLocatedIn(beg)', 'IsLocatedIn(len)']); - # Determine if this feature actually overlaps the region. The query insures that - # this will be the case if the segment is the maximum length, so to fine-tune - # the results we insure that the inequality from the query holds using the actual - # length. - my ($found, $end) = (0, 0); - if ($dir eq '+') { - $end = $beg + $len; - if ($end >= $start) { - # Denote we found a useful feature. - $found = 1; - } - } elsif ($dir eq '-') { - $end = $beg - $len; - if ($end <= $stop) { - # Denote we found a useful feature. - $found = 1; - } - } - if ($found) { - # Here we need to record the feature and update the minimum and maximum. - $featuresFound{$featureID} = 1; - if ($beg < $min) { $min = $beg; } - if ($end < $min) { $min = $end; } - if ($beg > $max) { $max = $beg; } - if ($end > $max) { $max = $end; } - } - } - } - # Compute a list of the IDs for the features found. - my @list = (sort (keys %featuresFound)); - # Return it along with the min and max. - return (\@list, $min, $max); + # Get the parameters. + my ($self, $contigID, $start, $stop) = @_; + # Get the maximum segment length. + my $maximumSegmentLength = $self->MaxSegment; + # Create a hash to receive the feature list. We use a hash so that we can eliminate + # duplicates easily. The hash key will be the feature ID. The value will be a two-element + # containing the minimum and maximum offsets. We will use the offsets to sort the results + # when we're building the result set. + my %featuresFound = (); + # Prime the values we'll use for the returned beginning and end. + my @initialMinMax = ($self->ContigLength($contigID), 0); + my ($min, $max) = @initialMinMax; + # Create a table of parameters for each query. Each query looks for features travelling in + # a particular direction. The query parameters include the contig ID, the feature direction, + # the lowest possible start position, and the highest possible start position. This works + # because each feature segment length must be no greater than the maximum segment length. + my %queryParms = (forward => [$contigID, '+', $start - $maximumSegmentLength + 1, $stop], + reverse => [$contigID, '-', $start, $stop + $maximumSegmentLength - 1]); + # Loop through the query parameters. + for my $parms (values %queryParms) { + # Create the query. + my $query = $self->Get(['IsLocatedIn'], + "IsLocatedIn(to-link)= ? AND IsLocatedIn(dir) = ? AND IsLocatedIn(beg) >= ? AND IsLocatedIn(beg) <= ?", + $parms); + # Loop through the feature segments found. + while (my $segment = $query->Fetch) { + # Get the data about this segment. + my ($featureID, $dir, $beg, $len) = $segment->Values(['IsLocatedIn(from-link)', + 'IsLocatedIn(dir)', 'IsLocatedIn(beg)', 'IsLocatedIn(len)']); + # Determine if this feature actually overlaps the region. The query insures that + # this will be the case if the segment is the maximum length, so to fine-tune + # the results we insure that the inequality from the query holds using the actual + # length. + my ($found, $end) = (0, 0); + if ($dir eq '+') { + $end = $beg + $len; + if ($end >= $start) { + # Denote we found a useful feature. + $found = 1; + } + } elsif ($dir eq '-') { + # Note we switch things around so that the beginning is to the left of the + # ending. + ($beg, $end) = ($beg - $len, $beg); + if ($beg <= $stop) { + # Denote we found a useful feature. + $found = 1; + } + } + if ($found) { + # Here we need to record the feature and update the minima and maxima. First, + # get the current entry for the specified feature. + my ($loc1, $loc2) = (exists $featuresFound{$featureID} ? @{$featuresFound{$featureID}} : + @initialMinMax); + # Merge the current segment's begin and end into the feature begin and end and the + # global min and max. + if ($beg < $loc1) { + $loc1 = $beg; + $min = $beg if $beg < $min; + } + if ($end > $loc2) { + $loc2 = $end; + $max = $end if $end > $max; + } + # Store the entry back into the hash table. + $featuresFound{$featureID} = [$loc1, $loc2]; + } + } + } + # Now we must compute the list of the IDs for the features found. We start with a list + # of midpoints / feature ID pairs. (It's not really a midpoint, it's twice the midpoint, + # but the result of the sort will be the same.) + my @list = map { [$featuresFound{$_}->[0] + $featuresFound{$_}->[1], $_] } keys %featuresFound; + # Now we sort by midpoint and yank out the feature IDs. + my @retVal = map { $_->[1] } sort { $a->[0] <=> $b->[0] } @list; + # Return it along with the min and max. + return (\@retVal, $min, $max); } =head3 FType @@ -942,18 +1014,17 @@ =cut #: Return Type $; sub FType { - # Get the parameters. - my $self = shift @_; - my ($featureID) = @_; - # Get the specified feature's type. - my ($retVal) = $self->GetEntityValues('Feature', $featureID, ['Feature(feature-type)']); - # Return the result. - return $retVal; + # Get the parameters. + my ($self, $featureID) = @_; + # Get the specified feature's type. + my ($retVal) = $self->GetEntityValues('Feature', $featureID, ['Feature(feature-type)']); + # Return the result. + return $retVal; } =head3 FeatureAnnotations -C<< my @descriptors = $sprout->FeatureAnnotations($featureID); >> +C<< my @descriptors = $sprout->FeatureAnnotations($featureID, $rawFlag); >> Return the annotations of a feature. @@ -963,13 +1034,18 @@ ID of the feature whose annotations are desired. +=item rawFlag + +If TRUE, the annotation timestamps will be returned in raw form; otherwise, they +will be returned in human-readable form. + =item RETURN Returns a list of annotation descriptors. Each descriptor is a hash with the following fields. * B ID of the relevant feature. -* B time the annotation was made, in user-friendly format. +* B time the annotation was made. * B ID of the user who made the annotation @@ -980,30 +1056,33 @@ =cut #: Return Type @%; sub FeatureAnnotations { - # Get the parameters. - my $self = shift @_; - my ($featureID) = @_; - # Create a query to get the feature's annotations and the associated users. - my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'], - "IsTargetOfAnnotation(from-link) = ?", [$featureID]); - # Create the return list. - my @retVal = (); - # Loop through the annotations. - while (my $annotation = $query->Fetch) { - # Get the fields to return. - my ($featureID, $timeStamp, $user, $text) = - $annotation->Values(['IsTargetOfAnnotation(from-link)', - 'Annotation(time)', 'MadeAnnotation(from-link)', - 'Annotation(annotation)']); - # Assemble them into a hash. + # Get the parameters. + my ($self, $featureID, $rawFlag) = @_; + # Create a query to get the feature's annotations and the associated users. + my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'], + "IsTargetOfAnnotation(from-link) = ?", [$featureID]); + # Create the return list. + my @retVal = (); + # Loop through the annotations. + while (my $annotation = $query->Fetch) { + # Get the fields to return. + my ($featureID, $timeStamp, $user, $text) = + $annotation->Values(['IsTargetOfAnnotation(from-link)', + 'Annotation(time)', 'MadeAnnotation(from-link)', + 'Annotation(annotation)']); + # Convert the time, if necessary. + if (! $rawFlag) { + $timeStamp = FriendlyTimestamp($timeStamp); + } + # Assemble them into a hash. my $annotationHash = { featureID => $featureID, - timeStamp => FriendlyTimestamp($timeStamp), - user => $user, text => $text }; - # Add it to the return list. - push @retVal, $annotationHash; - } - # Return the result list. - return @retVal; + timeStamp => $timeStamp, + user => $user, text => $text }; + # Add it to the return list. + push @retVal, $annotationHash; + } + # Return the result list. + return @retVal; } =head3 AllFunctionsOf @@ -1011,12 +1090,12 @@ C<< my %functions = $sprout->AllFunctionsOf($featureID); >> Return all of the functional assignments for a particular feature. The data is returned as a -hash of functional assignments to user IDs. A functional assignment is a type of annotation. -It has the format "XXXX\nset XXXX function to\nYYYYY". In this instance, XXXX is the user ID -and YYYYY is the functional assignment text. Its worth noting that we cannot filter on the content -of the annotation itself because it's a text field; however, this is not a big problem because most -features only have a small number of annotations. Finally, if a single user has multiple -functional assignments, we will only keep the most recent one. +hash of functional assignments to user IDs. A functional assignment is a type of annotation, +Functional assignments are described in the L function. Its worth noting that +we cannot filter on the content of the annotation itself because it's a text field; however, +this is not a big problem because most features only have a small number of annotations. +Finally, if a single user has multiple functional assignments, we will only keep the most +recent one. =over 4 @@ -1026,43 +1105,39 @@ =item RETURN -Returns a hash mapping the functional assignment IDs to user IDs. +Returns a hash mapping the user IDs to functional assignment IDs. =back =cut #: Return Type %; sub AllFunctionsOf { - # Get the parameters. - my $self = shift @_; - my ($featureID) = @_; - # Get all of the feature's annotations. - my @query = $self->GetAll(['IsTargetOfAnnotation', 'Annotation'], - "IsTargetOfAnnotation(from-link) = ?", - [$featureID], ['Annotation(time)', 'Annotation(annotation)']); - # Declare the return hash. - my %retVal; - # Declare a hash for insuring we only make one assignment per user. - my %timeHash = (); + # Get the parameters. + my ($self, $featureID) = @_; + # Get all of the feature's annotations. + my @query = $self->GetAll(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'], + "IsTargetOfAnnotation(from-link) = ?", + [$featureID], ['Annotation(time)', 'Annotation(annotation)', + 'MadeAnnotation(from-link)']); + # Declare the return hash. + my %retVal; # Now we sort the assignments by timestamp in reverse. my @sortedQuery = sort { -($a->[0] <=> $b->[0]) } @query; - # Loop until we run out of annotations. + # Loop until we run out of annotations. for my $annotation (@sortedQuery) { # Get the annotation