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

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