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lib/Bio/MUST/Apps/HmmCleaner/Process.pm  view on Meta::CPAN

package Bio::MUST::Apps::HmmCleaner::Process;
# ABSTRACT: Process class for HmmCleaner
# CONTRIBUTOR: Denis BAURAIN <denis.baurain@uliege.be>
$Bio::MUST::Apps::HmmCleaner::Process::VERSION = '0.243280';
use Moose;
use namespace::autoclean;

use Carp;
use Smart::Comments -ENV;
use Modern::Perl;

use Bio::MUST::Core 0.180230;
use Bio::MUST::Core::Constants qw(:gaps :files);
use Bio::FastParsers::Hmmer;
use aliased 'Bio::MUST::Core::Seq';

####### [PROCESS] Value of env verbosity : scalar(split ' ', $ENV{Smart_Comments})

# ATTRIBUTES
has 'ali' => (
    is          => 'ro',
    isa         => 'Bio::MUST::Core::Ali',
    required    => 1,
);

has 'seq' => (
    is          => 'ro',
    isa         => 'Bio::MUST::Core::Seq',
    required    => 1,
);

has 'model' => (
    is          => 'ro',
    isa         => 'Bio::MUST::Drivers::Hmmer::Model::Temporary',
    required    => 1,
);

has 'nogap_seq' => (
    is          => 'ro',
    isa         => 'Bio::MUST::Core::Seq',
    lazy        => 1,
    builder     => '_build_nogap_seq',
);

has 'parser' => (
    is          => 'ro',
    isa         => 'Bio::FastParsers::Hmmer::Standard',
    lazy        => 1,
    builder     => '_build_parser',
);

has 'score' => (
    is          => 'ro',
    isa         => 'Str',
    lazy        => 1,
    builder     => '_build_scoreseq',
);

has 'consider_X' => (
    is          => 'ro',
    isa         => 'Bool',
    default     => 1,
);

has 'debug_mode' => (
    is          => 'ro',