view release on metacpan or  search on metacpan

ABI.pm  view on Meta::CPAN

}

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;
}

=head1 METHODS

=head2 get_max_trace()

  Title    :  get_max_trace()
  Usage    :  $max = $abi->get_max_trace();
  Function :  Returns the maximum trace value of all the traces.
  Args     :  Nothing
  Returns  :  A scalar

=cut

sub get_max_trace {
	my $self = shift;
	return $self->{_maximum_trace};
}

=head2 get_trace()

  Title    :  get_trace()
  Usage    :  my @a = $abi->get_trace("A");
  Function :  Returns the raw traces as array.
  Args     :  "A" or "G" or "C" or "T"
  Returns  :  An array

=cut

sub get_trace {
	my $self   = shift;
	my $symbol = shift;
	if ( $symbol =~ /A/i ) {
		return @{ $self->{A} };
	} elsif ( $symbol =~ /G/i ) {
		return @{ $self->{G} };
	} elsif ( $symbol =~ /C/i ) {
		return @{ $self->{C} };
	} elsif ( $symbol =~ /T/i ) {
		return @{ $self->{T} };
	} else {
		croak "Illegal symbol\n";
	}
}

=head2 get_sequence()

  Title    : get_sequence()
  Usage    : my $seq = $abi->get_sequence();
  Function : Returns the original unedited sequence as string. If you want to access the edited
             sequence use "get_corrected_sequence()" instead.
  Args     : Nothing
  Returns  : A scalar

=cut

sub get_sequence {
	my $self = shift;
	return $self->{_sequence};
}

=head2 get_corrected_sequence()

  Title    : get_corrected_sequence()
  Usage    : my $seq = $abi->get_corrected_sequence();
  Function : Returns the corrected sequence as string. If you want to access the original 
             unedited sequence, use "get_sequence()" instead.
  Args     : Nothing
  Returns  : A scalar

=cut

sub get_corrected_sequence {
	my $self = shift;
	return $self->{_sequence_corrected};
}

=head2 get_sequence_length()

  Title    : get_sequence_length()
  Usage    : my $seq_length = $abi->get_sequence_length();
  Function : Returns the sequence length of the orginal unedited sequence.
  Args     : Nothing
  Returns  : A scalar

=cut

sub get_sequence_length {
	my $self = shift;
	return $self->{_seq_length};
}

=head2 get_corrected_sequence_length()

  Title    : get_corrected_sequence_length()
  Usage    : my $seq_length = $abi->get_corrected_sequence_length();
  Function : Returns the length of the edited sequence. 
  Args     : Nothing
  Returns  : A scalar

=cut

sub get_corrected_sequence_length {
	my $self = shift;

	#print STDERR "**ABI**",$self->{_seq_length_corrected},"\n";
	return $self->{_seq_length_corrected};
}

=head2 get_trace_length()

  Title    : get_trace_length()
  Usage    : my $trace_length = $abi->get_trace_length();
  Function : Returns the trace length
  Args     : Nothing
  Returns  : A scalar

=cut

sub get_trace_length {
	my $self = shift;
	return $self->{_trace_length};
}

=head2 get_base_calls()

  Title    : get_base_calls()
  Usage    : my @base_calls = $abi->get_base_calls();
  Function : Returns the called bases by the base caller. This method will return the unedited 
  	         original basecalls created by the basecaller.
  Args     : Nothing
  Returns  : An array

=cut

sub get_base_calls {
	my $self = shift;
	return @{ $self->{_basecalls} };
}

=head2 get_corrected_base_calls()

  Title    : get_corrected_base_calls()
  Usage    : my @base_calls = $abi->get_corrected_base_calls();
  Function : If you have edited the trace file you can get the corrected base call 
             with this method
  Args     : Nothing
  Returns  : An array

=cut

sub get_corrected_base_calls {
	my $self = shift;
	return @{ $self->{_basecalls_corrected} };
}

=head2 get_sample_name()

  Title    : get_sample_name()
  Usage    : my $sample = $abi->get_sample_name();
  Function : Returns hard coded sample name
  Args     : Nothing
  Returns  : A scalar

=cut

sub get_sample_name {
	my $self = shift;
	return $self->{_sample};
}

=head1 AUTHOR

Malay <malay@bioinformatics.org>

=head1 BUGS

Please report any bugs or feature requests to
C<bug-abi at rt.cpan.org>, or through the web interface at
L<http://rt.cpan.org/NoAuth/ReportBug.html?Queue=ABI>.
I will be notified, and then you'll automatically be notified of progress on
your bug as I make changes.

or 

You can directly contact me to my email address.


=head1 SUPPORT