fields. - my ($timeStamp, $text) = @{$annotation}; - # Check to see if this is a functional assignment. - my ($user, $function) = ParseAssignment($text); - if ($user && ! exists $timeHash{$user}) { + my ($timeStamp, $text, $user) = @{$annotation}; + # Check to see if this is a functional assignment. + my ($actualUser, $function) = _ParseAssignment($user, $text); + if ($actualUser && ! exists $retVal{$actualUser}) { # Here it is a functional assignment and there has been no # previous assignment for this user, so we stuff it in the # return hash. - $retVal{$function} = $user; - # Insure we don't assign to this user again. - $timeHash{$user} = 1; - } - } - # Return the hash of assignments found. - return %retVal; + $retVal{$actualUser} = $function; + } + } + # Return the hash of assignments found. + return %retVal; } =head3 FunctionOf @@ -1073,10 +1148,10 @@ The functional assignment is handled differently depending on the type of feature. If the feature is identified by a FIG ID (begins with the string C), then a functional -assignment is a type of annotation. It has the format "XXXX\nset XXXX function to\nYYYYY". In this -instance, XXXX is the user ID and YYYYY is the functional assignment text. Its worth noting that -we cannot filter on the content of the annotation itself because it's a text field; however, this -is not a big problem because most features only have a small number of annotations. +assignment is a type of annotation. The format of an assignment is described in +L. Its worth noting that we cannot filter on the content of the +annotation itself because it's a text field; however, this is not a big problem because +most features only have a small number of annotations. Each user has an associated list of trusted users. The assignment returned will be the most recent one by at least one of the trusted users. If no trusted user list is available, then @@ -1107,9 +1182,8 @@ =cut #: Return Type $; sub FunctionOf { - # Get the parameters. - my $self = shift @_; - my ($featureID, $userID) = @_; + # Get the parameters. + my ($self, $featureID, $userID) = @_; # Declare the return value. my $retVal; # Determine the ID type. @@ -1137,20 +1211,22 @@ } } # Build a query for all of the feature's annotations, sorted by date. - my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation'], + my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'], "IsTargetOfAnnotation(from-link) = ? ORDER BY Annotation(time) DESC", [$featureID]); my $timeSelected = 0; # Loop until we run out of annotations. while (my $annotation = $query->Fetch()) { # Get the annotation text. - my ($text, $time) = $annotation->Values(['Annotation(annotation)','Annotation(time)']); + my ($text, $time, $user) = $annotation->Values(['Annotation(annotation)', + 'Annotation(time)', 'MadeAnnotation(from-link)']); # Check to see if this is a functional assignment for a trusted user. - my ($user, $type, $function) = split(/\n/, $text); - if ($type =~ m/^set $user function to$/i) { + my ($actualUser, $function) = _ParseAssignment($user, $text); + Trace("Assignment user is $actualUser, text is $function.") if T(4); + if ($actualUser) { # Here it is a functional assignment. Check the time and the user # name. The time must be recent and the user must be trusted. - if ((exists $trusteeTable{$user}) && ($time > $timeSelected)) { + if ((exists $trusteeTable{$actualUser}) && ($time > $timeSelected)) { $retVal = $function; $timeSelected = $time; } @@ -1162,8 +1238,80 @@ # table. ($retVal) = $self->GetEntityValues('ExternalAliasFunc', $featureID, ['ExternalAliasFunc(func)']); } - # Return the assignment found. - return $retVal; + # Return the assignment found. + return $retVal; +} + +=head3 FunctionsOf + +C<< my @functionList = $sprout->FunctionOf($featureID, $userID); >> + +Return the functional assignments of a particular feature. + +The functional assignment is handled differently depending on the type of feature. If +the feature is identified by a FIG ID (begins with the string C), then a functional +assignment is a type of annotation. The format of an assignment is described in +L. Its worth noting that we cannot filter on the content of the +annotation itself because it's a text field; however, this is not a big problem because +most features only have a small number of annotations. + +If the feature is B identified by a FIG ID, then the functional assignment +information is taken from the B table. If the table does +not contain an entry for the feature, an empty list is returned. + +=over 4 + +=item featureID + +ID of the feature whose functional assignments are desired. + +=item RETURN + +Returns a list of 2-tuples, each consisting of a user ID and the text of an assignment by +that user. + +=back + +=cut +#: Return Type @@; +sub FunctionsOf { + # Get the parameters. + my ($self, $featureID) = @_; + # Declare the return value. + my @retVal = (); + # Determine the ID type. + if ($featureID =~ m/^fig\|/) { + # Here we have a FIG feature ID. We must build the list of trusted + # users. + my %trusteeTable = (); + # Build a query for all of the feature's annotations, sorted by date. + my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'], + "IsTargetOfAnnotation(from-link) = ? ORDER BY Annotation(time) DESC", + [$featureID]); + my $timeSelected = 0; + # Loop until we run out of annotations. + while (my $annotation = $query->Fetch()) { + # Get the annotation text. + my ($text, $time, $user) = $annotation->Values(['Annotation(annotation)', + 'Annotation(time)', + 'MadeAnnotation(user)']); + # Check to see if this is a functional assignment for a trusted user. + my ($actualUser, $function) = _ParseAssignment($user, $text); + if ($actualUser) { + # Here it is a functional assignment. + push @retVal, [$actualUser, $function]; + } + } + } else { + # Here we have a non-FIG feature ID. In this case the user ID does not + # matter. We simply get the information from the External Alias Function + # table. + my @assignments = $self->GetEntityValues('ExternalAliasFunc', $featureID, + ['ExternalAliasFunc(func)']); + push @retVal, map { ['master', $_] } @assignments; + } + # Return the assignments found. + return @retVal; } =head3 BBHList @@ -1185,34 +1333,111 @@ =item RETURN -Returns a reference to a hash that maps the IDs of the incoming features to the IDs of -their best hits. +Returns a reference to a hash that maps the IDs of the incoming features to the best hits +on the target genome. =back =cut #: Return Type %; sub BBHList { - # Get the parameters. - my $self = shift @_; - my ($genomeID, $featureList) = @_; - # Create the return structure. - my %retVal = (); - # Loop through the incoming features. - for my $featureID (@{$featureList}) { - # Create a query to get the feature's best hit. - my $query = $self->Get(['IsBidirectionalBestHitOf'], - "IsBidirectionalBestHitOf(from-link) = ? AND IsBidirectionalBestHitOf(genome) = ?", - [$featureID, $genomeID]); - # Look for the best hit. - my $bbh = $query->Fetch; - if ($bbh) { - my ($targetFeature) = $bbh->Value('IsBidirectionalBestHitOf(to-link)'); - $retVal{$featureID} = $targetFeature; - } - } - # Return the mapping. - return \%retVal; + # Get the parameters. + my ($self, $genomeID, $featureList) = @_; + # Create the return structure. + my %retVal = (); + # Loop through the incoming features. + for my $featureID (@{$featureList}) { + # Create a query to get the feature's best hit. + my $query = $self->Get(['IsBidirectionalBestHitOf'], + "IsBidirectionalBestHitOf(from-link) = ? AND IsBidirectionalBestHitOf(genome) = ?", + [$featureID, $genomeID]); + # Peel off the BBHs found. + my @found = (); + while (my $bbh = $query->Fetch) { + push @found, $bbh->Value('IsBidirectionalBestHitOf(to-link)'); + } + $retVal{$featureID} = \@found; + } + # Return the mapping. + return \%retVal; +} + +=head3 SimList + +C<< my %similarities = $sprout->SimList($featureID, $count); >> + +Return a list of the similarities to the specified feature. + +Sprout does not support real similarities, so this method just returns the bidirectional +best hits. + +=over 4 + +=item featureID + +ID of the feature whose similarities are desired. + +=item count + +Maximum number of similar features to be returned, or C<0> to return them all. + +=back + +=cut +#: Return Type %; +sub SimList { + # Get the parameters. + my ($self, $featureID, $count) = @_; + # Ask for the best hits. + my @lists = $self->GetAll(['IsBidirectionalBestHitOf'], + "IsBidirectionalBestHitOf(from-link) = ? ORDER BY IsBidirectionalBestHitOf(score) DESC", + [$featureID], ['IsBidirectionalBestHitOf(to-link)', 'IsBidirectionalBestHitOf(score)'], + $count); + # Create the return value. + my %retVal = (); + for my $tuple (@lists) { + $retVal{$tuple->[0]} = $tuple->[1]; + } + # Return the result. + return %retVal; +} + + + +=head3 IsComplete + +C<< my $flag = $sprout->IsComplete($genomeID); >> + +Return TRUE if the specified genome is complete, else FALSE. + +=over 4 + +=item genomeID + +ID of the genome whose completeness status is desired. + +=item RETURN + +Returns TRUE if the genome is complete, FALSE if it is incomplete, and C if it is +not found. + +=back + +=cut +#: Return Type $; +sub IsComplete { + # Get the parameters. + my ($self, $genomeID) = @_; + # Declare the return variable. + my $retVal; + # Get the genome's data. + my $genomeData = $self->GetEntity('Genome', $genomeID); + if ($genomeData) { + # The genome exists, so get the completeness flag. + ($retVal) = $genomeData->Value('Genome(complete)'); + } + # Return the result. + return $retVal; } =head3 FeatureAliases @@ -1237,117 +1462,280 @@ =cut #: Return Type @; sub FeatureAliases { - # Get the parameters. - my $self = shift @_; - my ($featureID) = @_; - # Get the desired feature's aliases - my @retVal = $self->GetEntityValues('Feature', $featureID, ['Feature(alias)']); - # Return the result. - return @retVal; + # Get the parameters. + my ($self, $featureID) = @_; + # Get the desired feature's aliases + my @retVal = $self->GetEntityValues('Feature', $featureID, ['Feature(alias)']); + # Return the result. + return @retVal; +} + +=head3 GenomeOf + +C<< my $genomeID = $sprout->GenomeOf($featureID); >> + +Return the genome that contains a specified feature or contig. + +=over 4 + +=item featureID + +ID of the feature or contig whose genome is desired. + +=item RETURN + +Returns the ID of the genome for the specified feature or contig. If the feature or contig is not +found, returns an undefined value. + +=back + +=cut +#: Return Type $; +sub GenomeOf { + # Get the parameters. + my ($self, $featureID) = @_; + # Create a query to find the genome associated with the incoming ID. + my $query = $self->Get(['IsLocatedIn', 'HasContig'], "IsLocatedIn(from-link) = ? OR HasContig(to-link) = ?", + [$featureID, $featureID]); + # Declare the return value. + my $retVal; + # Get the genome ID. + if (my $relationship = $query->Fetch()) { + ($retVal) = $relationship->Value('HasContig(from-link)'); + } + # Return the value found. + return $retVal; +} + +=head3 CoupledFeatures + +C<< my %coupleHash = $sprout->CoupledFeatures($featureID); >> + +Return the features functionally coupled with a specified feature. Features are considered +functionally coupled if they tend to be clustered on the same chromosome. + +=over 4 + +=item featureID + +ID of the feature whose functionally-coupled brethren are desired. + +=item RETURN + +A hash mapping the functionally-coupled feature IDs to the coupling score. + +=back + +=cut +#: Return Type %; +sub CoupledFeatures { + # Get the parameters. + my ($self, $featureID) = @_; + # Create a query to retrieve the functionally-coupled features. + my $query = $self->Get(['ParticipatesInCoupling', 'Coupling'], + "ParticipatesInCoupling(from-link) = ?", [$featureID]); + # This value will be set to TRUE if we find at least one coupled feature. + my $found = 0; + # Create the return hash. + my %retVal = (); + # Retrieve the relationship records and store them in the hash. + while (my $clustering = $query->Fetch()) { + # Get the ID and score of the coupling. + my ($couplingID, $score) = $clustering->Values(['Coupling(id)', + 'Coupling(score)']); + # Get the other feature that participates in the coupling. + my ($otherFeatureID) = $self->GetFlat(['ParticipatesInCoupling'], + "ParticipatesInCoupling(to-link) = ? AND ParticipatesInCoupling(from-link) <> ?", + [$couplingID, $featureID], 'ParticipatesInCoupling(to-link)'); + # Attach the other feature's score to its ID. + $retVal{$otherFeatureID} = $score; + $found = 1; + } + # Functional coupling is reflexive. If we found at least one coupled feature, we must add + # the incoming feature as well. + if ($found) { + $retVal{$featureID} = 9999; + } + # Return the hash. + return %retVal; +} + +=head3 CouplingEvidence + +C<< my @evidence = $sprout->CouplingEvidence($peg1, $peg2); >> + +Return the evidence for a functional coupling. + +A pair of features is considered evidence of a coupling between two other +features if they occur close together on a contig and both are similar to +the coupled features. So, if B and B are close together on a contig, +B and B are considered evidence for the coupling if (1) B and +B are close together, (2) B is similar to B, and (3) B is +similar to B. + +The score of a coupling is determined by the number of pieces of evidence +that are considered I. If several evidence items belong to +a group of genomes that are close to each other, only one of those items +is considered representative. The other evidence items are presumed to be +there because of the relationship between the genomes rather than because +the two proteins generated by the features have a related functionality. + +Each evidence item is returned as a three-tuple in the form C<[>I<$peg1a>C<,> +I<$peg2a>C<,> I<$rep>C<]>, where I<$peg1a> is similar to I<$peg1>, I<$peg2a> +is similar to I<$peg2>, and I<$rep> is TRUE if the evidence is representative +and FALSE otherwise. + +=over 4 + +=item peg1 + +ID of the feature of interest. + +=item peg2 + +ID of a feature functionally coupled to the feature of interest. + +=item RETURN + +Returns a list of 3-tuples. Each tuple consists of a feature similar to the feature +of interest, a feature similar to the functionally coupled feature, and a flag +that is TRUE for a representative piece of evidence and FALSE otherwise. + +=back + +=cut +#: Return Type @@; +sub CouplingEvidence { + # Get the parameters. + my ($self, $peg1, $peg2) = @_; + # Declare the return variable. + my @retVal = (); + # Our first task is to find out the nature of the coupling: whether or not + # it exists, its score, and whether the features are stored in the same + # order as the ones coming in. + my ($couplingID, $inverted, $score) = $self->GetCoupling($peg1, $peg2); + # Only proceed if a coupling exists. + if ($couplingID) { + # Determine the ordering to place on the evidence items. If we're + # inverted, we want to see feature 2 before feature 1 (descending); otherwise, + # we want feature 1 before feature 2 (normal). + Trace("Coupling evidence for ($peg1, $peg2) with inversion flag $inverted.") if T(Coupling => 4); + my $ordering = ($inverted ? "DESC" : ""); + # Get the coupling evidence. + my @evidenceList = $self->GetAll(['IsEvidencedBy', 'PCH', 'UsesAsEvidence'], + "IsEvidencedBy(from-link) = ? ORDER BY PCH(id), UsesAsEvidence(pos) $ordering", + [$couplingID], + ['PCH(used)', 'UsesAsEvidence(to-link)']); + # Loop through the evidence items. Each piece of evidence is represented by two + # positions in the evidence list, one for each feature on the other side of the + # evidence link. If at some point we want to generalize to couplings with + # more than two positions, this section of code will need to be re-done. + while (@evidenceList > 0) { + my $peg1Data = shift @evidenceList; + my $peg2Data = shift @evidenceList; + Trace("Peg 1 is " . $peg1Data->[1] . " and Peg 2 is " . $peg2Data->[1] . ".") if T(Coupling => 4); + push @retVal, [$peg1Data->[1], $peg2Data->[1], $peg1Data->[0]]; + } + Trace("Last index in evidence result is is $#retVal.") if T(Coupling => 4); + } + # Return the result. + return @retVal; } -=head3 GenomeOf +=head3 GetCoupling -C<< my $genomeID = $sprout->GenomeOf($featureID); >> +C<< my ($couplingID, $inverted, $score) = $sprout->GetCoupling($peg1, $peg2); >> -Return the genome that contains a specified feature. +Return the coupling (if any) for the specified pair of PEGs. If a coupling +exists, we return the coupling ID along with an indicator of whether the +coupling is stored as C<(>I<$peg1>C<, >I<$peg2>C<)> or C<(>I<$peg2>C<, >I<$peg1>C<)>. +In the second case, we say the coupling is I. The importance of an +inverted coupling is that the PEGs in the evidence will appear in reverse order. =over 4 -=item featureID +=item peg1 + +ID of the feature of interest. + +=item peg2 -ID of the feature whose genome is desired. +ID of the potentially coupled feature. =item RETURN -Returns the ID of the genome for the specified feature. If the feature is not found, returns -an undefined value. +Returns a three-element list. The first element contains the database ID of +the coupling. The second element is FALSE if the coupling is stored in the +database in the caller specified order and TRUE if it is stored in the +inverted order. The third element is the coupling's score. If the coupling +does not exist, all three list elements will be C. =back =cut -#: Return Type $; -sub GenomeOf { - # Get the parameters. - my $self = shift @_; - my ($featureID) = @_; - # Create a query to find the genome associated with the feature. - my $query = $self->Get(['IsLocatedIn', 'HasContig'], "IsLocatedIn(from-link) = ?", [$featureID]); - # Declare the return value. - my $retVal; - # Get the genome ID. - if (my $relationship = $query->Fetch()) { - ($retVal) = $relationship->Value('HasContig(from-link)'); - } - # Return the value found. - return $retVal; +#: Return Type $%@; +sub GetCoupling { + # Get the parameters. + my ($self, $peg1, $peg2) = @_; + # Declare the return values. We'll start with the coupling ID and undefine the + # flag and score until we have more information. + my ($retVal, $inverted, $score) = (CouplingID($peg1, $peg2), undef, undef); + # Find the coupling data. + my @pegs = $self->GetAll(['Coupling', 'ParticipatesInCoupling'], + "Coupling(id) = ? ORDER BY ParticipatesInCoupling(pos)", + [$retVal], ["ParticipatesInCoupling(from-link)", "Coupling(score)"]); + # Check to see if we found anything. + if (!@pegs) { + Trace("No coupling found.") if T(Coupling => 4); + # No coupling, so undefine the return value. + $retVal = undef; + } else { + # We have a coupling! Get the score and check for inversion. + $score = $pegs[0]->[1]; + my $firstFound = $pegs[0]->[0]; + $inverted = ($firstFound ne $peg1); + Trace("Coupling score is $score. First peg is $firstFound, peg 1 is $peg1.") if T(Coupling => 4); + } + # Return the result. + return ($retVal, $inverted, $score); } -=head3 CoupledFeatures - -C<< my %coupleHash = $sprout->CoupledFeatures($featureID); >> +=head3 CouplingID -Return the features functionally coupled with a specified feature. Features are considered -functionally coupled if they tend to be clustered on the same chromosome. +C<< my $couplingID = Sprout::CouplingID($peg1, $peg2); >> -=over 4 +Return the coupling ID for a pair of feature IDs. -=item featureID +The coupling ID is currently computed by joining the feature IDs in +sorted order with a space. Client modules (that is, modules which +use Sprout) should not, however, count on this always being the +case. This method provides a way for abstracting the concept of a +coupling ID. All that we know for sure about it is that it can be +generated easily from the feature IDs and the order of the IDs +in the parameter list does not matter (i.e. C +will have the same value as C. -ID of the feature whose functionally-coupled brethren are desired. +=over 4 -=item RETURN +=item peg1 -A hash mapping the functionally-coupled feature IDs to the coupling score. +First feature of interest. -=back +=item peg2 -=cut -#: Return Type %; -sub CoupledFeatures { - # Get the parameters. - my $self = shift @_; - my ($featureID) = @_; - # Create a query to retrieve the