Provided by: libbio-scf-perl_1.03-2build2_amd64 
NAME
Bio::SCF - Perl extension for reading and writing SCF sequence files
SYNOPSIS
use Bio::SCF;
# tied interface tie %hash,'Bio::SCF','my_scf_file.scf';
my $sequence_length = $hash{bases_length}; my $chromatogram_sample_length =
$hash{samples_length}; my $third_base = $hash{bases}[2]; my $quality_score =
$hash{$third_base}[2]; my $sample_A_at_time_1400 = $hash{samples}{A}[1400];
# change the third base and write out new file $hash{bases}[2] = 'C'; tied (%hash)->write('new.scf');
# object-oriented interface my $scf = Bio::SCF->new('my_scf_file.scf'); my
$sequence_length = $scf->bases_length; my $chromatogram_sample_length = $scf->samples_length;
my $third_base = $scf->bases(2); my $quality_score = $scf->score(2); my
$sample_A_at_time_1400 = $scf->sample('A',1400);
# change the third base and write out new file $scf->bases(2,'C'); $scf->write('new.scf');
DESCRIPTION
This module provides a perl interface to SCF DNA sequencing files. It has both tied hash and an object-
oriented interfaces. It provides the ability to read fields from SCF files and limited ability to modify
them and write them back.
Tied Methods
$obj = tie %hash,'Bio::SCF',$filename_or_handle
Tie the Bio::SCF module to a filename or filehandle. If successful, tie() will return the object.
$value = $hash{'key'}
Fetch a field from the SCF file. Valid keys are as follows:
Key Value
--- -----
bases_length Number of called bases in the sequence (read-only)
samples_length Number of samples in the file (read-only)
version SCF version (read-only)
code_set Code set used to code bases (read-only)
comments Structured comments (read-only)
bases Array reference to a list of the base calls
index Array reference to a list of the sample position
for each of the base calls (e.g. the position of
the base calling peak)
A An array reference that can be used to determine the
probability that the base in position $i is an "A".
G An array reference that can be used to determine the
probability that the base in position $i is a "G".
C An array reference that can be used to determine the
probability that the base in position $i is a "C".
T An array reference that can be used to determine the
probability that the base in position $i is a "T".
samples A hash reference with keys "A", "C", "G" and "T". The
value of each hash is an array reference to the list
of intensity values for each sample.
To get the length of the called sequence: $scf{bases_length}
To get the value of the called sequence at position 3: $scf{bases}[3]
To get the sample position at which base 3 was called: $scf{index}[3]
To get the value of the "C" curve under base 3: $scf{samples}{C}[$scf{index}[3]]
To get the probability that base 3 is a "C": $scf{C}[3]
To print out the chromatogram as a four-column list:
my $samples = $scf{samples};
for (my $i = 0; $i<$scf{samples_length}; $i++) {
print join "\t",$samples->{C}[$i],$samples->{G}[$i],
$samples->{A}[$i],$samples->{T}[$i],"\n";
}
$scf{bases}[$index] = $new_value
The base call probability scores, base call values, base call positions, and sample values are all
read/write, so that you can change them:
$samples->{C}[500] = 0;
each %scf
Will return keys and values for the tied object.
delete $scf{$key}
%scf = ()
These operations are not supported and will return a run-time error
Object Methods
$scf = Bio::SCF->new($scf_file_or_filehandle)
Create a new Bio::SCF object. The single argument is the name of a file or a previously-opened
filehandle. If successful, new() returns the Bio::SCF object.
$length = $scf->bases_length
Return the length of the called sequence.
$samples = $scf->samples_length
Return the length of the list of chromatogram samples in the file. There are four sample series, one
for each base.
$sample_size = $scf->sample_size
Returns the size of each sample (bytes).
$code_set = $scf->code_set
Return the code set used for base calling.
$base = $scf->base($base_no [,$new_base])
Get the base call at the indicated position. If a new value is provided, will change the base call to
the indicated base.
$index = $scf->index($base_no [,$new_index])
Translates the indicated base position into the sample index for that called base. Here is how to
fetch the intensity values at base number 5:
my $sample_index = $scf->index(5);
my ($g,$a,$t,$c) = map { $scf->sample($_,$sample_index) } qw(G A T C);
If you provide a new value for the sample index, it will be updated.
$base_score = $scf->base_score($base,$base_no [,$new_score])
Get the probability that the indicated base occurs at position $base_no. Here is how to fetch the
probabilities for the four bases at base position 5:
my ($g,$a,$t,$c) = map { $scf->base_score($_,5) } qw(G A T C);
If you provide a new value for the base probability score, it will be updated.
$score = $scf->score($base_no)
Get the quality score for the called base at the indicated position.
$intensity = $scf->sample($base,$sample_index [,$new_value])
Get the intensity value for the channel corresponding to the indicated base at the indicated sample
index. You may update the intensity by providing a new value.
$scf->write('file_path')
Write the updated SCF file to the indicated file path.
$scf->fwrite($file_handle)
Write the updated SCF file to the indicated filehandle. The file must previously have been opened for
writing. The filehandle is actually reopened in append mode, so you can call fwrite() multiple times
and interperse your own record separators.
EXAMPLES
Reading information from a preexisting file:
tie %scf, 'Bio::SCF', "data.scf";
print "Base calls:\n";
for ( my $i=0; $i<$scf{bases}; $i++ ){
print "$scf{base}[$i] ";
}
print "\n";
print "Intensity values for the A curve\n";
for ( my $i=0; $i<$scf{samples}; $i++ ){
print "$scf{sample}{A}[$i];
}
print "\n";
Another example, where we set all bases to "A", indexes to 10 and write the file back:
my $obj = tie %scf,'Bio::SCF','data.scf';
for (0...@{$scf{bases}}-1){
$scf{base}[$_] = "A";
$obj->set('index', $_, 10);
}
$obj->write('data.scf');
AUTHOR
Dmitri Priimak, priimak@cshl.org (1999)
with some cleanups by Lincoln Stein, lstein@cshl.edu (2006)
This package and its accompanying libraries is free software; you can redistribute it and/or modify it
under the terms of the GPL (either version 1, or at your option, any later version) or the Artistic
License 2.0. Refer to LICENSE for the full license text. In addition, please see DISCLAIMER for
disclaimers of warranty.
SEE ALSO
perl(1).