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.

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)