Bio::DB::GFF::Aggregator -- Aggregate GFF groups into composite features use Bio::DB::GFF; my $agg1 = Bio::DB::GFF::Aggregator->new(-method => 'cistron', -main_method => 'locus', -sub_parts => ['allele','variant'] ); my $agg2 = Bio::DB::GFF::Aggregator->new(-method => 'splice_group', -sub_parts => 'transcript'); my $db = Bio::DB::GFF->new( -adaptor => 'dbi:mysql', -aggregator => [$agg1,$agg2], -dsn => 'dbi:mysql:elegans42', ); Bio::DB::GFF::Aggregator is used to aggregate GFF groups into composite features. Each composite feature has a "main part", the top-level feature, and a series of zero or more subparts, retrieved with the sub_SeqFeature() method. The aggregator class is designed to be subclassable, allowing a variety of GFF feature types to be supported. The base Bio::DB::GFF::Aggregator class is generic, and can be used to create specific instances to be passed to the -aggregator argument of Bio::DB::GFF->new() call. The various subclasses of Bio::DB::GFF::Aggregator are tuned for specific common feature types such as clones, gapped alignments and transcripts. Instances of Bio::DB::GFF::Aggregator have three attributes: This is the GFF method field of the composite feature as a whole. For example, "transcript" may be used for a composite feature created by aggregating individual intron, exon and UTR features. Sometimes GFF groups are organized hierarchically, with one feature logically containing another. For example, in the C. elegans schema, methods of type "Sequence:curated" correspond to regions covered by curated genes. There can be zero or one main methods. This is a list of one or more methods that correspond to the component features of the aggregates. For example, in the C. elegans database, the subparts of transcript are "intron", "exon" and "CDS". Aggregators have two main methods that can be overridden in subclasses: This method is called by the Adaptor object prior to fetching a list of features. The method is passed an associative array containing the [method,source] pairs that the user has requested, and it returns a list of raw features that it would like the adaptor to fetch. This method is called by the Adaptor object after it has fetched features. The method is passed a list of raw features and is expected to add its composite features to the list. The disaggregate() and aggregate() methods provided by the base Aggregator class should be sufficient for many applications. In this case, it suffices for subclasses to override the following methods: Return the default method for the composite feature as a whole. Return the default main method name. Return a list of subpart method names. Provided that method() and part_names() are overridden (and optionally main_name() as well), then the bare name of the aggregator subclass can be passed to the -aggregator of Bio::DB::GFF->new(). For example, this is a small subclass that will aggregate features of type "allele" and "polymorphism" into an aggregate named "mutant": package Bio::DB::GFF::Aggregator::mutant; use strict; use Bio::DB::GFF::Aggregator; use vars '@ISA'; @ISA = 'Bio::DB::GFF::Aggregator'; sub method { 'mutant' } sub part_names { return qw(allele polymorphism); } 1; Once installed, this aggregator can be passed to Bio::DB::GFF->new() by name like so: my $db = Bio::DB::GFF->new( -adaptor => 'dbi:mysql', -aggregator => 'mutant', -dsn => 'dbi:mysql:elegans42', ); The remainder of this document describes the public and private methods implemented by this module.

new
Title : new Usage : $a = Bio::DB::GFF::Aggregator->new(@args) Function: create a new aggregator Returns : a Bio::DB::GFF::Aggregator object Args : see below Status : Public This is the constructor for Bio::DB::GFF::Aggregator. Named arguments are as follows: -method the method for the composite feature -main_method the top-level raw feature, if any -sub_parts the list of raw features that will form the subparts of the composite feature (array reference or scalar)

disaggregate
Title : disaggregate Usage : $a->disaggregate($types,$factory) Function: disaggregate type list into components Returns : a true value if this aggregator should be called to reaggregate Args : see below Status : Public This method is called to disaggregate a list of types into the set of low-level features to be retrieved from the GFF database. The list of types is passed as an array reference containing a series of [method,source] pairs. This method synthesizes a new set of [method,source] pairs, and appends them to the list of requested types, changing the list in situ. Arguments: $types reference to an array of [method,source] pairs $factory reference to the Adaptor object that is calling this method Note that the API allows disaggregate() to remove types from the type list. This feature is probably not desirable and may be deprecated in the future.

