/ 
BioPerl-Run-1.007001
River stage one • 2 direct dependents • 2 total dependents
/ Bio::Tools::Run::RepeatMasker

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