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Bio::Tools::Run::Meme(User Contributed Perl DocumentatBio::Tools::Run::Meme(3)

NAME
       Bio::Tools::Run::Meme - Wrapper for Meme Program

SYNOPSIS
	 use Bio::Tools::Run::Meme;

	 my $factory = Bio::Tools::Run::Meme->new(-dna => 1, -mod => 'zoops');

	 # return a Bio::AlignIO given Bio::PrimarySeqI objects
	 my $alignio = $factory->run($seq1, $seq2, $seq3...);

	 # add a Bio::Map::Prediction to the appropriate maps given Bio::Map::GeneMap
	 # objects (predict on the full map sequences supplied) or Bio::Map::Gene
	 # objects (predict on the full map sequences of the maps the supplied Genes
	 # are on) or Bio::Map::PositionWithSequence objects
	 my $prediction = $factory->run($biomap1, $biomap2, $biomap3...);

DESCRIPTION
       This is a wrapper for running meme, a transcription factor binding site
       prediction program. It can be found here:
       http://meme.sdsc.edu/meme4/meme-download.html

       You can try supplying normal meme command-line arguments to new(), eg.
       new(-mod => 'oops') or calling arg-named methods (excluding the initial
       hyphen(s), eg. $factory->mod('oops') to set the -mod option to 'oops').

       You will need to enable this MEME wrapper to find the meme program.
       During standard installation of meme you will have set up an
       environment variable called MEME_BIN which is used for this purpose.

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 - Sendu Bala
       Email bix@sendu.me.uk

APPENDIX
       The rest of the documentation details each of the object methods.
       Internal methods are usually preceded with a "_".

   new
	Title	: new
	Usage	: $rm->new($seq)
	Function: creates a new wrapper
	Returns:  Bio::Tools::Run::Meme
	Args	: Most options understood by meme can be supplied as key =>
		  value pairs, with a boolean value for switches. -quiet can also be
		  set to silence meme completely.

		  These options can NOT be used with this wrapper (they are handled
		  internally or don't make sense in this context):
		  -h -text -nostatus

   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	:

   version
	Title	: version
	Usage	: n/a
	Function: Determine the version number of the program, which is
		  non-discoverable for Meme
	Returns : undef
	Args	: none

   run
	Title	: run
	Usage	: $rm->run($seq1, $seq2, $seq3...);
	Function: Run Meme on the sequences/Bio::Map::* set as the argument
	Returns : Bio::AlignIO if sequence objects supplied, OR
		  Bio::Map::Prediction if Bio::Map::* objects supplied
		  undef if no executable found
	Args	: list of Bio::PrimarySeqI compliant objects, OR
		  list of Bio::Map::GeneMap objects, OR
		  list of Bio::Map::Gene objects, OR
		  list of Bio::Map::PositionWithSequence objects

   _run
	Title	: _run
	Usage	: $rm->_run ($filename,$param_string)
	Function: internal function that runs meme
	Returns : as per run(), undef if no executable found
	Args	: the filename to the input sequence file

   _setparams()
	Title	: _setparams
	Usage	: Internal function, not to be called directly
	Function: Create parameter inputs for meme program
	Returns : parameter string to be passed to meme
	Args	: none

   _setinput()
	Title	: _setinput
	Usage	: Internal function, not to be called directly
	Function: writes input sequence to file and return the file name
	Returns : string (file name)
	Args	: as per run()

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 v5.14.1			  2011-07-21	      Bio::Tools::Run::Meme(3)
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