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