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)