File Coverage

lib/Bio/Roary/AccessoryClustering.pm

Criterion	Covered	Total	%
statement	15	45	33.3
branch	0	4	0.0
condition			n/a
subroutine	5	7	71.4
pod			n/a
total	20	56	35.7

package Bio::Roary::AccessoryClustering;
$Bio::Roary::AccessoryClustering::VERSION = '3.10.2';
# ABSTRACT: Take an a clusters file from CD-hit and the fasta file and output a fasta file without full clusters


use Moose;
use Bio::Roary::External::Cdhit;
with 'Bio::Roary::ClustersRole';

has 'input_file'              => ( is => 'ro', isa => 'Str',     required => 1 );
has 'identity'                => ( is => 'ro', isa => 'Num',     default  => 0.9 );
has 'cpus'                    => ( is => 'ro', isa => 'Int',      default  => 1 );
has '_output_cd_hit_filename' => ( is => 'ro', isa => 'Str',     default  => '_accessory_clusters' );
has 'clusters_to_samples'     => ( is => 'ro', isa => 'HashRef', lazy     => 1, builder => '_build_clusters_to_samples' );
has 'samples_to_clusters'     => ( is => 'ro', isa => 'HashRef', lazy     => 1, builder => '_build_samples_to_clusters' );
has 'sample_weights'          => ( is => 'ro', isa => 'HashRef', lazy     => 1, builder => '_build_sample_weights' );
has 'clusters_filename'       => ( is => 'ro', isa => 'Str',     lazy     => 1, builder => '_build_clusters_filename' );
has 'clusters'                => ( is => 'ro', isa => 'HashRef', lazy     => 1, builder => '_build__clusters' );

sub _build_sample_weights {
    my ($self) = @_;
    my %sample_weights;
    for my $cluster_name ( keys %{ $self->clusters_to_samples } ) {
        my $cluster_size = @{ $self->clusters_to_samples->{$cluster_name} };
        for my $sample_name ( @{ $self->clusters_to_samples->{$cluster_name} } ) {
            $sample_weights{$sample_name} = 1 / $cluster_size;
        }
    }
    return \%sample_weights;
}

sub _build_samples_to_clusters {
    my ($self) = @_;
    my %samples_to_clusters;
    for my $cluster_name ( keys %{ $self->clusters_to_samples } ) {
        for my $sample_name ( @{ $self->clusters_to_samples->{$cluster_name} } ) {
            $samples_to_clusters{$sample_name} = $cluster_name;
        }
    }
    return \%samples_to_clusters;
}

sub _build_clusters_filename {
    my ($self) = @_;
    return $self->_output_cd_hit_filename . '.clstr';
}

sub _build_clusters_to_samples {
    my ($self) = @_;

    my $cdhit_obj = Bio::Roary::External::Cdhit->new(
        input_file                   => $self->input_file,
        output_base                  => $self->_output_cd_hit_filename,
        _length_difference_cutoff    => 1,
        _sequence_identity_threshold => $self->identity,
		cpus                         => $self->cpus
    );
    $cdhit_obj->run();
    my $clusterd_genes = $self->_clustered_genes;

    for my $cluster_name ( keys %{$clusterd_genes} ) {
        my $found = 0;
        for my $gene_name ( @{ $clusterd_genes->{$cluster_name} } ) {
            if ( $gene_name eq $cluster_name ) {
                $found = 1;
                last;
            }
        }

        if ( $found == 0 ) {
            push( @{ $clusterd_genes->{$cluster_name} }, $cluster_name );
        }
    }

    return $clusterd_genes;
}

no Moose;
__PACKAGE__->meta->make_immutable;

1;

__END__

=pod

=encoding UTF-8

=head1 NAME

Bio::Roary::AccessoryClustering - Take an a clusters file from CD-hit and the fasta file and output a fasta file without full clusters

=head1 VERSION

version 3.10.2

=head1 SYNOPSIS

Take an a clusters file from CD-hit and the fasta file and output a fasta file without full clusters
   use Bio::Roary::AccessoryClustering;

   my $obj = Bio::Roary::AccessoryClustering->new(
       input_file        => 'accessory_binary_genes.fa',
       identity           => 0.96,
       cpus => 10,
     );
   $obj->sample_weights();

=head1 AUTHOR

Andrew J. Page <[e-mail]>

=head1 COPYRIGHT AND LICENSE

This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.

This is free software, licensed under:

  The GNU General Public License, Version 3, June 2007

=cut