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

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

use autodie;

use List::AllUtils qw(mesh);

extends 'Bio::FastParsers::Base';

use Bio::FastParsers::Constants qw(:files);
use aliased 'Bio::FastParsers::Hmmer::Table::Hit';


# public attributes (inherited)


# private attributes

has '_line_iterator' => (
    traits   => ['Code'],
    is       => 'ro',
    isa      => 'CodeRef',
    init_arg => undef,
    lazy     => 1,
    builder  => '_build_line_iterator',
    handles  => {
        _next_line => 'execute',
    },
);

## no critic (ProhibitUnusedPrivateSubroutines)

sub _build_line_iterator {
    my $self = shift;

    open my $fh, '<', $self->file;      # autodie
    return sub { <$fh> };               # return closure
}

## use critic

my @attrs = qw(
    target_name target_accession
     query_name  query_accession
             evalue          score          bias
    best_dom_evalue best_dom_score best_dom_bias
    exp reg clu ov env dom rep inc
    target_description
);      # DID try to use MOP to get Hit attrs but order was not preserved


sub next_hit {
    my $self = shift;

    LINE:
    while (my $line = $self->_next_line) {

        # skip header/comments and empty lines
        chomp $line;
        next LINE if $line =~ $COMMENT_LINE
                  || $line =~ $EMPTY_LINE;