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)