Bio::Tools::Run::Mdust(3pm)				User Contributed Perl Documentation			       Bio::Tools::Run::Mdust(3pm)

NAME

       Mdust - Perl extension for Mdust nucleotide filtering

SYNOPSIS

	 use Bio::Tools::Run::Mdust;
	 my $mdust = Bio::Tools::Run::Mdust->new();

	 $mdust->run($bio_seq_object);

DESCRIPTION

       Perl wrapper for the nucleic acid complexity filtering program mdust as available from TIGR via <http://www.tigr.org/tdb/tgi/software/>.
       Takes a Bio::SeqI or Bio::PrimarySeqI object of type DNA as input.

       If a Bio::Seq::RichSeqI is passed then the low-complexity regions will be added to the feature table of the target object as
       Bio::SeqFeature::Generic items with primary tag = 'Excluded' .  Otherwise a new target object will be returned with low-complexity regions
       masked (by N's or other character as specified by maskchar()).

       The mdust executable must be in a directory specified with either the PATH or MDUSTDIR environment variable.

SEE ALSO

       mdust, Bio::PrimarySeq, Bio::Seq::RichSeq, Bio::SeqFeature::Generic

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the
       Bioperl mailing list.  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
       it. Please include a thorough description of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the
       web:

	 http://redmine.open-bio.org/projects/bioperl/

AUTHOR

       Donald Jackson (donald.jackson@bms.com)

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are usually preceded with a _

   new
	 Title	       : new
	 Usage	       : my $mdust = Bio::Tools::Run::Mdust->new( -target => $target_bioseq)
	 Purpose       : Create a new mdust object
	 Returns       : A Bio::Seq object
	 Args	       : target - Bio::Seq object for masking - alphabet MUST be DNA.
			 wsize - word size for masking (default = 3)
			 cutoff - cutoff score for masking (default = 28)
			 maskchar - character for replacing masked regions (default = N)
			 coords - boolean - indicate low-complexity regions as
				  Bio::SeqFeature::Generic
				  objects with primary tag 'Excluded',
				  do not change sequence (default 0)
			 tmpdir - directory for storing temporary files
			 debug - boolean - toggle debugging output,
				 do not remove temporary files
	 Notes	       : All of the arguments can also be get/set with their own accessors, such as:
			 my $wsize = $mdust->wsize();

			 When processing multiple sequences, call Bio::Tools::Run::Mdust->new() once
			 then pass each sequence as an argument to the target() or run() methods.

   run
	 Title	       : run
	 Usage	       : $mdust->run();
	 Purpose       : Run mdust on the target sequence
	 Args	       : target (optional) - Bio::Seq object of alphabet DNA for masking
	 Returns       : Bio::Seq object with masked sequence or low-complexity regions added to feature table.

   target
	 Title	       : target
	 Usage	       : $mdust->target($bio_seq)
	 Purpose       : Set/get the target (sequence to be filtered).
	 Returns       : Target Bio::Seq object
	 Args	       : Bio::SeqI or Bio::PrimarySeqI object using the DNA alphabet (optional)
	 Note	       : If coordinate parsing is selected ($mdust->coords = 1) then target
			 MUST be a Bio::Seq::RichSeqI object.  Passing a RichSeqI object automatically
			 turns on coordinate parsing.

   maskchar
	 Title	       : maskchar
	 Usage	       : $mdust->maskchar('N')
	 Purpose       : Set/get the character for masking low-complexity regions
	 Returns       : True on success
	 Args	       : Either N (default), X or L (lower case)

perl v5.12.3							    2011-06-18					       Bio::Tools::Run::Mdust(3pm)