functionally-coupled features. Note that we depend on the - # fact that the functional coupling is physically paired. If (A,B) is in the database, then - # (B,A) will also be found. - my $query = $self->Get(['IsClusteredOnChromosomeWith'], - "IsClusteredOnChromosomeWith(from-link) = ?", [$featureID]); - # This value will be set to TRUE if we find at least one coupled feature. - my $found = 0; - # Create the return hash. - my %retVal = (); - # Retrieve the relationship records and store them in the hash. - while (my $clustering = $query->Fetch()) { - my ($otherFeatureID, $score) = $clustering->Values(['IsClusteredOnChromosomeWith(to-link)', - 'IsClusteredOnChromosomeWith(score)']); - $retVal{$otherFeatureID} = $score; - $found = 1; - } - # Functional coupling is reflexive. If we found at least one coupled feature, we must add - # the incoming feature as well. - if ($found) { - $retVal{$featureID} = 9999; - } - # Return the hash. - return %retVal; -} +Second feature of interest. -=head3 GetEntityTypes +=item RETURN -C<< my @entityList = $sprout->GetEntityTypes(); >> +Returns the ID that would be used to represent a functional coupling of +the two specified PEGs. -Return the list of supported entity types. +=back =cut -#: Return Type @; -sub GetEntityTypes { - # Get the parameters. - my $self = shift @_; - # Get the underlying database object. - my $erdb = $self->{_erdb}; - # Get its entity type list. - my @retVal = $erdb->GetEntityTypes(); +#: Return Type $; +sub CouplingID { + return join " ", sort @_; } =head3 ReadFasta @@ -1377,40 +1765,43 @@ =cut #: Return Type %; sub ReadFasta { - # Get the parameters. - my ($fileName, $prefix) = @_; - # Create the return hash. - my %retVal = (); - # Open the file for input. - open FASTAFILE, '<', $fileName; - # Declare the ID variable and clear the sequence accumulator. - my $sequence = ""; - my $id = ""; - # Loop through the file. - while () { - # Get the current line. - my $line = $_; - # Check for a header line. - if ($line =~ m/^>\s*(.+?)(\s|\n)/) { - # Here we have a new header. Store the current sequence if we have one. - if ($id) { - $retVal{$id} = $sequence; - } - # Clear the sequence accumulator and save the new ID. - ($id, $sequence) = ("$prefix$1", ""); - } else { - # Here we have a data line, so we add it to the sequence accumulator. - # First, we get the actual data out. - $line =~ /^\s*(.*?)(\s|\n)/; - $sequence .= $1; - } - } - # Flush out the last sequence (if any). - if ($sequence) { - $retVal {$id} = $sequence; - } - # Return the hash constructed from the file. - return %retVal; + # Get the parameters. + my ($fileName, $prefix) = @_; + # Create the return hash. + my %retVal = (); + # Open the file for input. + open FASTAFILE, '<', $fileName; + # Declare the ID variable and clear the sequence accumulator. + my $sequence = ""; + my $id = ""; + # Loop through the file. + while () { + # Get the current line. + my $line = $_; + # Check for a header line. + if ($line =~ m/^>\s*(.+?)(\s|\n)/) { + # Here we have a new header. Store the current sequence if we have one. + if ($id) { + $retVal{$id} = lc $sequence; + } + # Clear the sequence accumulator and save the new ID. + ($id, $sequence) = ("$prefix$1", ""); + } else { + # Here we have a data line, so we add it to the sequence accumulator. + # First, we get the actual data out. Note that we normalize to lower + # case. + $line =~ /^\s*(.*?)(\s|\n)/; + $sequence .= $1; + } + } + # Flush out the last sequence (if any). + if ($sequence) { + $retVal{$id} = lc $sequence; + } + # Close the file. + close FASTAFILE; + # Return the hash constructed from the file. + return %retVal; } =head3 FormatLocations @@ -1419,7 +1810,9 @@ Insure that a list of feature locations is in the Sprout format. The Sprout feature location format is I_I where I<*> is C<+> for a forward gene and C<-> for a backward -gene. The old format is I_I_I. +gene. The old format is I_I_I. If a feature is in the new format already, +it will not be changed; otherwise, it will be converted. This method can also be used to +perform the reverse task-- insuring that all the locations are in the old format. =over 4 @@ -1445,36 +1838,35 @@ =cut #: Return Type @; sub FormatLocations { - # Get the parameters. - my $self = shift @_; - my ($prefix, $locations, $oldFormat) = @_; - # Create the return list. - my @retVal = (); - # Check to see if any locations were passed in. - if ($locations eq '') { - confess "No locations specified."; - } else { - # Loop through the locations, converting them to the new format. - for my $location (@{$locations}) { - # Parse the location elements. - my ($contig, $beg, $dir, $len) = ParseLocation($location); - # Process according to the desired output format. - if (!$oldFormat) { - # Here we're producing the new format. Add the location to the return list. - push @retVal, "$prefix${contig}_$beg$dir$len"; - } elsif ($dir eq '+') { - # Here we're producing the old format and it's a forward gene. - my $end = $beg + $len - 1; - push @retVal, "$prefix${contig}_${beg}_$end"; - } else { - # Here we're producting the old format and it's a backward gene. - my $end = $beg - $len + 1; - push @retVal, "$prefix${contig}_${beg}_$end"; - } - } - } - # Return the normalized list. - return @retVal; + # Get the parameters. + my ($self, $prefix, $locations, $oldFormat) = @_; + # Create the return list. + my @retVal = (); + # Check to see if any locations were passed in. + if ($locations eq '') { + Confess("No locations specified."); + } else { + # Loop through the locations, converting them to the new format. + for my $location (@{$locations}) { + # Parse the location elements. + my ($contig, $beg, $dir, $len) = ParseLocation($location); + # Process according to the desired output format. + if (!$oldFormat) { + # Here we're producing the new format. Add the location to the return list. + push @retVal, "$prefix${contig}_$beg$dir$len"; + } elsif ($dir eq '+') { + # Here we're producing the old format and it's a forward gene. + my $end = $beg + $len - 1; + push @retVal, "$prefix${contig}_${beg}_$end"; + } else { + # Here we're producting the old format and it's a backward gene. + my $end = $beg - $len + 1; + push @retVal, "$prefix${contig}_${beg}_$end"; + } + } + } + # Return the normalized list. + return @retVal; } =head3 DumpData @@ -1486,12 +1878,12 @@ =cut sub DumpData { - # Get the parameters. - my $self = shift @_; - # Get the data directory name. - my $outputDirectory = $self->{_options}->{dataDir}; - # Dump the relations. - $self->{_erdb}->DumpRelations($outputDirectory); + # Get the parameters. + my ($self) = @_; + # Get the data directory name. + my $outputDirectory = $self->{_options}->{dataDir}; + # Dump the relations. + $self->DumpRelations($outputDirectory); } =head3 XMLFileName @@ -1503,8 +1895,8 @@ =cut #: Return Type $; sub XMLFileName { - my $self = shift @_; - return $self->{_xmlName}; + my ($self) = @_; + return $self->{_xmlName}; } =head3 Insert @@ -1523,7 +1915,7 @@ The next statement inserts a C relationship between feature C and property C<4> with an evidence URL of C. -C<< $sprout->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence = 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >> +C<< $sprout->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence => 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >> =over 4 @@ -1540,11 +1932,10 @@ =cut #: Return Type ; sub Insert { - # Get the parameters. - my $self = shift @_; - my ($objectType, $fieldHash) = @_; - # Call the underlying method. - $self->{_erdb}->InsertObject($objectType, $fieldHash); + # Get the parameters. + my ($self, $objectType, $fieldHash) = @_; + # Call the underlying method. + $self->InsertObject($objectType, $fieldHash); } =head3 Annotate @@ -1582,33 +1973,31 @@ =cut #: Return Type $; sub Annotate { - # Get the parameters. - my $self = shift @_; - my ($fid, $timestamp, $user, $text) = @_; - # Create the annotation ID. - my $aid = "$fid:$timestamp"; - # Insert the Annotation object. - my $retVal = $self->Insert('Annotation', { id => $aid, time => $timestamp, annotation => $text }); - if ($retVal) { - # Connect it to the user. - $retVal = $self->Insert('MadeAnnotation', { 'from-link' => $user, 'to-link' => $aid }); - if ($retVal) { - # Connect it to the feature. - $retVal = $self->Insert('IsTargetOfAnnotation', { 'from-link' => $fid, - 'to-link' => $aid }); - } - } - # Return the success indicator. - return $retVal; + # Get the parameters. + my ($self, $fid, $timestamp, $user, $text) = @_; + # Create the annotation ID. + my $aid = "$fid:$timestamp"; + # Insert the Annotation object. + my $retVal = $self->Insert('Annotation', { id => $aid, time => $timestamp, annotation => $text }); + if ($retVal) { + # Connect it to the user. + $retVal = $self->Insert('MadeAnnotation', { 'from-link' => $user, 'to-link' => $aid }); + if ($retVal) { + # Connect it to the feature. + $retVal = $self->Insert('IsTargetOfAnnotation', { 'from-link' => $fid, + 'to-link' => $aid }); + } + } + # Return the success indicator. + return $retVal; } =head3 AssignFunction -C<< my $ok = $sprout->AssignFunction($featureID, $user, $function); >> +C<< my $ok = $sprout->AssignFunction($featureID, $user, $function, $assigningUser); >> This method assigns a function to a feature. Functions are a special type of annotation. The general -format is "XXXX\nset XXXX function to\nYYYYY" where XXXX is the feature type and YYYY is the functional -assignment text. +format is described in L. =over 4 @@ -1618,12 +2007,16 @@ =item user -Name of the user making the assignment. This is frequently a group name, like C or C. +Name of the user group making the assignment, such as C or C. =item function Text of the function being assigned. +=item assigningUser (optional) + +Name of the individual user making the assignment. If omitted, defaults to the user group. + =item RETURN Returns 1 if successful, 0 if an error occurred. @@ -1633,27 +2026,30 @@ =cut #: Return Type $; sub AssignFunction { - # Get the parameters. - my $self = shift @_; - my ($featureID, $user, $function) = @_; - # Create an annotation string from the parameters. - my $annotationText = "$user\nset $user function to\n$function"; - # Get the current time. - my $now = time; - # Declare the return variable. - my $retVal = 1; - # Locate the genome containing the feature. - my $genome = $self->GenomeOf($featureID); - if (!