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lib/Bio/MUST/Core/PostPred/Composition.pm  view on Meta::CPAN

package Bio::MUST::Core::PostPred::Composition;
# ABSTRACT: Posterior predictive test for compositional bias
$Bio::MUST::Core::PostPred::Composition::VERSION = '0.252040';
use Moose;
use namespace::autoclean;

use autodie;
use feature qw(say);

# use Smart::Comments;

use List::AllUtils qw(sum);
use Tie::IxHash;

use Bio::MUST::Core::Types;


has 'seqs' => (
    is       => 'ro',
    isa      => 'Bio::MUST::Core::Ali',
    required => 1,
    coerce   => 1,
    handles  => [
        qw(gapmiss_regex all_seqs)
    ],
);

# TODO: consider a role if more tests are implemented

# private hash containing compositional biases
# Note: this hash is actually a Tie::IxHash (see builder)
has '_stat_for' => (
    traits   => ['Hash'],
    is       => 'ro',
    isa      => 'HashRef[Num]',
    init_arg => undef,
    lazy     => 1,
    builder  => '_build_stat_for',
    handles  => {
         all_ids => 'keys',
        stat_for => 'get',
    },
);

## no critic (ProhibitUnusedPrivateSubroutines)

sub _build_stat_for {
    my $self = shift;

        my %glb_freq_for;
    tie my %seq_freq_for, 'Tie::IxHash';

    my $regex = $self->gapmiss_regex;
    my $glb_tot = 0;

    # loop through seqs to store state freqs
    for my $seq ($self->all_seqs) {
        my %freq_for;
        my $seq_tot = 0;

        STATE:
        for my $state ($seq->all_states) {
            $state = uc $state;

            # skip missing/gap states