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lib/GenOO/Data/File/FASTA.pm  view on Meta::CPAN

# POD documentation - main docs before the code

=head1 NAME

GenOO::Data::File::FASTA - Object implementing methods for accessing fasta formatted files (http://genome.ucsc.edu/FAQ/FAQformat#format1)

=head1 SYNOPSIS

    # Object that manages a fasta file.

    # To initialize
    my $fasta_parser = GenOO::Data::File::FASTA->new(
        file            => undef,
    );

=head1 DESCRIPTION

    This object offers methods to read a fasta file line by line.

=head1 EXAMPLES

    # Create object
    my $fasta_parser = GenOO::Data::File::FASTA->new(
          file => 't/sample_data/sample.fasta.gz'
    );

    # Read one record at a time
    my $record = $fasta_parser->next_record;

    # Get the number of records read
    my $count = $fasta_parser->records_read_count;

=cut

# Let the code begin...

package GenOO::Data::File::FASTA;
$GenOO::Data::File::FASTA::VERSION = '1.5.2';

#######################################################################
#######################   Load External modules   #####################
#######################################################################
use Modern::Perl;
use autodie;
use Moose;
use namespace::autoclean;


#######################################################################
#########################   Load GenOO modules   ######################
#######################################################################
use GenOO::Data::File::FASTA::Record;


#######################################################################
#######################   Interface attributes   ######################
#######################################################################
has 'file' => (
	isa      => 'Maybe[Str]',
	is       => 'rw',
	required => 1
);

has 'records_read_count' => (
	is        => 'rw',
	default   => 0,
	init_arg  => undef,
);

has '_filehandle' => (
	is        => 'ro',
	builder   => '_open_filehandle',
	init_arg  => undef,
	lazy      => 1,
);

has '_stored_record_header' => (
	is        => 'rw',
	clearer   => '_clear_stored_record_header',
	predicate => '_has_stored_record_header',
	init_arg  => undef,
);

has '_stored_record_sequence_parts' => (
        traits  => ['Array'],
        is      => 'rw',
        isa     => 'ArrayRef[Str]',
        default => sub { [] },
        handles => {
            _all_record_sequence_parts    => 'elements',
            _add_record_sequence_part     => 'push',
            _join_record_sequence_parts   => 'join',
            _clear_record_sequence_parts  => 'clear',
        },
    );

has '_eof' => (
	is        => 'rw',
	predicate => '_reached_eof',
	init_arg  => undef
);