NAME

       Bio::Tools::Run::RepeatMasker - Wrapper for RepeatMasker Program

SYNOPSIS

         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;

DESCRIPTION

       To use this module, the RepeatMasker program (and probably database) must be installed.
       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://www.repeatmasker.org/.

       Having installed RepeatMasker, you must let Bioperl know where it is.  This can be done in
       (at least) three ways:

        1. Make sure the RepeatMasker executable is in your path.
        2. Define an environmental variable REPEATMASKERDIR which is a
           directory which contains the RepeatMasker executable:
           In bash:

           export REPEATMASKERDIR=/home/username/RepeatMasker/

           In csh/tcsh:

           setenv REPEATMASKERDIR /home/username/RepeatMasker/

        3. Include a definition of an environmental variable REPEATMASKERDIR in
           every script that will use this RepeatMasker wrapper module, e.g.:

           BEGIN { $ENV{REPEATMASKERDIR} = '/home/username/RepeatMasker/' }
           use Bio::Tools::Run::RepeatMasker;

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 one of the Bioperl mailing lists. 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 the bugs and their
       resolution.  Bug reports can be submitted via the web:

         http://redmine.open-bio.org/projects/bioperl/

AUTHOR - Shawn Hoon

       Email shawnh@fugu-sg.org

APPENDIX

       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, obtained 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

Bio::Tools::Run::Wrapper methods

   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