Bio::Tools::Run::RNAMotif.3pm

Langue: en

Autres versions - même langue

Version: 2009-11-04 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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://bugzilla.open-bio.org/
 
 

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    :