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lib/Bio/MUST/Apps/Debrief42/TaxReport.pm  view on Meta::CPAN

package Bio::MUST::Apps::Debrief42::TaxReport;
# ABSTRACT: Front-end class for tabular tax-report parser
# CONTRIBUTOR: Mick VAN VLIERBERGHE <mvanvlierberghe@doct.uliege.be>
$Bio::MUST::Apps::Debrief42::TaxReport::VERSION = '0.213470';
use Moose;
use namespace::autoclean;

use autodie;
use feature qw(say);

use List::AllUtils qw(mesh);

extends 'Bio::FastParsers::Base';

use Bio::MUST::Core;
use Bio::MUST::Core::Utils qw(change_suffix);
use Bio::FastParsers::Constants qw(:files);
use aliased 'Bio::MUST::Apps::Debrief42::TaxReport::NewSeq';

use Smart::Comments;

# 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 = ( NewSeq->heads, 'outfile' );

sub next_seq {
    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;

        # process TaxReport line