Bio::SAGE::DataProcessing::AveragePhredFilter - A filter that validates sequences based on average Phred score.
use Bio::SAGE::DataProcessing::AveragePhredFilter; $filter = new Bio::SAGE::DataProcessing::AveragePhredFilter->new( 30, 15 );
This module is a concrete subclass of Bio::SAGE::DataProcessing::Filter. The implementation considers a sequence valid if the average quality of all nucleotides meet a given value.
Included with Bio::SAGE::DataProcessing.
This module requires the Bio::SAGE::DataProcessing::Filter package.
1.10 2004.06.19 - Initial release. 0.01 2004.05.02 - prototype
Constructor.
Arguments
$avgPhred
The average phred value of all nucleotides required for a sequence to be considered valid.
$minPhred (optional)
The minimum phred value that all nucleotides in a sequence must have in order to be considered valid. The default value if this argument is not specified is 0.
Usage
my $filter = Bio::SAGE::DataProcessing::MinimumPhredFilter->new( 30, 20 ); if( $filter->is_tag_valid( "AAAAAA", "20 40 40 40 30 35" ) ) { print "VALID!\n"; }
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( "AAAAAA", "20 40 40 40 30 35" ) ) { print "VALID!\n"; }
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(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.
Scott Zuyderduyn <scottz@bccrc.ca> BC Cancer Research Centre
1.20
Bio::SAGE::DataProcessing(1). Bio::SAGE::DataProcessing::Filter(1).
Nothing yet.