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

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

use autodie;
use feature qw(say);

use Smart::Comments -ENV;

use Carp;
use Const::Fast;
use File::Basename;
use List::AllUtils qw(first part partition_by pairmap);
use Path::Class qw(file);
use POSIX;
use Sort::Naturally;
use Tie::IxHash;

use Bio::MUST::Core;
use Bio::MUST::Core::Utils qw(:filenames secure_outfile);
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::Apps::SlaveAligner::Local';
use aliased 'Bio::MUST::Apps::FortyTwo::OrgProcessor';
use aliased 'Bio::MUST::Apps::Debrief42::TaxReport::NewSeq';

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


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


has '+ali' => (
    handles  => [ qw(all_new_seqs all_but_new_seqs) ],
);


has 'lookup' => (
    is       => 'ro',
    isa      => 'Bio::MUST::Core::IdList',
    init_arg => undef,
    lazy     => 1,
    builder  => '_build_lookup',
);


has 'blastdb' => (
    is       => 'ro',
    isa      => 'Bio::MUST::Drivers::Blast::Database::Temporary',
    init_arg => undef,
    lazy     => 1,
    builder  => '_build_blastdb',
);