Provided by: libbio-perl-perl_1.6.923-1_all 
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.