$genome) { - # Here the genome was not found. This probably means the feature ID is invalid. - Trace("No genome found for feature $featureID.") if T(0); - $retVal = 0; - } else { - # Here we know we have a feature with a genome. Store the annotation. + # Get the parameters. + my ($self, $featureID, $user, $function, $assigningUser) = @_; + # Default the assigning user. + if (! $assigningUser) { + $assigningUser = $user; + } + # Create an annotation string from the parameters. + my $annotationText = "$assigningUser\nset $user function to\n$function"; + # Get the current time. + my $now = time; + # Declare the return variable. + my $retVal = 1; + # Locate the genome containing the feature. + my $genome = $self->GenomeOf($featureID); + if (!$genome) { + # Here the genome was not found. This probably means the feature ID is invalid. + Trace("No genome found for feature $featureID.") if T(0); + $retVal = 0; + } else { + # Here we know we have a feature with a genome. Store the annotation. $retVal = $self->Annotate($featureID, $now, $user, $annotationText); - } - # Return the success indicator. - return $retVal; + } + # Return the success indicator. + return $retVal; } =head3 FeaturesByAlias @@ -1681,22 +2077,21 @@ =cut #: Return Type @; sub FeaturesByAlias { - # Get the parameters. - my $self = shift @_; - my ($alias) = @_; - # Declare the return variable. - my @retVal = (); - # Parse the alias. - my ($mappedAlias, $flag) = FIGRules::NormalizeAlias($alias); - # If it's a FIG alias, we're done. - if ($flag) { - push @retVal, $mappedAlias; - } else { - # Here we have a non-FIG alias. Get the features with the normalized alias. - @retVal = $self->GetFlat(['Feature'], 'Feature(alias) = ?', [$mappedAlias], 'Feature(id)'); - } - # Return the result. - return @retVal; + # Get the parameters. + my ($self, $alias) = @_; + # Declare the return variable. + my @retVal = (); + # Parse the alias. + my ($mappedAlias, $flag) = FIGRules::NormalizeAlias($alias); + # If it's a FIG alias, we're done. + if ($flag) { + push @retVal, $mappedAlias; + } else { + # Here we have a non-FIG alias. Get the features with the normalized alias. + @retVal = $self->GetFlat(['Feature'], 'Feature(alias) = ?', [$mappedAlias], 'Feature(id)'); + } + # Return the result. + return @retVal; } =head3 Exists @@ -1724,14 +2119,14 @@ =cut #: Return Type $; sub Exists { - # Get the parameters. - my $self = shift @_; - my ($entityName, $entityID) = @_; - # Check for the entity instance. - my $testInstance = $self->GetEntity($entityName, $entityID); - # Return an existence indicator. - my $retVal = ($testInstance ? 1 : 0); - return $retVal; + # Get the parameters. + my ($self, $entityName, $entityID) = @_; + # Check for the entity instance. + Trace("Checking existence of $entityName with ID=$entityID.") if T(4); + my $testInstance = $self->GetEntity($entityName, $entityID); + # Return an existence indicator. + my $retVal = ($testInstance ? 1 : 0); + return $retVal; } =head3 FeatureTranslation @@ -1755,12 +2150,11 @@ =cut #: Return Type $; sub FeatureTranslation { - # Get the parameters. - my $self = shift @_; - my ($featureID) = @_; - # Get the specified feature's translation. - my ($retVal) = $self->GetEntityValues("Feature", $featureID, ['Feature(translation)']); - return $retVal; + # Get the parameters. + my ($self, $featureID) = @_; + # Get the specified feature's translation. + my ($retVal) = $self->GetEntityValues("Feature", $featureID, ['Feature(translation)']); + return $retVal; } =head3 Taxonomy @@ -1788,21 +2182,20 @@ =cut #: Return Type @; sub Taxonomy { - # Get the parameters. - my $self = shift @_; - my ($genome) = @_; - # Find the specified genome's taxonomy string. - my ($list) = $self->GetEntityValues('Genome', $genome, ['Genome(taxonomy)']); - # Declare the return variable. - my @retVal = (); - # If we found the genome, return its taxonomy string. - if ($list) { - @retVal = split /\s*;\s*/, $list; - } else { - Trace("Genome \"$genome\" does not have a taxonomy in the database.\n") if T(0); - } - # Return the value found. - return @retVal; + # Get the parameters. + my ($self, $genome) = @_; + # Find the specified genome's taxonomy string. + my ($list) = $self->GetEntityValues('Genome', $genome, ['Genome(taxonomy)']); + # Declare the return variable. + my @retVal = (); + # If we found the genome, return its taxonomy string. + if ($list) { + @retVal = split /\s*;\s*/, $list; + } else { + Trace("Genome \"$genome\" does not have a taxonomy in the database.\n") if T(0); + } + # Return the value found. + return @retVal; } =head3 CrudeDistance @@ -1832,29 +2225,28 @@ =cut #: Return Type $; sub CrudeDistance { - # Get the parameters. - my $self = shift @_; - my ($genome1, $genome2) = @_; - # Insure that the distance is commutative by sorting the genome IDs. - my ($genomeA, $genomeB); - if ($genome2 < $genome2) { - ($genomeA, $genomeB) = ($genome1, $genome2); - } else { - ($genomeA, $genomeB) = ($genome2, $genome1); - } - my @taxA = $self->Taxonomy($genomeA); - my @taxB = $self->Taxonomy($genomeB); - # Initialize the distance to 1. We'll reduce it each time we find a match between the - # taxonomies. - my $retVal = 1.0; - # Initialize the subtraction amount. This amount determines the distance reduction caused - # by a mismatch at the current level. - my $v = 0.5; - # Loop through the taxonomies. - for (my $i = 0; ($i < @taxA) && ($i < @taxB) && ($taxA[$i] eq $taxB[$i]); $i++) { - $retVal -= $v; - $v /= 2; - } + # Get the parameters. + my ($self, $genome1, $genome2) = @_; + # Insure that the distance is commutative by sorting the genome IDs. + my ($genomeA, $genomeB); + if ($genome2 < $genome2) { + ($genomeA, $genomeB) = ($genome1, $genome2); + } else { + ($genomeA, $genomeB) = ($genome2, $genome1); + } + my @taxA = $self->Taxonomy($genomeA); + my @taxB = $self->Taxonomy($genomeB); + # Initialize the distance to 1. We'll reduce it each time we find a match between the + # taxonomies. + my $retVal = 1.0; + # Initialize the subtraction amount. This amount determines the distance reduction caused + # by a mismatch at the current level. + my $v = 0.5; + # Loop through the taxonomies. + for (my $i = 0; ($i < @taxA) && ($i < @taxB) && ($taxA[$i] eq $taxB[$i]); $i++) { + $retVal -= $v; + $v /= 2; + } return $retVal; } @@ -1880,17 +2272,16 @@ =cut #: Return Type $; sub RoleName { - # Get the parameters. - my $self = shift @_; - my ($roleID) = @_; - # Get the specified role's name. - my ($retVal) = $self->GetEntityValues('Role', $roleID, ['Role(name)']); - # Use the ID if the role has no name. - if (!$retVal) { - $retVal = $roleID; - } - # Return the name. - return $retVal; + # Get the parameters. + my ($self, $roleID) = @_; + # Get the specified role's name. + my ($retVal) = $self->GetEntityValues('Role', $roleID, ['Role(name)']); + # Use the ID if the role has no name. + if (!$retVal) { + $retVal = $roleID; + } + # Return the name. + return $retVal; } =head3 RoleDiagrams @@ -1914,14 +2305,96 @@ =cut #: Return Type @; sub RoleDiagrams { - # Get the parameters. - my $self = shift @_; - my ($roleID) = @_; - # Query for the diagrams. - my @retVal = $self->GetFlat(['RoleOccursIn'], "RoleOccursIn(from-link) = ?", [$roleID], - 'RoleOccursIn(to-link)'); - # Return the result. - return @retVal; + # Get the parameters. + my ($self, $roleID) = @_; + # Query for the diagrams. + my @retVal = $self->GetFlat(['RoleOccursIn'], "RoleOccursIn(from-link) = ?", [$roleID], + 'RoleOccursIn(to-link)'); + # Return the result. + return @retVal; +} + +=head3 GetProperties + +C<< my @list = $sprout->GetProperties($fid, $key, $value, $url); >> + +Return a list of the properties with the specified characteristics. + +Properties are arbitrary key-value pairs associated with a feature. (At some point they +will also be associated with genomes.) A property value is represented by a 4-tuple of +the form B<($fid, $key, $value, $url)>. These exactly correspond to the parameter + +=over 4 + +=item fid + +ID of the feature possessing the property. + +=item key + +Name or key of the property. + +=item value + +Value of the property. + +=item url + +URL of the document that indicated the property should have this particular value, or an +empty string if no such document exists. + +=back + +The parameters act as a filter for the desired data. Any non-null parameter will +automatically match all the tuples returned. So, specifying just the I<$fid> will +return all the properties of the specified feature; similarly, specifying the I<$key> +and I<$value> parameters will return all the features having the specified property +value. + +A single property key can have many values, representing different ideas about the +feature in question. For example, one paper may declare that a feature C is +virulent, and another may declare that it is not virulent. A query about the virulence of +C would be coded as + + my @list = $sprout->GetProperties('fig|83333.1.peg.10', 'virulence', '', ''); + +Here the I<$value> and I<$url> fields are left blank, indicating that those fields are +not to be filtered. The tuples returned would be + + ('fig|83333.1.peg.10', 'virulence', 'yes', 'http://www.somewhere.edu/first.paper.pdf') + ('fig|83333.1.peg.10', 'virulence', 'no', 'http://www.somewhere.edu/second.paper.pdf') + +=cut +#: Return Type @@; +sub GetProperties { + # Get the parameters. + my ($self, @parms) = @_; + # Declare the return variable. + my @retVal = (); + # Now we need to create a WHERE clause that will get us the data we want. First, + # we create a list of the columns containing the data for each parameter. + my @colNames = ('HasProperty(from-link)', 'Property(property-name)', + 'Property(property-value)', 'HasProperty(evidence)'); + # Now we build the WHERE clause and the list of parameter values. + my @where = (); + my @values = (); + for (my $i = 0; $i <= $#colNames; $i++) { + my $parm = $parms[$i]; + if (defined $parm && ($parm ne '')) { + push @where, "$colNames[$i] = ?"; + push @values, $parm; + } + } + # Format the WHERE clause. + my $filter = (@values > 0 ? (join " AND ", @where) : undef); + # Ask for all the propertie values with the desired characteristics. + my $query = $self->Get(['HasProperty', 'Property'], $filter, \@values); + while (my $valueObject = $query->Fetch()) { + my @tuple = $valueObject->Values(\@colNames); + push @retVal, \@tuple; + } + # Return the result. + return @retVal; } =head3 FeatureProperties @@ -1952,15 +2425,14 @@ =cut #: Return Type @@; sub FeatureProperties { - # Get the parameters. - my $self = shift @_; - my ($featureID) = @_; - # Get the properties. - my @retVal = $self->GetAll(['HasProperty', 'Property'], "HasProperty(from-link) = ?", [$featureID], - ['Property(property-name)', 'Property(property-value)', - 'HasProperty(evidence)']); - # Return the resulting list. - return @retVal; + # Get the parameters. + my ($self, $featureID) = @_; + # Get the properties. + my @retVal = $self->GetAll(['HasProperty', 'Property'], "HasProperty(from-link) = ?", [$featureID], + ['Property(property-name)', 'Property(property-value)', + 'HasProperty(evidence)']); + # Return the resulting list. + return @retVal; } =head3 DiagramName @@ -1984,12 +2456,11 @@ =cut #: Return Type $; sub DiagramName { - # Get the parameters. - my $self = shift @_; - my ($diagramID) = @_; - # Get the specified diagram's name and return it. - my ($retVal) = $self->GetEntityValues('Diagram', $diagramID, ['Diagram(name)']); - return $retVal; + # Get the parameters. + my ($self, $diagramID) = @_; + # Get the specified diagram's name and return it. + my ($retVal) = $self->GetEntityValues('Diagram', $diagramID, ['Diagram(name)']); + return $retVal; } =head3 MergedAnnotations @@ -2017,29 +2488,28 @@ =cut #: Return Type @; sub MergedAnnotations { - # Get the parameters. - my $self = shift @_; - my ($list) = @_; - # Create a list to hold the annotation tuples found. - my @tuples = (); - # Loop through the features in the input list. - for my $fid (@{$list}) { - # Create a list of this feature's annotation tuples. - my @newTuples = $self->GetAll(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'], - "IsTargetOfAnnotation(from-link) = ?", [$fid], - ['IsTargetOfAnnotation(from-link)', 'Annotation(time)', - 'MadeAnnotation(from-link)', 'Annotation(annotation)']); - # Put it in the result list. - push @tuples, @newTuples; - } - # Sort the result list by timestamp. - my @retVal = sort { $a->[1] <=> $b->[1] } @tuples; + # Get the parameters. + my ($self, $list) = @_; + # Create a list to hold the annotation tuples found. + my @tuples = (); + # Loop through the features in the input list. + for my $fid (@{$list}) { + # Create a list of this feature's annotation tuples. + my @newTuples = $self->GetAll(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'], + "IsTargetOfAnnotation(from-link) = ?", [$fid], + ['IsTargetOfAnnotation(from-link)', 'Annotation(time)', + 'MadeAnnotation(from-link)', 'Annotation(annotation)']); + # Put it in the result list. + push @tuples, @newTuples; + } + # Sort the result list by timestamp. + my @retVal = sort { $a->[1] <=> $b->[1] } @tuples; # Loop through and make the time stamps friendly. for my $tuple (@retVal) { $tuple->[1] = FriendlyTimestamp($tuple->[1]); } - # Return the sorted list. - return @retVal; + # Return the sorted list. + return @retVal; } =head3 RoleNeighbors @@ -2066,24 +2536,23 @@ =cut #: Return Type @; sub RoleNeighbors { - # Get the parameters. - my $self = shift @_; - my ($roleID) = @_; - # Get all the diagrams containing this role. - my @diagrams = $self->GetFlat(['RoleOccursIn'], "RoleOccursIn(from-link) = ?", [$roleID], - 'RoleOccursIn(to-link)'); - # Create the return list. - my @retVal = (); - # Loop through the diagrams. - for my $diagramID (@diagrams) { - # Get all the roles in this diagram. - my @roles = $self->GetFlat(['RoleOccursIn'], "RoleOccursIn(to-link) = ?", [$diagramID], - 'RoleOccursIn(from-link)'); - # Add them to the return list. - push @retVal, @roles; - } - # Merge the duplicates from the list. - return Tracer::Merge(@retVal); + # Get the parameters. + my ($self, $roleID) = @_; + # Get all the diagrams containing this role. + my @diagrams = $self->GetFlat(['RoleOccursIn'], "RoleOccursIn(from-link) = ?", [$roleID], + 'RoleOccursIn(to-link)'); + # Create the return list. + my @retVal = (); + # Loop through the diagrams. + for my $diagramID (@diagrams) { + # Get all the roles in this diagram. + my @roles = $self->GetFlat(['RoleOccursIn'], "RoleOccursIn(to-link) = ?", [$diagramID], + 'RoleOccursIn(from-link)'); + # Add them to the return list. + push @retVal, @roles; + } + # Merge the duplicates from the list. + return Tracer::Merge(@retVal); } =head3 FeatureLinks @@ -2109,13 +2578,12 @@ =cut #: Return Type @; sub FeatureLinks { - # Get the parameters. - my $self = shift @_; - my ($featureID) = @_; - # Get the feature's links. - my @retVal = $self->GetEntityValues('Feature', $featureID, ['Feature(link)']); - # Return the feature's links. - return @retVal; + # Get the parameters. + my ($self, $featureID) = @_; + # Get the feature's links. + my @retVal = $self->GetEntityValues('Feature', $featureID, ['Feature(link)']); + # Return the feature's links. + return @retVal; } =head3 SubsystemsOf @@ -2123,7 +2591,7 @@ C<< my %subsystems = $sprout->SubsystemsOf($featureID); >> Return a hash describing all the subsystems in which a feature participates. Each subsystem is mapped -to the role the feature performs. +to the roles the feature performs. =over 4 @@ -2133,30 +2601,73 @@ =item RETURN -Returns a hash mapping all the feature's subsystems to the feature's role. +Returns a hash mapping all the feature's subsystems to a list of the feature's roles. =back =cut -#: Return Type %; +#: Return Type %@; sub SubsystemsOf { - # Get the parameters. - my $self = shift @_; - my ($featureID) = @_; - # Use the SSCell to connect features to subsystems. - my @subsystems = $self->GetAll(['ContainsFeature', 'HasSSCell', 'IsRoleOf'], - "ContainsFeature(to-link) = ?", [$featureID], - ['HasSSCell(from-link)', 'IsRoleOf(from-link)']); - # Create the return value. - my %retVal = (); - # Loop through the results, adding them to the hash. - for my $record (@subsystems) { - $retVal{$record->[0]} = $record->[1]; - } - # Return the hash. - return %retVal; + # Get the parameters. + my ($self, $featureID) = @_; + # Get the subsystem list. + my @subsystems = $self->GetAll(['ContainsFeature', 'HasSSCell', 'IsRoleOf'], + "ContainsFeature(to-link) = ?", [$featureID], + ['HasSSCell(from-link)', 'IsRoleOf(from-link)']); + # Create the return value. + my %retVal = (); + # Build a hash to weed out duplicates. Sometimes the same PEG and role appears + # in two spreadsheet cells. + my %dupHash = (); + # Loop through the results, adding them to the hash. + for my $record (@subsystems) { + # Get this subsystem and role. + my ($subsys, $role) = @{$record}; + # Insure it's the first time for both. + my $dupKey = "$subsys\n$role"; + if (! exists $dupHash{"$subsys\n$role"}) { + $dupHash{$dupKey} = 1; + push @{$retVal{$subsys}}, $role; + } + } + # Return the hash. + return %retVal; +} + +=head3 SubsystemList + +C<< my @subsystems = $sprout->SubsystemList($featureID); >> + +Return a list containing the names of the subsystems in which the specified +feature participates. Unlike L, this method only returns the +subsystem names, not the roles. + +=over 4 + +=item featureID + +ID of the feature whose subsystem names are desired. + +=item RETURN + +Returns a list of the names of the subsystems in which the feature participates. + +=back + +=cut +#: Return Type @; +sub SubsystemList { + # Get the parameters. + my ($self, $featureID) = @_; + # Get the list of names. + my @retVal = $self->GetFlat(['ContainsFeature', 'HasSSCell'], "ContainsFeature(to-link) = ?", + [$featureID], 'HasSSCell(from-link)'); + # Return the result. + return @retVal; } + + =head3 RelatedFeatures C<< my @relatedList = $sprout->RelatedFeatures($featureID, $function, $userID); >> @@ -2189,26 +2700,25 @@ =cut #: Return Type @; sub RelatedFeatures { - # Get the parameters. - my $self = shift @_; - my ($featureID, $function, $userID) = @_; - # Get a list of the features that are BBHs of the incoming feature. - my @bbhFeatures = $self->GetFlat(['IsBidirectionalBestHitOf'], - "IsBidirectionalBestHitOf(from-link) = ?", [$featureID], - 'IsBidirectionalBestHitOf(to-link)'); - # Now we loop through the features, pulling out the ones that have the correct - # functional assignment. - my @retVal = (); - for my $bbhFeature (@bbhFeatures) { - # Get this feature's functional assignment. - my $newFunction = $self->FunctionOf($bbhFeature, $userID); - # If it matches, add it to the result list. - if ($newFunction eq $function) { - push @retVal, $bbhFeature; - } - } - # Return the result list. - return @retVal; + # Get the parameters. + my ($self, $featureID, $function, $userID) = @_; + # Get a list of the features that are BBHs of the incoming feature. + my @bbhFeatures = $self->GetFlat(['IsBidirectionalBestHitOf'], + "IsBidirectionalBestHitOf(from-link) = ?", [$featureID], + 'IsBidirectionalBestHitOf(to-link)'); + # Now we loop through the features, pulling out the ones that have the correct + # functional assignment. + my @retVal = (); + for my $bbhFeature (@bbhFeatures) { + # Get this feature's functional assignment. + my $newFunction = $self->FunctionOf($bbhFeature, $userID); + # If it matches, add it to the result list. + if ($newFunction eq $function) { + push @retVal, $bbhFeature; + } + } + # Return the result list. + return @retVal; } =head3 TaxonomySort @@ -2238,164 +2748,25 @@ =cut #: Return Type @; sub TaxonomySort { - # Get the parameters. - my $self = shift @_; - my ($featureIDs) = @_; - # Create the working hash table. - my %hashBuffer = (); - # Loop through the features. - for my $fid (@{$featureIDs}) { - # Get the taxonomy of the feature's genome. - my ($taxonomy) = $self->GetFlat(['IsLocatedIn', 'HasContig', 'Genome'], "IsLocatedIn(from-link) = ?", - [$fid], 