Bio::Tools::Run::RepeatMasker.3pm

Langue: en

Version: 2009-11-04 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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://bugzilla.open-bio.org/
 
 

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