Mdust - Perl extension for Mdust nucleotide filtering
use Bio::Tools::Run::Mdust; my $mdust = Bio::Tools::Run::Mdust->new(); $mdust->run($bio_seq_object);
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.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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.
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.
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.
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)