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lib/Bio/MUST/Apps/SlaveAligner/Local.pm  view on Meta::CPAN

package Bio::MUST::Apps::SlaveAligner::Local;
# ABSTRACT: Internal class for slave-aligner
$Bio::MUST::Apps::SlaveAligner::Local::VERSION = '0.213470';
use Moose;
use namespace::autoclean;

use autodie;
use feature qw(say switch);
use experimental qw(smartmatch);        # to suppress warnings about 'when'

use Smart::Comments -ENV;

use List::AllUtils qw(max);
use Sort::Naturally;

use Bio::MUST::Core;
use aliased 'Bio::MUST::Core::Seq';


# _delayed_indels is a hash (site) of hashes (new_seq id)
# storing the number of insertions caused by each new_seq at each
# pos (as if each new_seq was added on its own to the Ali)

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


has '_delayed_indels' => (
    traits   => ['Hash'],
    is       => 'ro',
    isa      => 'HashRef[HashRef[Num]]',
    init_arg => undef,
    default  => sub { {} },
    handles  => {
        all_sites => 'keys',
        indels_at => 'get',
    },
);


sub align {                                 ## no critic (RequireArgUnpacking)
    my $self = shift;
    my %args = @_;

	my (
	    $query,                 #  new_seq as aligned in BLAST report
	    $sbjct,                 # template as aligned in BLAST report
	    $tmplt,                 # template as aligned in Ali
	    $splcd,
	    $start                  # pairwise alignment start in template
	) = @args{ qw(new_seq subject template cds_seq start) };

    # determine mode (prot/nucl) based on absence/presence of a DNA seq
    # setup multiplier according to mode
    my $mul = defined $splcd ? 3 : 1;

    # align query left-end on template
    for (my $u = 0; $u < $start; $u++) {
        $start++ if $tmplt->is_gap($u);
    }
    my $aligned_seq = q{ } x ( ($start-1) * $mul );