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.\" ========================================================================
.\"
.IX Title "Bio::Tools::Run::RNAMotif 3pm"
.TH Bio::Tools::Run::RNAMotif 3pm "2023-01-22" "perl v5.36.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
Bio::Tools::Run::RNAMotif \- Wrapper for local execution of rnamotif, rm2ct,
rmfmt, rmprune
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  #run rnamotif|rmfmt|rm2ct
\&
\&  my @params = (
\&              descr => \*(AqpyrR.descr\*(Aq,
\&              fmt   => \*(Aqgb\*(Aq,
\&              setvar => \*(Aqctx_maxlen=20\*(Aq,
\&              context => 1,
\&              sh    => 1,
\&             );
\&
\&  my $factory = Bio::Tools::Run::RNAMotif\->new(\-program =>\*(Aqrnamotif\*(Aq,
\&                                               \-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("\et", ( $r\->query_name,
\&                               $hit\->name,
\&                               $hsp\->hit\->start,
\&                               $hsp\->hit\->end,
\&                               $hsp\->meta,
\&                               $hsp\->score,
\&                               )), "\en";
\&    }
\&   }
\&  }
\&
\&  # Pass a finished report through rmfmt (\-a format only)
\&  # Returns Bio::AlignIO object
\&
\&  my $aio = Bio::AlignIO\->new(\-file=>"rna.msf",\-format=>\*(Aqmsf\*(Aq);
\&  my $factory =  Bio::Tools::Run::RNAMotif\->new(\*(Aqprogram\*(Aq=>\*(Aqrmfmt\*(Aq,
\&                                                \*(Aqa\*(Aq => 1);
\&  my $alnin = $factory\->run(\*(Aqtrna.rnamotif\*(Aq);
\&
\&  my $aln = $alnin\->next_aln;
\&
\&  $aio\->write_aln($aln);
.Ve
.SH "DESCRIPTION"
.IX Header "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.
.PP
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 \s-1STDERR,\s0 for rm2ct which requires '\-verbose' set to 1).
.PP
\&\s-1WARNING:\s0 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.
.SH "NOTES ON PROGRAM PARAMETERS"
.IX Header "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).
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  http://redmine.open\-bio.org/projects/bioperl/
.Ve
.SH "AUTHOR \- Chris Fields"
.IX Header "AUTHOR - Chris Fields"
.Vb 1
\& Email: cjfields\-at\-uiuc\-dot\-edu
.Ve
.SH "CONTRIBUTORS"
.IX Header "CONTRIBUTORS"
.Vb 1
\& cjfields\-at\-uiuc\-dot\-edu
.Ve
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
.SS "new"
.IX Subsection "new"
.Vb 8
\& 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)
.Ve
.SS "program_name"
.IX Subsection "program_name"
.Vb 5
\& Title   : program_name
\& Usage   : $factory>program_name()
\& Function: holds the program name
\& Returns:  string
\& Args    : None
.Ve
.SS "program_dir"
.IX Subsection "program_dir"
.Vb 5
\& Title   : program_dir
\& Usage   : $factory\->program_dir(@params)
\& Function: returns the program directory, obtained from ENV variable.
\& Returns:  string
\& Args    :
.Ve
.SS "version"
.IX Subsection "version"
.Vb 6
\& Title   : version
\& Usage   : $v = $prog\->version();
\& Function: Determine the version number of the program
\& Example :
\& Returns : float or undef
\& Args    : none
.Ve
.SS "run"
.IX Subsection "run"
.Vb 7
\& Title   :  run
\& Usage   :  $obj\->run($seqFile)
\& Function:  Runs RNAMotif programs, returns Bio::SearchIO/Bio::AlignIO
\& Returns :  Depends on program:
\&            \*(Aqrnamotif\*(Aq \- returns Bio::SearchIO
\&            \*(Aqrmfmt \-a\*(Aq \- 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()
.Ve
.SS "search"
.IX Subsection "search"
.Vb 7
\& Title   :  search
\& Usage   :  $searchio = $obj\->search($seqFile)
\& Function:  Runs \*(Aqrnamotif\*(Aq on seqs, returns Bio::SearchIO
\& Returns :  A Bio::SearchIO
\& Args    :  A Bio::PrimarySeqI or file name
\& Note    :  Runs \*(Aqrnamotif\*(Aq only, regardless of program setting; all other
\&            parameters loaded
.Ve
.SS "get_AlignIO"
.IX Subsection "get_AlignIO"
.Vb 7
\& Title   :  get_AlignIO
\& Usage   :  $aln = $obj\->get_AlignIO($seqFile)
\& Function:  Runs \*(Aqrmfmt \-a\*(Aq on file, returns Bio::AlignIO
\& Returns :  A Bio::AlignIO
\& Args    :  File name
\& Note    :  Runs \*(Aqrmfmt \-a\*(Aq only, regardless of program setting; only file
\&            name and outfile (if any) are set
.Ve
.SS "tempfile"
.IX Subsection "tempfile"
.Vb 6
\& 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
.Ve
.SS "prune"
.IX Subsection "prune"
.Vb 6
\& 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
.Ve
.SS "_run"
.IX Subsection "_run"
.Vb 5
\& Title   :   _run
\& Usage   :   $obj\->_run()
\& Function:   Internal(not to be used directly)
\& Returns :   
\& Args    :
.Ve
.SS "_setparams"
.IX Subsection "_setparams"
.Vb 6
\& Title   :  _setparams
\& Usage   :  Internal function, not to be called directly
\& Function:  creates a string of params to be used in the command string
\& Example :
\& Returns :  string of params
\& Args    :
.Ve
.SS "_writeSeqFile"
.IX Subsection "_writeSeqFile"
.Vb 6
\& Title   : _writeSeqFile
\& Usage   : obj\->_writeSeqFile($seq)
\& Function: Internal(not to be used directly)
\& Returns : writes passed Seq objects to tempfile, to be used as input
\&           for program
\& Args    :
.Ve