NAME
Bio::SAGE::DataProcessing::MinimumPhredFilter - A filter that validates sequences based on minimum Phred score.
SYNOPSIS
$filter
= new Bio::SAGE::DataProcessing::MinimumPhredFilter->new( 20 );
DESCRIPTION
This module is a concrete subclass of Bio::SAGE::DataProcessing::Filter. The implementation considers a sequence valid if all nucleotides have a Phred score that exceeds that specified for the filter.
INSTALLATION
Included with Bio::SAGE::DataProcessing.
PREREQUISITES
This module requires the Bio::SAGE::DataProcessing::Filter
package.
CHANGES
1.10 2004.06.19 - Initial release.
0.01 2004.05.02 -
prototype
CLASS METHODS
new $minPhred
Constructor.
Arguments
$minPhred
The minimum phred value that all nucleotides in a
sequence must have in order to be considered valid.
Usage
my
$filter
= Bio::SAGE::DataProcessing::MinimumPhredFilter->new( 20 );
if
(
$filter
->is_tag_valid(
"AAAAAAAAAA"
) ) {
"VALID!\n"
;
}
INSTANCE METHODS
is_valid $sequence, $scores
This implements the is_valid subroutine required in concrete subclasses of Bio::SAGE::DataProcessing::Filter.
Arguments
$sequence
The tag sequence.
$scores
A space-separated string of Phred scores
for
the
specified sequence.
Returns
Returns non-zero
if
the valid, zero
if
invalid.
Usage
my
$filter
= Bio::SAGE::DataProcessing::MinimumPhredFilter->new();
if
(
$filter
->is_tag_valid(
"AAAAAAAAAA"
) ) {
"VALID!\n"
;
}
compare $scores1, $scores2
The default implementation provided by the base class Bio::SAGE::DataProcessing::Filter is used. See the documentation for the base class for more information.
COPYRIGHT
Copyright(c)2004 Scott Zuyderduyn <scottz@bccrc.ca>. All rights reserved.
This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
AUTHOR
Scott Zuyderduyn <scottz@bccrc.ca> BC Cancer Research Centre
VERSION
1.20
SEE ALSO
Bio::SAGE::DataProcessing(1).
Bio::SAGE::DataProcessing::Filter(1).
TODO
Nothing yet.