Bio::Tools::Run::RepeatMasker - Wrapper for RepeatMasker Program use Bio::Tools::Run::RepeatMasker; my @params=("mam" => 1,"noint"=>1); my $factory = Bio::Tools::Run::RepeatMasker->new(@params); $in = Bio::SeqIO->new(-file => "contig1.fa", -format => 'fasta'); my $seq = $in->next_seq(); #return an array of Bio::SeqFeature::FeaturePair objects my @feats = $factory->run($seq); # or $factory->run($seq); my @feats = $factory->repeat_features; #return the masked sequence, a Bio::SeqI object my $masked_seq = $factory->run; RepeatMasker is a program that screens DNA sequences for interspersed repeats known to exist in mammalian genomes as well as for low complexity DNA sequences. For more information, on the program and its usage, please refer to http://repeatmasker.genome.washington.edu/.

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Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: http://bugzilla.bioperl.org/ Email shawnh@fugu-sg.org The rest of the documentation details each of the object methods. Internal methods are usually preceded with a "_".

program_name
Title : program_name Usage : $factory>program_name() Function: holds the program name Returns: string Args : None

program_dir
Title : program_dir Usage : $factory->program_dir(@params) Function: returns the program directory, obtiained from ENV variable. Returns: string Args :

new
Title : new Usage : $rm->new($seq) Function: creates a new wrapper Returns: Bio::Tools::Run::RepeatMasker Args : self

version
Title : version Usage : Function: Determine the version number of the program Example : Returns : float or undef Args : none

run
Title : run Usage : $rm->run($seq); Function: Run Repeatmasker on the sequence set as the argument Returns : an array of repeat features that are Bio::SeqFeature::FeaturePairs Args : Bio::PrimarySeqI compliant object

mask
Title : mask Usage : $rm->mask($seq) Function: This method is deprecated. Call run() instead Example : Returns : an array of repeat features that are Bio::SeqFeature::FeaturePairs Args : Bio::PrimarySeqI compliant object

_run
Title : _run Usage : $rm->_run ($filename,$param_string) Function: internal function that runs the repeat masker Example : Returns : an array of repeat features Args : the filename to the input sequence and the parameter string

masked_seq
Title : masked_seq Usage : $rm->masked_seq($seq) Function: get/set for masked sequence Example : Returns : the masked sequence Args : Bio::Seq object

repeat_features
Title : repeat_features Usage : $rm->repeat_features(\@rf) Function: get/set for repeat features array Example : Returns : the array of repeat features Args :

_setparams()
Title : _setparams Usage : Internal function, not to be called directly Function: Create parameter inputs for repeatmasker program Example : Returns : parameter string to be passed to repeatmasker Args : name of calling object

_setinput()
Title : _setinput Usage : Internal function, not to be called directly Function: writes input sequence to file and return the file name Example : Returns : string Args : a Bio::PrimarySeqI compliant object

no_param_checks
Title : no_param_checks Usage : $obj->no_param_checks($newval) Function: Boolean flag as to whether or not we should trust the sanity checks for parameter values Returns : value of no_param_checks Args : newvalue (optional)

save_tempfiles
Title : save_tempfiles Usage : $obj->save_tempfiles($newval) Function: Returns : value of save_tempfiles Args : newvalue (optional)

outfile_name
Title : outfile_name Usage : my $outfile = $codeml->outfile_name(); Function: Get/Set the name of the output file for this run (if you wanted to do something special) Returns : string Args : [optional] string to set value to

tempdir
Title : tempdir Usage : my $tmpdir = $self->tempdir(); Function: Retrieve a temporary directory name (which is created) Returns : string which is the name of the temporary directory Args : none

cleanup
Title : cleanup Usage : $codeml->cleanup(); Function: Will cleanup the tempdir directory Returns : none Args : none

io
Title : io Usage : $obj->io($newval) Function: Gets a L<Bio::Root::IO> object Returns : L<Bio::Root::IO> Args : none