| Bio::Tools::Run::Meme(3pm) | User Contributed Perl Documentation | Bio::Tools::Run::Meme(3pm) |
Bio::Tools::Run::Meme - Wrapper for Meme Program
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...);
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.
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
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.
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:
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Email bix@sendu.me.uk
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a "_".
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
Title : program_name Usage : $factory>program_name() Function: holds the program name Returns: string Args : None
Title : program_dir Usage : $factory->program_dir(@params) Function: returns the program directory, obtained from ENV variable. Returns: string Args :
Title : version
Usage : n/a
Function: Determine the version number of the program, which is
non-discoverable for Meme
Returns : undef
Args : none
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
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
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
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()
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)
Title : save_tempfiles Usage : $obj->save_tempfiles($newval) Function: Returns : value of save_tempfiles Args : newvalue (optional)
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
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
Title : cleanup Usage : $codeml->cleanup(); Function: Will cleanup the tempdir directory Returns : none Args : none
Title : io Usage : $obj->io($newval) Function: Gets a L<Bio::Root::IO> object Returns : L<Bio::Root::IO> Args : none
| 2018-09-14 | perl v5.26.2 |