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://redmine.open-bio.org/projects/bioperl/

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