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

BioPerl documentation Contained in the BioPerl distribution.

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NAME

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

SYNOPSIS

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 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

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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:

Aggregators have two main methods that can be overridden in subclasses:

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:

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

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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

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None known yet.

SEE ALSO

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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

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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.

BioPerl documentation Contained in the BioPerl distribution. 
package Bio::DB::GFF::Aggregator;

use strict;
use Bio::DB::GFF::Util::Rearrange;  # for rearrange()
use Bio::DB::GFF::Feature;

use base qw(Bio::Root::Root);

my $ALWAYS_TRUE   = sub { 1 };


sub new {
  my $class = shift;
  my ($method,$main,$sub_parts,$whole_object) = rearrange(['METHOD',
							   ['MAIN_PART','MAIN_METHOD'],
							   ['SUB_METHODS','SUB_PARTS'],
							   'WHOLE_OBJECT'
							  ],@_);
  return bless {
		method      => $method,
		main_method => $main,
		sub_parts   => $sub_parts,
		require_whole_object => $whole_object,
	       },$class;
}


# this is called at the beginning to turn the pseudo-type 
# into its component feature types
sub disaggregate {
  my $self  = shift;
  my $types = shift;
  my $factory = shift;

  my $sub_features = $factory->parse_types($self->get_part_names);
  my $main_feature = $factory->parse_types($self->get_main_name);

  if (@$types) {
    my (@synthetic_types,@unchanged);
    foreach (@$types) {
      my ($method,$source) = @$_;
      if (lc $method eq lc $self->get_method) { # e.g. "transcript"
	push @synthetic_types,map { [$_->[0],$_->[1] || $source] } @$sub_features,@$main_feature;
      }
      else {
	push @unchanged,$_;
      }
    }
    # remember what we're searching for
    $self->components(\@synthetic_types);
    $self->passthru(\@unchanged);
    @$types = (@unchanged,@synthetic_types);
  }

  # we get here when no search types are listed
  else {
    my @stypes = map { [$_->[0],$_->[1]] }  @$sub_features,@$main_feature;
    $self->components(\@stypes);
    $self->passthru(undef);
  }

  return $self->component_count > 0;
}



sub aggregate {
  my $self = shift;
  my $features = shift;
  my $factory  = shift;

  my $main_method = $self->get_main_name;
  my $matchsub    = $self->match_sub($factory) or return;
  my $strictmatch = $self->strict_match();
  my $passthru    = $self->passthru_sub($factory);

  my (%aggregates,@result);
  for my $feature (@$features) {

    if ($feature->group && $matchsub->($feature)) {
      my $key = $strictmatch->{lc $feature->method,lc $feature->source} 
          ? join ($;,$feature->group,$feature->refseq,$feature->source)
          : join ($;,$feature->group,$feature->refseq);
      if ($main_method && lc $feature->method eq lc $main_method) {
	$aggregates{$key}{base} ||= $feature->clone;
      } else {
	push @{$aggregates{$key}{subparts}},$feature;
      }
      push @result,$feature if $passthru && $passthru->($feature);

    } else {
      push @result,$feature;
    }
  }

  # aggregate components
  my $pseudo_method        = $self->get_method;
  my $require_whole_object = $self->require_whole_object;
  foreach (keys %aggregates) {
    if ($require_whole_object && $self->components) {
      next unless $aggregates{$_}{base}; # && $aggregates{$_}{subparts};
    }
    my $base = $aggregates{$_}{base};
    unless ($base) { # no base, so create one
      my $first = $aggregates{$_}{subparts}[0];
      $base = $first->clone;     # to inherit parent coordinate system, etc
      $base->score(undef);
      $base->phase(undef);
    }
    $base->method($pseudo_method);
    $base->add_subfeature($_) foreach @{$aggregates{$_}{subparts}};
    $base->adjust_bounds;
    $base->compound(1);  # set the compound flag
    push @result,$base;
  }
  @$features = @result;
}



# default method - override in subclasses
sub method {
  my $self = shift;
  $self->{method};
}


# no default main method
sub main_name {
  my $self = shift;
  return;
}


# no default part names
sub part_names {
  my $self = shift;
  return;
}


sub require_whole_object {
  my $self = shift;
  my $d    = $self->{require_whole_object};
  $self->{require_whole_object} = shift if @_;
  $d;
}


#' make emacs happy

sub match_sub {
  my $self    = shift;
  my $factory = shift;
  my $types_to_aggregate = $self->components() or return;  # saved from disaggregate call
  return unless @$types_to_aggregate;
  return $factory->make_match_sub($types_to_aggregate);
}


sub strict_match {
  my $self = shift;
  my $types_to_aggregate = $self->components();
  my %strict;
  for my $t (@$types_to_aggregate) {
    $strict{lc $t->[0],lc $t->[1]}++ if defined $t->[1];
  }
  \%strict;
}

sub passthru_sub {
  my $self    = shift;
  my $factory = shift;
  my $passthru = $self->passthru() or return;
  return unless @$passthru;
  return $factory->make_match_sub($passthru);
}


sub components {
  my $self = shift;
  my $d = $self->{components};
  $self->{components} = shift if @_;
  return unless ref $d;
  return wantarray ? @$d : $d;
}

sub component_count {
  my @c = shift->components;
  scalar @c;
}

sub passthru {
  my $self = shift;
  my $d = $self->{passthru};
  $self->{passthru} = shift if @_;
  return unless ref $d;
  return wantarray ? @$d : $d;
}

sub clone {
  my $self = shift;
  my %new = %{$self};
  return bless \%new,ref($self);
}


sub get_part_names {
  my $self = shift;
  if ($self->{sub_parts}) {
    return ref $self->{sub_parts} ? @{$self->{sub_parts}} : $self->{sub_parts};
  } else {
    return $self->part_names;
  }
}


sub get_main_name {
  my $self = shift;
  return $self->{main_method} if defined $self->{main_method};
  return $self->main_name;
}


sub get_method {
  my $self = shift;
  return $self->{method} if defined $self->{method};
  return $self->method;
}

1;