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.
[email protected] - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list: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 :