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
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()
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
Title : io
Usage : $obj->io($newval)
Function: Gets a L<Bio::Root::IO> object
Returns : L<Bio::Root::IO>
Args : none