Bio::Tools::Run::RNAMotif(3pm)				User Contributed Perl Documentation			    Bio::Tools::Run::RNAMotif(3pm)

NAME

       Bio::Tools::Run::RNAMotif - Wrapper for local execution of rnamotif, rm2ct, rmfmt, rmprune

SYNOPSIS

	 #run rnamotif|rmfmt|rm2ct

	 my @params = (
		     descr => 'pyrR.descr',
		     fmt   => 'gb',
		     setvar => 'ctx_maxlen=20',
		     context => 1,
		     sh    => 1,
		    );

	 my $factory = Bio::Tools::Run::RNAMotif->new(-program =>'rnamotif',
						      -prune  => 1,
						       @params);

	 # Pass the factory a Bio::Seq object or a file name
	 # Returns a Bio::SearchIO object

	 #my $searchio = $factory->run("B_sub.gb");
	 my $searchio = $factory->run($seq);
	 while (my $result = $searchio->next_result){
	  while(my $hit = $result->next_hit){
	   while (my $hsp = $hit->next_hsp){
		   print join("	", ( $r->query_name,
				      $hit->name,
				      $hsp->hit->start,
				      $hsp->hit->end,
				      $hsp->meta,
				      $hsp->score,
				      )), "
";
	   }
	  }
	 }

	 # Pass a finished report through rmfmt (-a format only)
	 # Returns Bio::AlignIO object

	 my $aio = Bio::AlignIO->new(-file=>"rna.msf",-format=>'msf');
	 my $factory =	Bio::Tools::Run::RNAMotif->new('program'=>'rmfmt',
						       'a' => 1);
	 my $alnin = $factory->run('trna.rnamotif');

	 my $aln = $alnin->next_aln;

	 $aio->write_aln($aln);

DESCRIPTION

       Wrapper module for Tom Macke and David Cases's RNAMotif suite of programs. This allows running of rnamotif, rmprune, rm2ct, and rmfmt.
       Binaries are available at http://www.scripps.edu/mb/case/casegr-sh-3.5.html.

       This wrapper allows for one to save output to an optional named file or tempfile using the '-outfile_name' or '-tempfile' parameters; this
       is primarily for saving output from the rm2ct program, which currently does not have a parser available. If both a named output file and
       tempfile flag are set, the output file name is used. The default setting is piping output into a filehandle for parsing (or output to
       STDERR, for rm2ct which requires '-verbose' set to 1).

       WARNING: At this time, there is very little checking of parameter settings, so one could have an error if setting the worng parameter for a
       program. Future versions will likely add some error checking.

NOTES ON PROGRAM PARAMETERS

       All program parameters are currently supported. Of note, the 'D' parameter, used for setting the value of a variable to a value, is changed
       to 'set_var' to avoid name collisions with 'd' (used for dumping internal data structures).

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 - Chris Fields
	Email: cjfields-at-uiuc-dot-edu

CONTRIBUTORS

	cjfields-at-uiuc-dot-edu

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

   new
	Title	: new
	Usage	: my $wrapper = Bio::Tools::Run::RNAMotif->new(@params)
	Function: creates a new RNAMotif factory
	Returns:  Bio::Tools::Run::RNAMotif
	Args	: list of parameters
		  -tempfile	   => set tempfile flag (default 0)
		  -outfile_name    => set file to send output to (default none)
		  -prune	   => set rmprune postprocess flag (default 0)

   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	: $v = $prog->version();
	Function: Determine the version number of the program
	Example :
	Returns : float or undef
	Args	: none

   run
	Title	:  run
	Usage	:  $obj->run($seqFile)
	Function:  Runs RNAMotif programs, returns Bio::SearchIO/Bio::AlignIO
	Returns :  Depends on program:
		   'rnamotif' - returns Bio::SearchIO
		   'rmfmt -a' - returns Bio::AlignIO
		   all others - sends output to outfile, tempfile, STDERR

		   Use search() (for Bio::SearchIO stream) or get_AlignIO() (for
		   Bio::AlignIO stream) for a uniform Bioperl object interface.

	Args	:  A Bio::PrimarySeqI or file name
	Note	:  This runs any RNAMotif program set via program()

   search
	Title	:  search
	Usage	:  $searchio = $obj->search($seqFile)
	Function:  Runs 'rnamotif' on seqs, returns Bio::SearchIO
	Returns :  A Bio::SearchIO
	Args	:  A Bio::PrimarySeqI or file name
	Note	:  Runs 'rnamotif' only, regardless of program setting; all other
		   parameters loaded

   get_AlignIO
	Title	:  get_AlignIO
	Usage	:  $aln = $obj->get_AlignIO($seqFile)
	Function:  Runs 'rmfmt -a' on file, returns Bio::AlignIO
	Returns :  A Bio::AlignIO
	Args	:  File name
	Note	:  Runs 'rmfmt -a' only, regardless of program setting; only file
		   name and outfile (if any) are set

   tempfile
	Title	: tempfile
	Usage	: $obj->tempfile(1)
	Function: Set tempfile flag.  When set, writes output to a tempfile; this
		  is overridden by outfile_name() if set
	Returns : Boolean setting (or undef if not set)
	Args	: [OPTIONAL] Boolean

   prune
	Title	: prune
	Usage	: $obj->prune(1)
	Function: Set rmprune flag.  When set, follows any searches with a call to
		  rmprune (this deletes some redundant sequence hits)
	Returns : Boolean setting (or undef if not set)
	Args	: [OPTIONAL] Boolean

   _run
	Title	:   _run
	Usage	:   $obj->_run()
	Function:   Internal(not to be used directly)
	Returns :
	Args	:

   _setparams
	Title	:  _setparams
	Usage	:  Internal function, not to be called directly
	Function:  creates a string of params to be used in the command string
	Example :
	Returns :  string of params
	Args	:

   _writeSeqFile
	Title	: _writeSeqFile
	Usage	: obj->_writeSeqFile($seq)
	Function: Internal(not to be used directly)
	Returns : writes passed Seq objects to tempfile, to be used as input
		  for program
	Args	:

perl v5.12.3							    2011-06-18					    Bio::Tools::Run::RNAMotif(3pm)