aggregate
Title : aggregate Usage : $features = $a->aggregate($features,$factory) Function: aggregate a feature list into composite features Returns : an array reference containing modified features Args : see below Status : Public This method is called to aggregate a list of raw GFF features into the set of composite features. The method is called an array reference to a set of Bio::DB::GFF::Feature objects. It runs through the list, creating new composite features when appropriate. The method result is an array reference containing the composite features. Arguments: $features reference to an array of Bio::DB::GFF::Feature objects $factory reference to the Adaptor object that is calling this method NOTE: The reason that the function result contains the raw features as well as the aggregated ones is to allow queries like this one: @features = $segment->features('exon','transcript:curated'); Assuming that "transcript" is the name of an aggregated feature and that "exon" is one of its components, we do not want the transcript aggregator to remove features of type "exon" because the user asked for them explicitly.

method
Title : method Usage : $string = $a->method Function: get the method type for the composite feature Returns : a string Args : none Status : Protected This method is called to get the method to be assigned to the composite feature once it is aggregated. It is called if the user did not explicitly supply a -method argument when the aggregator was created. This is the method that should be overridden in aggregator subclasses.

main_name
Title : main_name Usage : $string = $a->main_name Function: get the method type for the "main" component of the feature Returns : a string Args : none Status : Protected This method is called to get the method of the "main component" of the composite feature. It is called if the user did not explicitly supply a -main-method argument when the aggregator was created. This is the method that should be overridden in aggregator subclasses.

part_names
Title : part_names Usage : @methods = $a->part_names Function: get the methods for the non-main various components of the feature Returns : a list of strings Args : none Status : Protected This method is called to get the list of methods of the "main component" of the composite feature. It is called if the user did not explicitly supply a -main-method argument when the aggregator was created. This is the method that should be overridden in aggregator subclasses.

require_whole_object
Title : require_whole_object Usage : $bool = $a->require_whole_object Function: see below Returns : a boolean flag Args : none Status : Internal This method returns true if the aggregator should refuse to aggregate an object unless both its main part and its subparts are present.

match_sub
Title : match_sub Usage : $coderef = $a->match_sub($factory) Function: generate a code reference that will match desired features Returns : a code reference Args : see below Status : Internal This method is used internally to generate a code sub that will quickly filter out the raw features that we're interested in aggregating. The returned sub accepts a Feature and returns true if we should aggregate it, false otherwise.

components
Title : components Usage : @array= $a->components([$components]) Function: get/set stored list of parsed raw feature types Returns : an array in list context, an array ref in scalar context Args : new arrayref of feature types Status : Internal This method is used internally to remember the parsed list of raw features that we will aggregate. The need for this subroutine is seen when a user requests a composite feature of type "clone:cosmid". This generates a list of components in which the source is appended to the method, like "clone_left_end:cosmid" and "clone_right_end:cosmid". components() stores this information for later use.

get_part_names
Title : get_part_names Usage : @array = $a->get_part_names Function: get list of sub-parts for this type of feature Returns : an array Args : none Status : Internal This method is used internally to fetch the list of feature types that form the components of the composite feature. Type names in the format "method:source" are recognized, as are "method" and Bio::DB::GFF::Typename objects as well. It checks instance variables first, and if not defined calls the part_names() method.

get_main_name
Title : get_main_name Usage : $string = $a->get_main_name Function: get the "main" method type for this feature Returns : a string Args : none Status : Internal This method is used internally to fetch the type of the "main part" of the feature. It checks instance variables first, and if not defined calls the main_name() method.

get_method
Title : get_method Usage : $string = $a->get_method Function: get the method type for the composite feature Returns : a string Args : none Status : Internal This method is used internally to fetch the type of the method that will be assigned to the composite feature once it is synthesized. None known yet. Bio::DB::GFF, Bio::DB::GFF::Aggregator::alignment, Bio::DB::GFF::Aggregator::clone, Bio::DB::GFF::Aggregator::coding, Bio::DB::GFF::Aggregator::match, Bio::DB::GFF::Aggregator::processed_transcript, Bio::DB::GFF::Aggregator::transcript, Bio::DB::GFF::Aggregator::none Lincoln Stein <lstein@cshl.org>. Copyright (c) 2001 Cold Spring Harbor Laboratory. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.