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Bio::Tools::Run::Meme.3pm

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