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lib/Bio/MUST/Apps/FortyTwo/RunProcessor.pm  view on Meta::CPAN

package Bio::MUST::Apps::FortyTwo::RunProcessor;
# ABSTRACT: Internal class for forty-two tool
$Bio::MUST::Apps::FortyTwo::RunProcessor::VERSION = '0.213470';
use Moose;
use namespace::autoclean;

use autodie;
use feature qw(say);

use Smart::Comments;                    # logging always enabled here

use Carp;
use List::AllUtils;
use Path::Class qw(dir file);

use Parallel::Batch;

use Bio::MUST::Core;
use Bio::MUST::Drivers;
use aliased 'Bio::MUST::Apps::FortyTwo::AliProcessor';

with 'Bio::MUST::Apps::Roles::RunProcable',
     'Bio::MUST::Core::Roles::Taxable';


has 'run_mode' => (
    is       => 'ro',
    isa      => 'Str',
    default  => 'phylogenomic',
);

has '+out_suffix' => (
    default  => '-42',
);


has 'query_orgs' => (
    traits   => ['Array'],
    is       => 'ro',
    isa      => 'ArrayRef[Str]',
    required => 1,
    handles  => {
        'count_query_orgs' => 'count',
          'all_query_orgs' => 'elements',
    },
);


# blast_args


has 'ref_brh' => (
    is       => 'ro',
    isa      => 'Str',
    default  => 'on',
);

has 'ref_bank_dir' => (
    is       => 'ro',
    isa      => 'Str',
);

has 'ref_org_mapper' => (
    is       => 'ro',
    isa      => 'Bio::MUST::Core::IdMapper',