'Genome(taxonomy)'); - # Add this feature to the hash buffer. - if (exists $hashBuffer{$taxonomy}) { - push @{$hashBuffer{$taxonomy}}, $fid; - } else { - $hashBuffer{$taxonomy} = [$fid]; - } - } - # Sort the keys and get the elements. - my @retVal = (); - for my $taxon (sort keys %hashBuffer) { - push @retVal, @{$hashBuffer{$taxon}}; - } - # Return the result. - return @retVal; -} - -=head3 GetAll - -C<< my @list = $sprout->GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count); >> - -Return a list of values taken from the objects returned by a query. The first three -parameters correspond to the parameters of the L method. The final parameter is -a list of the fields desired from each record found by the query. The field name -syntax is the standard syntax used for fields in the B system-- -B(I)>-- where I is the name of the relevant entity -or relationship and I is the name of the field. - -The list returned will be a list of lists. Each element of the list will contain -the values returned for the fields specified in the fourth parameter. If one of the -fields specified returns multiple values, they are flattened in with the rest. For -example, the following call will return a list of the features in a particular -spreadsheet cell, and each feature will be represented by a list containing the -feature ID followed by all of its aliases. - -C<< $query = $sprout->Get(['ContainsFeature', 'Feature'], "ContainsFeature(from-link) = ?", [$ssCellID], ['Feature(id)', 'Feature(alias)']); >> - -=over 4 - -=item objectNames - -List containing the names of the entity and relationship objects to be retrieved. - -=item filterClause - -WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can -be parameterized with parameter markers (C). Each field used must be specified in the standard form -B(I)>. Any parameters specified in the filter clause should be added to the -parameter list as additional parameters. The fields in a filter clause can come from primary -entity relations, relationship relations, or secondary entity relations; however, all of the -entities and relationships involved must be included in the list of object names. - -=item parameterList - -List of the parameters to be substituted in for the parameters marks in the filter clause. - -=item fields - -List of the fields to be returned in each element of the list returned. - -=item count - -Maximum number of records to return. If omitted or 0, all available records will be returned. - -=item RETURN - -Returns a list of list references. Each element of the return list contains the values for the -fields specified in the B parameter. - -=back - -=cut -#: Return Type @@; -sub GetAll { - # Get the parameters. - my $self = shift @_; - my ($objectNames, $filterClause, $parameterList, $fields, $count) = @_; - # Create the query. - my $query = $self->Get($objectNames, $filterClause, $parameterList); - # Set up a counter of the number of records read. - my $fetched = 0; - # Insure the counter has a value. - if (!defined $count) { - $count = 0; - } - # Loop through the records returned, extracting the fields. Note that if the - # counter is non-zero, we stop when the number of records read hits the count. - my @retVal = (); - while (($count == 0 || $fetched < $count) && (my $row = $query->Fetch())) { - my @rowData = $row->Values($fields); - push @retVal, \@rowData; - $fetched++; - } - # Return the resulting list. - return @retVal; -} - -=head3 GetFlat - -C<< my @list = $sprout->GetFlat(\@objectNames, $filterClause, $parameterList, $field); >> - -This is a variation of L that asks for only a single field per record and -returns a single flattened list. - -=over 4 - -=item objectNames - -List containing the names of the entity and relationship objects to be retrieved. - -=item filterClause - -WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can -be parameterized with parameter markers (C). Each field used must be specified in the standard form -B(I)>. Any parameters specified in the filter clause should be added to the -parameter list as additional parameters. The fields in a filter clause can come from primary -entity relations, relationship relations, or secondary entity relations; however, all of the -entities and relationships involved must be included in the list of object names. - -=item parameterList - -List of the parameters to be substituted in for the parameters marks in the filter clause. - -=item field - -Name of the field to be used to get the elements of the list returned. - -=item RETURN - -Returns a list of values. - -=back - -=cut -#: Return Type @; -sub GetFlat { - # Get the parameters. - my $self = shift @_; - my ($objectNames, $filterClause, $parameterList, $field) = @_; - # Construct the query. - my $query = $self->Get($objectNames, $filterClause, $parameterList); - # Create the result list. - my @retVal = (); - # Loop through the records, adding the field values found to the result list. - while (my $row = $query->Fetch()) { - push @retVal, $row->Value($field); - } - # Return the list created. - return @retVal; + # Get the parameters. + my ($self, $featureIDs) = @_; + # Create the working hash table. + my %hashBuffer = (); + # Loop through the features. + for my $fid (@{$featureIDs}) { + # Get the taxonomy of the feature's genome. + my ($taxonomy) = $self->GetFlat(['IsLocatedIn', 'HasContig', 'Genome'], "IsLocatedIn(from-link) = ?", + [$fid], 'Genome(taxonomy)'); + # Add this feature to the hash buffer. + Tracer::AddToListMap(\%hashBuffer, $taxonomy, $fid); + } + # Sort the keys and get the elements. + my @retVal = (); + for my $taxon (sort keys %hashBuffer) { + push @retVal, @{$hashBuffer{$taxon}}; + } + # Return the result. + return @retVal; } =head3 Protein @@ -2425,62 +2796,62 @@ # This is the translation table for protein synthesis. my $ProteinTable = { AAA => 'K', AAG => 'K', AAT => 'N', AAC => 'N', - AGA => 'R', AGG => 'R', AGT => 'S', AGC => 'S', - ATA => 'I', ATG => 'M', ATT => 'I', ATC => 'I', - ACA => 'T', ACG => 'T', ACT => 'T', ACC => 'T', - GAA => 'E', GAG => 'E', GAT => 'D', GAC => 'D', - GTA => 'V', GTG => 'V', GTT => 'V', GTC => 'V', - GGA => 'G', GGG => 'G', GGT => 'G', GGC => 'G', - GCA => 'A', GCG => 'A', GCT => 'A', GCC => 'A', - CAA => 'Q', CAG => 'Q', CAT => 'H', CAC => 'H', - CTA => 'L', CTG => 'L', CTT => 'L', CTC => 'L', - CGA => 'R', CGG => 'R', CGT => 'R', CGC => 'R', - CCA => 'P', CCG => 'P', CCT => 'P', CCC => 'P', - TAA => '*', TAG => '*', TAT => 'Y', TAC => 'Y', - TGA => '*', TGG => 'W', TGT => 'C', TGC => 'C', - TTA => 'L', TTG => 'L', TTT => 'F', TTC => 'F', - TCA => 'S', TCG => 'S', TCT => 'S', TCC => 'S', - AAR => 'K', AAY => 'N', - AGR => 'R', AGY => 'S', - ATY => 'I', - ACR => 'T', ACY => 'T', 'ACX' => 'T', - GAR => 'E', GAY => 'D', - GTR => 'V', GTY => 'V', GTX => 'V', - GGR => 'G', GGY => 'G', GGX => 'G', - GCR => 'A', GCY => 'A', GCX => 'A', - CAR => 'Q', CAY => 'H', - CTR => 'L', CTY => 'L', CTX => 'L', - CGR => 'R', CGY => 'R', CGX => 'R', - CCR => 'P', CCY => 'P', CCX => 'P', - TAR => '*', TAY => 'Y', - TGY => 'C', - TTR => 'L', TTY => 'F', - TCR => 'S', TCY => 'S', TCX => 'S' - }; + AGA => 'R', AGG => 'R', AGT => 'S', AGC => 'S', + ATA => 'I', ATG => 'M', ATT => 'I', ATC => 'I', + ACA => 'T', ACG => 'T', ACT => 'T', ACC => 'T', + GAA => 'E', GAG => 'E', GAT => 'D', GAC => 'D', + GTA => 'V', GTG => 'V', GTT => 'V', GTC => 'V', + GGA => 'G', GGG => 'G', GGT => 'G', GGC => 'G', + GCA => 'A', GCG => 'A', GCT => 'A', GCC => 'A', + CAA => 'Q', CAG => 'Q', CAT => 'H', CAC => 'H', + CTA => 'L', CTG => 'L', CTT => 'L', CTC => 'L', + CGA => 'R', CGG => 'R', CGT => 'R', CGC => 'R', + CCA => 'P', CCG => 'P', CCT => 'P', CCC => 'P', + TAA => '*', TAG => '*', TAT => 'Y', TAC => 'Y', + TGA => '*', TGG => 'W', TGT => 'C', TGC => 'C', + TTA => 'L', TTG => 'L', TTT => 'F', TTC => 'F', + TCA => 'S', TCG => 'S', TCT => 'S', TCC => 'S', + AAR => 'K', AAY => 'N', + AGR => 'R', AGY => 'S', + ATY => 'I', + ACR => 'T', ACY => 'T', 'ACX' => 'T', + GAR => 'E', GAY => 'D', + GTR => 'V', GTY => 'V', GTX => 'V', + GGR => 'G', GGY => 'G', GGX => 'G', + GCR => 'A', GCY => 'A', GCX => 'A', + CAR => 'Q', CAY => 'H', + CTR => 'L', CTY => 'L', CTX => 'L', + CGR => 'R', CGY => 'R', CGX => 'R', + CCR => 'P', CCY => 'P', CCX => 'P', + TAR => '*', TAY => 'Y', + TGY => 'C', + TTR => 'L', TTY => 'F', + TCR => 'S', TCY => 'S', TCX => 'S' + }; sub Protein { - # Get the paraeters. - my ($sequence, $table) = @_; - # If no table was specified, use the default. - if (!$table) { - $table = $ProteinTable; - } - # Create the return value. - my $retVal = ""; - # Loop through the input triples. - my $n = length $sequence; - for (my $i = 0; $i < $n; $i += 3) { - # Get the current triple from the sequence. - my $triple = substr($sequence, $i, 3); - # Translate it using the table. - my $protein = "X"; - if (exists $table->{$triple}) { $protein = $table->{$triple}; } - $retVal .= $protein; - } - # Remove the stop codon (if any). - $retVal =~ s/\*$//; - # Return the result. - return $retVal; + # Get the paraeters. + my ($sequence, $table) = @_; + # If no table was specified, use the default. + if (!$table) { + $table = $ProteinTable; + } + # Create the return value. + my $retVal = ""; + # Loop through the input triples. + my $n = length $sequence; + for (my $i = 0; $i < $n; $i += 3) { + # Get the current triple from the sequence. + my $triple = substr($sequence, $i, 3); + # Translate it using the table. + my $protein = "X"; + if (exists $table->{$triple}) { $protein = $table->{$triple}; } + $retVal .