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.\" ========================================================================
.\"
.IX Title "Bio::Tools::Run::Meme 3pm"
.TH Bio::Tools::Run::Meme 3pm "2018-09-14" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
Bio::Tools::Run::Meme \- Wrapper for Meme Program
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  use Bio::Tools::Run::Meme;
\&
\&  my $factory = Bio::Tools::Run::Meme\->new(\-dna => 1, \-mod => \*(Aqzoops\*(Aq);
\&
\&  # 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, $biomap3...);
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This is a wrapper for running meme, a transcription factor binding site
prediction program. It can be found here:
http://meme.sdsc.edu/meme4/meme\-download.html
.PP
You can try supplying normal meme command-line arguments to \fInew()\fR, eg.
new(\-mod => 'oops') or calling arg-named methods (excluding the initial
hyphen(s), eg. \f(CW$factory\fR\->mod('oops') to set the \-mod option to 'oops').
.PP
You will need to enable this \s-1MEME\s0 wrapper to find the meme program. During
standard installation of meme you will have set up an environment variable
called \s-1MEME_BIN\s0 which is used for this purpose.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  http://redmine.open\-bio.org/projects/bioperl/
.Ve
.SH "AUTHOR \- Sendu Bala"
.IX Header "AUTHOR - Sendu Bala"
Email bix@sendu.me.uk
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a \*(L"_\*(R".
.SS "new"
.IX Subsection "new"
.Vb 7
\& 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\*(Aqt make sense in this context):
\&           \-h \-text \-nostatus
.Ve
.SS "program_name"
.IX Subsection "program_name"
.Vb 5
\& Title   : program_name
\& Usage   : $factory>program_name()
\& Function: holds the program name
\& Returns:  string
\& Args    : None
.Ve
.SS "program_dir"
.IX Subsection "program_dir"
.Vb 5
\& Title   : program_dir
\& Usage   : $factory\->program_dir(@params)
\& Function: returns the program directory, obtained from ENV variable.
\& Returns:  string
\& Args    :
.Ve
.SS "version"
.IX Subsection "version"
.Vb 6
\& Title   : version
\& Usage   : n/a
\& Function: Determine the version number of the program, which is
\&           non\-discoverable for Meme
\& Returns : undef
\& Args    : none
.Ve
.SS "run"
.IX Subsection "run"
.Vb 10
\& 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
.Ve
.SS "_run"
.IX Subsection "_run"
.Vb 5
\& 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
.Ve
.SS "\fI_setparams()\fP"
.IX Subsection "_setparams()"
.Vb 5
\& 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
.Ve
.SS "\fI_setinput()\fP"
.IX Subsection "_setinput()"
.Vb 5
\& 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()
.Ve
.SH "Bio::Tools::Run::Wrapper methods"
.IX Header "Bio::Tools::Run::Wrapper methods"
.SS "no_param_checks"
.IX Subsection "no_param_checks"
.Vb 6
\& 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)
.Ve
.SS "save_tempfiles"
.IX Subsection "save_tempfiles"
.Vb 5
\& Title   : save_tempfiles
\& Usage   : $obj\->save_tempfiles($newval)
\& Function: 
\& Returns : value of save_tempfiles
\& Args    : newvalue (optional)
.Ve
.SS "outfile_name"
.IX Subsection "outfile_name"
.Vb 6
\& 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
.Ve
.SS "tempdir"
.IX Subsection "tempdir"
.Vb 5
\& 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
.Ve
.SS "cleanup"
.IX Subsection "cleanup"
.Vb 5
\& Title   : cleanup
\& Usage   : $codeml\->cleanup();
\& Function: Will cleanup the tempdir directory
\& Returns : none
\& Args    : none
.Ve
.SS "io"
.IX Subsection "io"
.Vb 5
\& Title   : io
\& Usage   : $obj\->io($newval)
\& Function:  Gets a L<Bio::Root::IO> object
\& Returns : L<Bio::Root::IO>
\& Args    : none
.Ve