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()
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 :