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Manual Reference Pages  -  BIO::TOOLS::RUN::RNAMOTIF (3)

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NAME

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

CONTENTS

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    :



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perl v5.20.3 BIO::TOOLS::RUN::RNAMOTIF (3) 2016-04-05

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