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)