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("\t", ( $r->query_name,
                               $hit->name,
                               $hsp->hit->start,
                               $hsp->hit->end,
                               $hsp->meta,
                               $hsp->score,
                               )), "\n";
    }
   }
  }

  # 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    :