Bio-Trace-ABIF

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lib/Bio/Trace/ABIF.pm  view on Meta::CPAN

  Returns   : The average peak spacing used in last analysis;
              undef if the data item is not in the file.
  ABIF Tag  : SPAC1
  ABIF Type : float
  File Type : ab1
  
This data item is from SeqScape(R) v2.5 and Sequencing Analysis v5.2 Software.

=cut

sub avg_peak_spacing() {
	my $self = shift;
	unless (defined $self->{'_SPAC1'}) {
		my $s = undef;
		($s) = $self->get_data_item('SPAC', 1, 'B32');
		$self->{'_SPAC1'} = $self->_ieee2decimal($s) if (defined $s);
	}
	return $self->{'_SPAC1'};
}

=head2 basecaller_apsf()

lib/Bio/Trace/ABIF.pm  view on Meta::CPAN

  Returns   : The spacing;
              undef if the data item is not in the file.
  ABIF Tag  : SPAC3
  ABIF Type : float
  File Type : ab1
 
This data item is from SeqScape(R) v2.5 and Sequencing Analysis v5.2 Software.

=cut

sub base_spacing() {
	my $self = shift;
	unless (defined $self->{'_SPAC3'}) {
		my $s = undef;
		($s) = $self->get_data_item('SPAC', 3, 'B32');
		$self->{'_SPAC3'} = $self->_ieee2decimal($s) if (defined $s);

	}
	return $self->{'_SPAC3'};
}

lib/Bio/Trace/ABIF.pm  view on Meta::CPAN

=head2 edited_sequence_length()

  Usage     : $l = edited_sequence_length();
  Returns   : The length of the basecalled sequence;
              0 if the sequence is not in the file.
  File Type : ab1
  
=cut

sub edited_sequence_length() {
	my $self = shift;
	my $seq = $self->edited_sequence();
	return 0 unless defined $seq;
	return length($seq);
}

=head2 electrophoresis_voltage()

  Usage     : $v = $abif->electrophoresis_voltage();
  Returns   : The electrophoresis voltage setting in volts;

lib/Bio/Trace/ABIF.pm  view on Meta::CPAN

=head2 sequence_length()

  Usage    : $l = sequence_length();
  Returns  : The length of the base called sequence;
             0 if the sequence is not in the file.
  File Type : ab1
  
=cut

sub sequence_length() {
	my $self = shift;
	my $seq = $self->sequence();
	return 0 unless defined $seq;
	return length($seq);
}

=head2 sequencing_analysis_param_filename()

  Usage     : $f = sequencing_analysis_param_filename();
  Returns   : The Sequencing Analysis parameters filename;