Bio::SCF - Perl extension for reading and writing SCF sequence files
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');
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.
- $obj = tie %hash,'Bio::SCF',$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
- $scf = Bio::SCF->new($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.
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');
Dmitri Priimak,
[email protected] (1999)
with some cleanups by Lincoln Stein,
[email protected] (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.
perl(1).