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|
=head1 NAME
Bio::DB::GFF::Aggregator::clone -- Clone aggregator
=head1 SYNOPSIS
use Bio::DB::GFF;
# Open the sequence database
my $db = Bio::DB::GFF->new( -adaptor => 'dbi:mysql',
-dsn => 'dbi:mysql:elegans42',
-aggregator => ['transcript','clone'],
);
----------------------------------------------------------------------------
Aggregator method: clone
Main method: -none-
Sub methods: Clone_left_end Clone_right_end region:Genomic_canonical
----------------------------------------------------------------------------
=head1 DESCRIPTION
Bio::DB::GFF::Aggregator::clone is one of the default aggregators, and
was written to be compatible with the C elegans GFF files. It
aggregates raw "Clone_left_end", "Clone_right_end", and
"region:Genomic_canonical" features into composite features of type
"clone".
=cut
package Bio::DB::GFF::Aggregator::clone;
$Bio::DB::GFF::Aggregator::clone::VERSION = '1.7.4';
use strict;
use base qw(Bio::DB::GFF::Aggregator);
=head2 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 L<Bio::DB::GFF::Aggregator>
Status : Public
The WormBase GFF model is unusual in that clones aren't identified as
a single feature with start and stop positions, but as two features, a
"left end" and a "right end". One or both of these features may be
absent. In order to accommodate this, the aggregator will return undef
for the start and/or stop if one or both of the ends are missing.
=cut
#'
# we look for features of type Sequence and add them to a pseudotype transcript
sub aggregate {
my $self = shift;
my $features = shift;
my $factory = shift;
my $matchsub = $self->match_sub($factory) or return;
my $passthru = $self->passthru_sub($factory);
my $method = $self->get_method;
my (%clones,%types,@result);
for my $feature (@$features) {
if ($feature->group && $matchsub->($feature)) {
if ($feature->method =~ /^region|Sequence$/ && $feature->source eq 'Genomic_canonical') {
$clones{$feature->group}{canonical} = $feature;
} elsif ($feature->method eq 'Clone_left_end') {
$clones{$feature->group}{left} = $feature;
} elsif ($feature->method eq 'Clone_right_end') {
$clones{$feature->group}{right} = $feature;
}
push @result,$feature if $passthru && $passthru->($feature);
} else {
push @result,$feature;
}
}
for my $clone (keys %clones) {
my $canonical = $clones{$clone}{canonical} or next;
# the genomic_canonical doesn't tell us where the clone starts and stops
# so don't assume it
my $duplicate = $canonical->clone; # make a duplicate of the feature
# munge the method and source fields
my $source = $duplicate->source;
my $type = $types{$method,$source} ||= Bio::DB::GFF::Typename->new($method,$source);
$duplicate->type($type);
my ($start,$stop) = $duplicate->strand > 0 ? ('start','stop') : ('stop','start');
@{$duplicate}{$start,$stop} =(undef,undef);
$duplicate->{$start} = $clones{$clone}{left}{$start} if exists $clones{$clone}{left};
$duplicate->{$stop} = $clones{$clone}{right}{$stop} if exists $clones{$clone}{right};
$duplicate->method($self->method);
push @result,$duplicate;
}
@$features = @result;
}
=head2 method
Title : method
Usage : $aggregator->method
Function: return the method for the composite object
Returns : the string "clone"
Args : none
Status : Public
=cut
sub method { 'clone' }
=head2 part_names
Title : part_names
Usage : $aggregator->part_names
Function: return the methods for the sub-parts
Returns : the list ("Clone_left_end", "Clone_right_end", "region:Genomic_canonical")
Args : none
Status : Public
=cut
sub part_names {
my $self = shift;
return qw(Clone_left_end Clone_right_end region:Genomic_canonical Sequence:Genomic_canonical);
}
1;
__END__
=head1 BUGS
None reported.
=head1 SEE ALSO
L<Bio::DB::GFF>, L<Bio::DB::GFF::Aggregator>
=head1 AUTHOR
Lincoln Stein E<lt>lstein@cshl.orgE<gt>.
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.
=cut
|
