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lib/Bio/FastParsers/Hmmer/Standard/Iteration.pm  view on Meta::CPAN

package Bio::FastParsers::Hmmer::Standard::Iteration;
# ABSTRACT: Front-end class for standard HMMER parser
# CONTRIBUTOR: Arnaud DI FRANCO <arnaud.difranco@gmail.com>
$Bio::FastParsers::Hmmer::Standard::Iteration::VERSION = '0.221230';
use Moose;
use namespace::autoclean;

use autodie;

use List::AllUtils qw(indexes firstidx mesh);

use Bio::FastParsers::Constants qw(:files);
use aliased 'Bio::FastParsers::Hmmer::Standard::Target';


# public attributes

has 'query' => (
    is       => 'ro',
    isa      => 'Str',
    required => 1,
);

has 'query_length' => (
    is       => 'ro',
    isa      => 'Int',
    required => 1,
);

has 'targets' => (
    traits   => ['Array'],
    is       => 'ro',
    isa      => 'ArrayRef[Bio::FastParsers::Hmmer::Standard::Target]',
    required => 1,
    handles  => {
         next_target  => 'shift',
          get_target  => 'get',
          all_targets => 'elements',
        count_targets => 'count',
    },
);

## no critic (ProhibitUnusedPrivateSubroutines)

around BUILDARGS => sub {
    my ($orig, $class, $iter_block) = @_;

    my %outargs;
    my @hits;

    # Parse Iteration to separate header information (q, qlen), header hit
    # table (Hit) and main output information per target (Target).
    # Hit and Target are the same entity but Hit is close to what is retrieved
    # from a Hmmer::Table output. For now, we chose to conserve Target as
    # primary name since it is how it is called in the file.

    my @lines = split /\n/xms, $iter_block;

    LINE:
    for my $line (@lines) {

        # parse header
        if ($line =~ m/Query:/xms) {
            my @fields = split /\s+/xms, $line;
              $outargs{'query'}        = $fields[1];
            ( $outargs{'query_length'} = $fields[2] ) =~ s/\D//xmsg;