Bio::SAGE::DataProcessing::MinimumPhredFilter - A filter that validates sequences based on minimum Phred score.

Bio-SAGE-DataProcessing documentation

Contained in the Bio-SAGE-DataProcessing distribution.

Index

NAME
SYNOPSIS
DESCRIPTION
INSTALLATION
PREREQUISITES
CHANGES
CLASS METHODS
- new $minPhred
INSTANCE METHODS
- is_valid $sequence, $scores
- compare $scores1, $scores2
COPYRIGHT
AUTHOR
VERSION
SEE ALSO
TODO

Code Index:

package Bio::SAGE::DataProcessing::MinimumPhredFilter
- new
- is_valid
__END__
EOF

NAME

Bio::SAGE::DataProcessing::MinimumPhredFilter - A filter that validates sequences based on minimum Phred score.

SYNOPSIS

  use Bio::SAGE::DataProcessing::MinimumPhredFilter;
  $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" ) ) {
      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( "AAAAAAAAAA" ) ) {
      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.

Bio-SAGE-DataProcessing documentation

Contained in the Bio-SAGE-DataProcessing distribution.

# *%) $Id: MinimumPhredFilter.pm,v 1.5 2004/10/15 22:30:46 scottz Exp $
#
# 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.

package Bio::SAGE::DataProcessing::MinimumPhredFilter;

use Bio::SAGE::DataProcessing::Filter;
use base qw( Bio::SAGE::DataProcessing::Filter );
use strict;
use diagnostics;
use vars qw( $VERSION @ISA @EXPORT @EXPORT_OK );

#require Exporter;
#require AutoLoader;

#@ISA = qw( Exporter AutoLoader );
@ISA = qw( Bio::SAGE::DataProcessing::Filter );
@EXPORT = qw();
$VERSION = $Bio::SAGE::DataProcessing::VERSION;

my $PACKAGE = "Bio::SAGE::DataProcessing::MinimumPhredFilter";

#######################################################
sub new {
#######################################################

    my $class = shift;
    $class->SUPER::new( @_ );

}

#######################################################
sub is_valid {
#######################################################

    my $this = shift;
    my $sequence = shift || die( $PACKAGE . "::is_valid no sequence defined." );
    my $scores = shift;

    if( $Bio::SAGE::DataProcessing::DEBUG >= 1 ) {
        print STDERR $PACKAGE . "::is_valid looking at " . $scores . "\n";
    }

    if( !defined( $scores ) ) { return 1; }

    my $min_phred = $this->{'args'}[0];

    if( $min_phred == 0 ) {
        if( $Bio::SAGE::DataProcessing::DEBUG >= 1 ) {
            print STDERR $PACKAGE . "::is_valid no need to check, minimum phred is 0\n";
        }
        return 1;
    }

    my @scores = split( /\s/, $scores );
    foreach my $score ( @scores ) {
        if( $score < $min_phred ) {
            if( $Bio::SAGE::DataProcessing::DEBUG >= 1 ) {
                print STDERR $PACKAGE . "::is_valid $score does not meet minimum $min_phred\n";
            }
            return 0;
        }
    }

    if( $Bio::SAGE::DataProcessing::DEBUG >= 1 ) {
        print STDERR $PACKAGE . "::is_valid scores passed\n";
    }

    return 1;

}

#######################################################
#######################################################

1;

__END__