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lib/Bio/MUST/Drivers/CdHit.pm  view on Meta::CPAN

package Bio::MUST::Drivers::CdHit;
# ABSTRACT: Bio::MUST driver for running the CD-HIT program
# CONTRIBUTOR: Amandine BERTRAND <amandine.bertrand@doct.uliege.be>
# CONTRIBUTOR: Valerian LUPO <valerian.lupo@uliege.be>
$Bio::MUST::Drivers::CdHit::VERSION = '0.252830';
use Moose;
use namespace::autoclean;

use autodie;
use feature qw(say);

# use Smart::Comments;

use Array::Utils qw(:all);
use Carp;
use IPC::System::Simple qw(system);
use List::AllUtils qw(sort_by);
use Module::Runtime qw(use_module);
use Path::Class qw(file);
use Tie::IxHash;

use Bio::MUST::Core;
extends 'Bio::MUST::Core::Ali::Temporary';

use Bio::MUST::Drivers::Utils qw(stringify_args);
use aliased 'Bio::MUST::Core::Ali';
use aliased 'Bio::MUST::Core::SeqId';
use aliased 'Bio::FastParsers::CdHit';


has 'cdhit_args' => (
    is       => 'ro',
    isa      => 'HashRef',
    default  => sub { {} },
);

has '_cluster_seq_ids' => (
    traits   => ['Hash'],
    is       => 'ro',
    isa      => 'HashRef[ArrayRef[Bio::MUST::Core::SeqId]]',
    init_arg => undef,
    writer   => '_set_cluster_seq_ids',
    handles  => {
        all_cluster_names   => 'keys',
        all_cluster_seq_ids => 'values',
        seq_ids_for         => 'get',
    },
);

has '_representatives' => (
    is       => 'ro',
    isa      => 'Bio::MUST::Core::Ali',
    init_arg => undef,
    writer   => '_set_representatives',
    handles  => {
          all_representatives        =>   'all_seqs',
        count_representatives        => 'count_seqs',
          get_representative_with_id =>   'get_seq_with_id',    # useless?
    },
);

has '_representative_for' => (
    traits   => ['Hash'],
    is       => 'ro',
    isa      => 'HashRef[Bio::MUST::Core::Seq]',
    init_arg => undef,
    lazy     => 1,