ABI

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ABI.pm  view on Meta::CPAN

	#print "****", $self->{_mac_header}, "\n";
	return $self;
}

sub _init {
	my ( $self, @args ) = @_;
	my ($file) = $self->_rearrange( ["FILE"], @args );
	if ( !defined($file) ) {
		croak "Can't open the input file\n";
	} else {
		$self->set_file_handle($file);
	}
	$self->{_sequence}             = "";
	$self->{_sequence_corrected}   = "";
	$self->{_sample}               = "";
	$self->{A}                     = [];
	$self->{T}                     = [];
	$self->{G}                     = [];
	$self->{C}                     = [];
	$self->{_basecalls}            = [];
	$self->{_basecalls_corrected}  = [];

ABI.pm  view on Meta::CPAN

	$self->{DATA12}                = undef;
	$self->{PBAS1}                 = undef;
	$self->{PBAS2}                 = undef;
	$self->{FWO}                   = undef;
	$self->{_mac_header}           = 0;
	$self->{_maximum_trace}        = 0;

	if ( $self->_is_abi() ) {

		#print "ABI FILE\n";
		$self->_set_index();
		$self->_set_base_calls();
		$self->_set_corrected_base_calls();
		$self->_set_seq();
		$self->_set_corrected_seq();
		$self->_set_traces();
		$self->_set_max_trace();
		$self->_set_sample_name();
		close( $self->{_fh} );
	}
	return $self;
}

sub set_file_handle {
	my $self = shift;
	my $path = shift;
	my $fh   = IO::File->new();
	if ( $fh->open("< $path") ) {
		binmode($fh);
		$self->{_fh} = $fh;
	} else {
		croak "Could not open $path in ABITrace::set_file_handle\n";
	}
}

sub _rearrange {
	my ( $self, $order, @param ) = @_;
	return unless @param;
	return @param unless ( defined( $param[0] ) && $param[0] =~ /^-/ );
	for ( my $i = 0 ; $i < @param ; $i += 2 ) {
		$param[$i] =~ s/^\-//;
		$param[$i] =~ tr/a-z/A-Z/;

ABI.pm  view on Meta::CPAN

	seek( $fh, 0, 0 );
	read( $fh, $buf, 3 );

	#my $a = unpack("n*", $buf);
	if ( $buf eq "ABI" ) {
		return 1;
	} else {
		seek( $fh, 128, 0 );
		read( $fh, $buf, 3 );
		if ( $buf eq "ABI" ) {
			$self->_set_mac_header();
			return 1;
		} else {
			return 0;
		}
	}
}

sub _set_mac_header {
	my $self = shift;
	$self->{_mac_header} = 128;
}

sub _set_index {
	my $self         = shift;
	my $data_counter = 0;
	my $pbas_counter = 0;
	my $ploc_counter = 0;
	my ( $num_records, $buf );

	#print $self->{_fh}, "\n";
	#print $self->{_mac_header}, "\n";
	seek( $self->{_fh}, $self->{_abs_index} + $self->{_mac_header}, 0 );
	read( $self->{_fh}, $buf, 4 );

ABI.pm  view on Meta::CPAN

	$self->{PLOC1}  = $self->_get_int( $self->{PLOC1} ) + $self->{_mac_header};
	$self->{DATA9}  = $self->_get_int( $self->{DATA9} ) + $self->{_mac_header};
	$self->{DATA10} = $self->_get_int( $self->{DATA10} ) + $self->{_mac_header};
	$self->{DATA11} = $self->_get_int( $self->{DATA11} ) + $self->{_mac_header};
	$self->{DATA12} = $self->_get_int( $self->{DATA12} ) + $self->{_mac_header};
	$self->{PBAS1}  = $self->_get_int( $self->{PBAS1} ) + $self->{_mac_header};
	$self->{PBAS2}  = $self->_get_int( $self->{PBAS2} ) + $self->{_mac_header};
	$self->{SMPL} += $self->{_mac_header};
}

sub _set_base_calls {
	my $self = shift;
	my $buf;
	my $length = $self->{_seq_length} * 2;
	my $fh     = $self->{_fh};
	seek( $fh, $self->{PLOC}, 0 );
	read( $fh, $buf, $length );
	@{ $self->{_basecalls} } = unpack( "n" x $length, $buf );

	# print "@{$self->{_basecalls}}" , "\n";
}

sub _set_corrected_base_calls {
	my $self = shift;
	my $buf;
	my $length = $self->{_seq_length_corrected} * 2;
	my $fh     = $self->{_fh};
	seek( $fh, $self->{PLOC1}, 0 );
	read( $fh, $buf, $length );
	@{ $self->{_basecalls_corrected} } = unpack( "n" x $length, $buf );
}

sub _set_seq {
	my $self = shift;
	my $buf;
	my $length = $self->{_seq_length};
	my $fh     = $self->{_fh};
	seek( $fh, $self->{PBAS2}, 0 );
	read( $fh, $buf, $length );
	$self->{_sequence} = $buf;

	#my @seq = unpack( "C" x $length, $buf);
	#print $buf, "\n";
}

sub _set_corrected_seq {
	my $self = shift;
	my $buf;
	my $length = $self->{_seq_length_corrected};
	my $fh     = $self->{_fh};
	seek( $fh, $self->{PBAS1}, 0 );
	read( $fh, $buf, $length );
	$self->{_sequence_corrected} = $buf;
}

sub _set_traces {
	my $self = shift;
	my $buf;
	my ( @pointers, @A, @G, @C, @T );
	my (@datas) =
	  ( $self->{DATA9}, $self->{DATA10}, $self->{DATA11}, $self->{DATA12} );
	my $fh = $self->{_fh};
	seek( $fh, $self->{FWO}, 0 );
	read( $fh, $buf, 4 );
	my @order = split( //, $buf );

ABI.pm  view on Meta::CPAN

sub _get_int {
	my $self = shift;
	my $buf;
	my $pos = shift;
	my $fh  = $self->{_fh};
	seek( $fh, $pos, 0 );
	read( $fh, $buf, 4 );
	return unpack( "N", $buf );
}

sub _set_max_trace {
	my $self = shift;
	my @A    = @{ $self->{A} };
	my @T    = @{ $self->{T} };
	my @G    = @{ $self->{G} };
	my @C    = @{ $self->{C} };
	my $max  = 0;
	for ( my $i = 0 ; $i < @T ; $i++ ) {
		if ( $T[$i] > $max ) { $max = $T[$i]; }
		if ( $A[$i] > $max ) { $max = $A[$i]; }
		if ( $G[$i] > $max ) { $max = $G[$i]; }
		if ( $C[$i] > $max ) { $max = $C[$i]; }
	}
	$self->{_maximum_trace} = $max;
}

sub _set_sample_name {
	my $self = shift;
	my $buf;
	my $fh = $self->{_fh};
	seek( $fh, $self->{SMPL}, 0 );
	read( $fh, $buf, 1 );
	my $length = unpack( "C", $buf );
	read( $fh, $buf, $length );
	$self->{_sample} = $buf;
}