Author image Scott Zuyderduyn

NAME

Bio::SAGE::DataProcessing::AveragePhredFilter - A filter that validates sequences based on average Phred score.

SYNOPSIS

  use Bio::SAGE::DataProcessing::AveragePhredFilter;
  $filter = new Bio::SAGE::DataProcessing::AveragePhredFilter->new( 30, 15 );

DESCRIPTION

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.

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 $avgPhred, <$minPhred>

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";
  }

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( "AAAAAA", "20 40 40 40 30 35" ) ) {
      print "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.