/ 
BioPerl-Run-1.007000
River stage one • 2 direct dependents • 2 total dependents
/ Bio::Tools::Run::RNAMotif

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()
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    :