= $protein; + } + # Remove the stop codon (if any). + $retVal =~ s/\*$//; + # Return the result. + return $retVal; } =head3 LoadInfo @@ -2494,19 +2865,19 @@ =cut #: Return Type @; sub LoadInfo { - # Get the parameters. - my $self = shift @_; - # Create the return list, priming it with the name of the data directory. - my @retVal = ($self->{_options}->{dataDir}); - # Concatenate the table names. - push @retVal, $self->{_erdb}->GetTableNames(); - # Return the result. - return @retVal; + # Get the parameters. + my ($self) = @_; + # Create the return list, priming it with the name of the data directory. + my @retVal = ($self->{_options}->{dataDir}); + # Concatenate the table names. + push @retVal, $self->GetTableNames(); + # Return the result. + return @retVal; } =head3 LowBBHs -C<< my %bbhMap = $sprout->GoodBBHs($featureID, $cutoff); >> +C<< my %bbhMap = $sprout->LowBBHs($featureID, $cutoff); >> Return the bidirectional best hits of a feature whose score is no greater than a specified cutoff value. A higher cutoff value will allow inclusion of hits with @@ -2531,29 +2902,178 @@ =cut #: Return Type %; sub LowBBHs { - # Get the parsameters. - my $self = shift @_; - my ($featureID, $cutoff) = @_; - # Create the return hash. - my %retVal = (); - # Create a query to get the desired BBHs. - my @bbhList = $self->GetAll(['IsBidirectionalBestHitOf'], - 'IsBidirectionalBestHitOf(sc) <= ? AND IsBidirectionalBestHitOf(from-link) = ?', - [$cutoff, $featureID], - ['IsBidirectionalBestHitOf(to-link)', 'IsBidirectionalBestHitOf(sc)']); - # Form the results into the return hash. - for my $pair (@bbhList) { - $retVal{$pair->[0]} = $pair->[1]; - } - # Return the result. - return %retVal; + # Get the parsameters. + my ($self, $featureID, $cutoff) = @_; + # Create the return hash. + my %retVal = (); + # Create a query to get the desired BBHs. + my @bbhList = $self->GetAll(['IsBidirectionalBestHitOf'], + 'IsBidirectionalBestHitOf(sc) <= ? AND IsBidirectionalBestHitOf(from-link) = ?', + [$cutoff, $featureID], + ['IsBidirectionalBestHitOf(to-link)', 'IsBidirectionalBestHitOf(sc)']); + # Form the results into the return hash. + for my $pair (@bbhList) { + $retVal{$pair->[0]} = $pair->[1]; + } + # Return the result. + return %retVal; } =head3 GetGroups +C<< my %groups = $sprout->GetGroups(\@groupList); >> + +Return a hash mapping each group to the IDs of the genomes in the group. +A list of groups may be specified, in which case only those groups will be +shown. Alternatively, if no parameter is supplied, all groups will be +included. Genomes that are not in any group are omitted. + =cut #: Return Type %@; sub GetGroups { + # Get the parameters. + my ($self, $groupList) = @_; + # Declare the return value. + my %retVal = (); + # Determine whether we are getting all the groups or just some. + if (defined $groupList) { + # Here we have a group list. Loop through them individually, + # getting a list of the relevant genomes. + for my $group (@{$groupList}) { + my @genomeIDs = $self->GetFlat(['Genome'], "Genome(group-name) = ?", + [$group], "Genome(id)"); + $retVal{$group} = \@genomeIDs; + } + } else { + # Here we need all of the groups. In this case, we run through all + # of the genome records, putting each one found into the appropriate + # group. Note that we use a filter clause to insure that only genomes + # in groups are included in the return set. + my @genomes = $self->GetAll(['Genome'], "Genome(group-name) > ' '", [], + ['Genome(id)', 'Genome(group-name)']); + # Loop through the genomes found. + for my $genome (@genomes) { + # Pop this genome's ID off the current list. + my @groups = @{$genome}; + my $genomeID = shift @groups; + # Loop through the groups, adding the genome ID to each group's + # list. + for my $group (@groups) { + Tracer::AddToListMap(\%retVal, $group, $genomeID); + } + } + } + # Return the hash we just built. + return %retVal; +} + +=head3 MyGenomes + +C<< my @genomes = Sprout::MyGenomes($dataDir); >> + +Return a list of the genomes to be included in the Sprout. + +This method is provided for use during the Sprout load. It presumes the Genome load file has +already been created. (It will be in the Sprout data directory and called either C +or C.) Essentially, it reads in the Genome load file and strips out the genome +IDs. + +=over 4 + +=item dataDir + +Directory containing the Sprout load files. + +=back + +=cut +#: Return Type @; +sub MyGenomes { + # Get the parameters. + my ($dataDir) = @_; + # Compute the genome file name. + my $genomeFileName = LoadFileName($dataDir, "Genome"); + # Extract the genome IDs from the files. + my @retVal = map { $_ =~ /^(\S+)/; $1 } Tracer::GetFile($genomeFileName); + # Return the result. + return @retVal; +} + +=head3 LoadFileName + +C<< my $fileName = Sprout::LoadFileName($dataDir, $tableName); >> + +Return the name of the load file for the specified table in the specified data +directory. + +=over 4 + +=item dataDir + +Directory containing the Sprout load files. + +=item tableName + +Name of the table whose load file is desired. + +=item RETURN + +Returns the name of the file containing the load data for the specified table, or +C if no load file is present. + +=back + +=cut +#: Return Type $; +sub LoadFileName { + # Get the parameters. + my ($dataDir, $tableName) = @_; + # Declare the return variable. + my $retVal; + # Check for the various file names. + if (-e "$dataDir/$tableName") { + $retVal = "$dataDir/$tableName"; + } elsif (-e "$dataDir/$tableName.dtx") { + $retVal = "$dataDir/$tableName.dtx"; + } + # Return the result. + return $retVal; +} + +=head3 DeleteGenome + +C<< my $stats = $sprout->DeleteGenome($genomeID, $testFlag); >> + +Delete a genome from the database. + +=over 4 + +=item genomeID + +ID of the genome to delete + +=item testFlag + +If TRUE, then the DELETE statements will be traced, but no deletions will occur. + +=item RETURN + +Returns a statistics object describing the rows deleted. + +=back + +=cut +#: Return Type $%; +sub DeleteGenome { + # Get the parameters. + my ($self, $genomeID, $testFlag) = @_; + # Perform the delete for the genome's features. + my $retVal = $self->Delete('Feature', "fig|$genomeID.%", $testFlag); + # Perform the delete for the primary genome data. + my $stats = $self->Delete('Genome', $genomeID, $testFlag); + $retVal->Accumulate($stats); + # Return the result. + return $retVal; } =head2 Internal Utility Methods @@ -2561,13 +3081,28 @@ =head3 ParseAssignment Parse annotation text to determine whether or not it is a functional assignment. If it is, -the user and function text will be returned as a 2-element list. If it isn't, an empty list -will be returned. +the user, function text, and assigning user will be returned as a 3-element list. If it +isn't, an empty list will be returned. + +A functional assignment is always of the form + + CIC< function to\n>I + +where I is the B, and I is the actual functional role. In most cases, +the user and the assigning user (from MadeAnnotation) will be the same, but that is +not always the case. + +In addition, the functional role may contain extra data that is stripped, such as +terminating spaces or a comment separated from the rest of the text by a tab. This is a static method. =over 4 +=item user + +Name of the assigning user. + =item text Text of the annotation. @@ -2581,19 +3116,27 @@ =cut -sub ParseAssignment { - # Get the parameters. - my ($text) = @_; - # Declare the return value. - my @retVal = (); - # Check to see if this is a functional assignment. - my ($user, $type, $function) = split(/\n/, $text); - if ($type =~ m/^set $user function to$/i) { - # Here it is, so we return the user name and function text. - @retVal = ($user, $function); - } - # Return the result list. - return @retVal; +sub _ParseAssignment { + # Get the parameters. + my ($user, $text) = @_; + # Declare the return value. + my @retVal = (); + # Check to see if this is a functional assignment. + my ($type, $function) = split(/\n/, $text); + if ($type =~ m/^set function to$/i) { + # Here we have an assignment without a user, so we use the incoming user ID. + @retVal = ($user, $function); + } elsif ($type =~ m/^set (\S+) function to$/i) { + # Here we have an assignment with a user that is passed back to the caller. + @retVal = ($1, $function); + } + # If we have an assignment, we need to clean the function text. There may be + # extra junk at the end added as a note from the user. + if (@retVal) { + $retVal[1] =~ s/(\t\S)?\s*$//; + } + # Return the result list. + return @retVal; } =head3 FriendlyTimestamp @@ -2618,8 +3161,66 @@ sub FriendlyTimestamp { my ($timeValue) = @_; - my $retVal = strftime("%a %b %e %H:%M:%S %Y", localtime($timeValue)); + my $retVal = localtime($timeValue); return $retVal; } +=head3 AddProperty + +C<< my = $sprout->AddProperty($featureID, $key, $value, $url); >> + +Add a new attribute value (Property) to a feature. In the SEED system, attributes can +be added to almost any object. In Sprout, they can only be added to features. In +Sprout, attributes are implemented using I. A property represents a key/value +pair. If the particular key/value pair coming in is not already in the database, a new +B record is created to hold it. + +=over 4 + +=item peg + +ID of the feature to which the attribute is to be replied. + +=item key + +Name of the attribute (key). + +=item value + +Value of the attribute. + +=item url + +URL or text citation from which the property was obtained. + +=back + +=cut +#: Return Type ; +sub AddProperty { + # Get the parameters. + my ($self, $featureID, $key, $value, $url) = @_; + # Declare the variable to hold the desired property ID. + my $propID; + # Attempt to find a property record for this key/value pair. + my @properties = $self->GetFlat(['Property'], + "Property(property-name) = ? AND Property(property-value) = ?", + [$key, $value], 'Property(id)'); + if (@properties) { + # Here the property is already in the database. We save its ID. + $propID = $properties[0]; + # Here the property value does not exist. We need to generate an ID. It will be set + # to a number one greater than the maximum value in the database. This call to + # GetAll will stop after one record. + my @maxProperty = $self->GetAll(['Property'], "ORDER BY Property(id) DESC", [], ['Property(id)'], + 1); + $propID = $maxProperty[0]->[0] + 1; + # Insert the new property value. + $self->Insert('Property', { 'property-name' => $key, 'property-value' => $value, id => $propID }); + } + # Now we connect the incoming feature to the property. + $self->Insert('HasProperty', { 'from-link' => $featureID, 'to-link' => $propID, evidence => $url }); +} + + 1; \ No newline at end of file