Bio::SAGE::DataProcessing::Filter - An abstract filter for determining whether a [di]tag is worth keeping.
use Bio::SAGE::DataProcessing::Filter; $filter = Bio::SAGE::DataProcessing::Filter->new();
This module encapsulates an abstract filtering procedure that is used during library processing with Bio::SAGE::DataProcessing. For example, a concrete implementation might indicate a tag is not worth keeping because the Phred scores are too low.
Included with Bio::SAGE::DataProcessing.
This module requires the Bio::SAGE::DataProcessing package.
Bio::SAGE::DataProcessing
1.10 2004.06.19 - Initial release. 0.01 2004.05.02 - prototype
Globals
$PROTOCOL_SAGE
Hashref containing protocol parameters for the regular/original SAGE protocol (see set_protocol documentation for more information).
$PROTOCOL_LONGSAGE
Hashref containing protocol parameters for the LongSAGE protocol (see set_protocol documentation for more information).
Settings
$DEBUG = 0
Prints debugging output if value if >= 1.
Constructor for a new Bio::SAGE::DataProcessing::Filter object.
Arguments
$arg1,$arg2,... (optional)
Any arguments can be specified. These are stored in the 'args' hash element (ie. $self->{'args'}). Concrete subclasses must call this constructor explictly from within their constructor. i.e. $class->SUPER::new( @_ ); The required parameters are dependent on the concrete implementation of a Filter.
Usage
Not explicitly called.
This method must be implementated by the developer in a concrete subclass. The contract of this method is to return a boolean value indicating whether the tag is valid or not.
The subclass implementation should always work for cases where the \@scores argument is not provided (i.e. !defined(\@scores)).
$sequence
The tag sequence.
\@scores (optional)
An arrayref to scores for this tag (it should be assumed that the quality scores for the leading anchoring enzyme site nucleotides are included).
my $filter = Bio::SAGE::DataProcessing::Filter->new(); if( $filter->is_tag_valid( "AAAAAAAAAA" ) ) { print "VALID!\n"; }
This method determines which set of scores is "better" (defined by the implementation).
This method can be overridden by the developer in a subclass. The default method chooses the scores that have the highest cumulative sum.
$scores1,$scores2
Space-separated strings of Phred scores (for example, "20 20 25 12 35").
Returns
Returns <0 if the first scores are best, >0 if the second scores are best, and 0 if the two score sets are equivalent.
my $filter = Bio::SAGE::DataProcessing::Filter->new(); my $res = $filter->compare( "20 20 20", "40 40 40" ); if( $res == -1 ) { # this would be the result in this example print "First set is better.\n"; } if( $res == +1 ) { print "Second set is better.\n"; } if( $res == 0 ) { print "Both sets are equivalent.\n"; }
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).
Nothing yet.
To install Bio::SAGE::DataProcessing, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::SAGE::DataProcessing
CPAN shell
perl -MCPAN -e shell install Bio::SAGE::DataProcessing
For more information on module installation, please visit the detailed CPAN module installation guide.