NAME

Bio::DB::GFF::Aggregator -- Aggregate GFF groups into composite features

SYNOPSIS

 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',
				 );

DESCRIPTION

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:

• method

  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.

• main method

  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.

• subparts

  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:

• disaggregate()

  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.

• aggregate()

  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:

• method()

  Return the default method for the composite feature as a whole.

• main_name()

  Return the default main method name.

• part_names()

  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 base qw(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',
				 );

API

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.

strict_match

Title   : strict_match
Usage   : $strict = $a->strict_match
Function: generate a hashref that indicates which subfeatures
          need to be tested strictly for matching sources before
          aggregating
Returns : a hash ref
Status  : Internal

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.

BUGS

None known yet.

SEE ALSO

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

AUTHOR

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.

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq