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

package Bio::MUST::Apps::Leel::AliProcessor;
# ABSTRACT: Internal class for leel tool
$Bio::MUST::Apps::Leel::AliProcessor::VERSION = '0.213470';
use Moose;
use namespace::autoclean;

use autodie;
use feature qw(say);

use Smart::Comments -ENV;

use Carp;
use File::Basename;
use List::AllUtils 'uniq';
use Path::Class qw(file);
use Test::Deep::NoTest 'eq_deeply';

use Bio::MUST::Core;
use Bio::MUST::Core::Utils qw(:filenames secure_outfile);
use aliased 'Bio::MUST::Core::Ali';
use aliased 'Bio::MUST::Core::GeneticCode::Factory';
use aliased 'Bio::MUST::Apps::SlaveAligner::Local';
use aliased 'Bio::MUST::Apps::Leel::OrgProcessor';

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


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


has '+ali' => (
    handles  => {
        protein_for => 'get_seq_with_id',
    },
);


has 'cds_ali' => (
    is       => 'ro',
    isa      => 'Bio::MUST::Core::Ali',
    init_arg => undef,
    lazy     => 1,
    builder  => '_build_cds_ali',
);


## no critic (ProhibitUnusedPrivateSubroutines)

sub _build_cds_ali {
    return Ali->new( file => shift->ali->filename );
}


sub _build_integrator {
    return Local->new( ali => shift->cds_ali );
}

## use critic


sub _check_ali_by_translation {