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Bio::Tools::Run::RepeaUserkContributed Perl DoBio::Tools::Run::RepeatMasker(3)

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

perl v5.32.1			  2021-03-01  Bio::Tools::Run::RepeatMasker(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Shawn Hoon | APPENDIX | Bio::Tools::Run::Wrapper methods

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