File Coverage

blib/lib/GenOO/Data/File/SAM.pm

Criterion	Covered	Total	%
statement	47	51	92.1
branch	11	14	78.5
condition			n/a
subroutine	10	11	90.9
pod	0	3	0.0
total	68	79	86.0

# POD documentation - main docs before the code

=head1 NAME

GenOO::Data::File::SAM - Object implementing methods for accessing SAM formatted files

=head1 SYNOPSIS

    # Object that manages a sam file.

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


=head1 DESCRIPTION

    This object implements methods to read a sam file line by line.

=head1 EXAMPLES

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

    # Read one record at a time
    my $sam_record = $sam_file->next_record();

=cut

# Let the code begin...

package GenOO::Data::File::SAM;
$GenOO::Data::File::SAM::VERSION = '1.4.6';

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


#######################################################################
#######################   Interface attributes   ######################
#######################################################################
has 'file' => (
	isa      => 'Maybe[Str]', # undef value makes the parser read from STDIN
	is       => 'ro',
	required => 1,
);

has 'records_read_count' => (
	traits  => ['Counter'],
	is      => 'ro',
	isa     => 'Num',
	default => 0,
	handles => {
		_inc_records_read_count   => 'inc',
		_reset_records_read_count => 'reset',
	},
);

has 'records_class' => (
	is        => 'ro',
	default   => 'GenOO::Data::File::SAM::Record',
);

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

has '_is_eof_reached' => (
	traits  => ['Bool'],
	is      => 'rw',
	isa     => 'Bool',
	default => 0,
	handles => {
		_set_eof_reached   => 'set',
		_unset_eof_reached => 'unset',
		_eof_not_reached   => 'not',
	},
);

has '_cached_header_lines' => (
	traits  => ['Array'],
	is      => 'ro',
	default => sub { [] },
	handles => {
		_all_cached_header_lines    => 'elements',
		_add_header_line_in_cache   => 'push',
		_shift_cached_header_line   => 'shift',
		_has_cached_header_lines    => 'count',
		_has_no_cached_header_lines => 'is_empty',
		_cached_header_lines_count  => 'count',
		_clear_cached_header_lines  => 'clear'
	},
);

has '_cached_record' => (
	is        => 'rw',
	clearer   => '_clear_cached_record',
	predicate => '_has_cached_record',
);


#######################################################################
##############################   BUILD   ##############################
#######################################################################
sub BUILD {
	my $self = shift;

	eval "require ".$self->records_class;
	$self->_parse_header_section;
}


#######################################################################
########################   Interface Methods   ########################
#######################################################################
sub next_record {
	my ($self) = @_;

	my $record;
	if ($self->_has_cached_record) {
		$record = $self->_cached_record;
		$self->_clear_cached_record;
	}
	else {
		$record = $self->_next_record_from_file;
	}

	$self->_inc_records_read_count if defined $record;

	return $record;
}

sub header {
	my ($self) = @_;

	return join("\n", $self->_all_cached_header_lines);
}


#######################################################################
#########################   Private Methods   #########################
#######################################################################
sub _parse_header_section {
	my ($self) = @_;

	while (my $line = $self->_filehandle->getline) {
		if ($line =~ /^\@/) {
			chomp($line);
			$self->_add_header_line_in_cache($line);
		}
		else {
			# When the while reads the first line after the header section
			# we need to process it immediatelly because in zipped files we cannot go back
			my $record = $self->_parse_record_line($line);
			$self->_cached_record($record);
			return;
		}
	}
}

sub _next_record_from_file {
	my ($self) = @_;

	my $line = $self->_filehandle->getline;
	if (defined $line) {
		return $self->_parse_record_line($line);
	}
	else {
		$self->_set_eof_reached;
		return undef;
	}
}

sub _parse_record_line {
	my ($self,$line) = @_;

	chomp $line;
	my @fields = split(/\t/,$line);
	return $self->records_class->new(fields => \@fields);
}

sub _open_filehandle {
	my ($self) = @_;

	my $read_mode;
	my $HANDLE;
	if (!defined $self->file) {
		open ($HANDLE, '<-', $self->file);
	}
	elsif ($self->file =~ /\.gz$/) {
		die 'Cannot open file ' . $self->file . "\n" if ! -e $self->file;
		open($HANDLE, 'gzip -dc ' . $self->file . ' |');
	}
	else {
		open ($HANDLE, '<', $self->file);
	}

	return $HANDLE;
}


#######################################################################
############################   Finalize   #############################
#######################################################################
__PACKAGE__->meta->make_immutable;

1;