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bio::tools::run::mdust(3pm) [debian man page]

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)
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