Bio::Tools::Run::Meme(3pm) User Contributed Perl Documentation 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://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
perl v5.12.3 2011-06-18 Bio::Tools::Run::Meme(3pm)