view release on metacpan or  search on metacpan

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

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

use autodie;
use feature qw(say);

use Smart::Comments -ENV;

use Carp;
use Const::Fast;
use List::AllUtils qw(each_array pairmap);
use Path::Class qw(file);
use Tie::IxHash;

use Bio::MUST::Core;
use Bio::MUST::Core::Constants qw(:gaps :ncbi);
use Bio::MUST::Core::Utils qw(:filenames);
use Bio::MUST::Drivers;
use aliased 'Bio::MUST::Core::Ali';
use aliased 'Bio::MUST::Core::Ali::Temporary';
use aliased 'Bio::MUST::Core::IdList';
use aliased 'Bio::MUST::Core::Seq';
use aliased 'Bio::MUST::Core::SeqId';
use aliased 'Bio::MUST::Core::SeqMask';
use aliased 'Bio::MUST::Drivers::Cap3';
use aliased 'Bio::MUST::Apps::Debrief42::TaxReport::NewSeq';

with 'Bio::MUST::Apps::Roles::OrgProcable';


# org

# banks

# code


has 'ali_proc' => (
    is       => 'ro',
    isa      => 'Bio::MUST::Apps::FortyTwo::AliProcessor',
    required => 1,
);


has 'tax_filter' => (
    is       => 'ro',
    isa      => 'Maybe[ArrayRef[Str]]',
);


has '_tax_filter' => (
    is       => 'ro',
    isa      => 'Maybe[Bio::MUST::Core::Taxonomy::Filter]',
    init_arg => undef,
    writer   => '_set_tax_filter',
    handles  => [ qw(is_allowed) ],
);


has $_ . '_seqs' => (
    is       => 'ro',
    isa      => 'Bio::MUST::Core::Ali::Temporary',