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ABI.pm  view on Meta::CPAN

  my @trace_g = $abi->get_trace("G"); # Get the raw traces for "G"
  my @base_calls = $abi->get_base_calls(); # Get the base calls

=head1 DESCRIPTION

An ABI chromatogram file is in binary format. It contain several 
information only some of which is required for normal use. This
module only gives access to the most used information stored in
ABI file. All the accesses are read only.

If you have edited the file using a trace editor, then you can use the corresponding 
method to access the edited sequence and base calls.



=head1 CONSTRUCTOR

=head2 new()

  Usage : $abi = ABI->new(-file=>"filename");
          $abi = ABI->new("filename"); # same thing

ABI.pm  view on Meta::CPAN

		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};

ABI.pm  view on Meta::CPAN

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} };
}