Bio::Tools::Run::InferUser3Contributed Perl DocumeBio::Tools::Run::Infernal(3)NAMEBio::Tools::Run::Infernal - Wrapper for local execution of cmalign,
cmbuild, cmsearch, cmscore
SYNOPSIS
# parameters which are switches are set with any value that evals TRUE,
# others are set to a specific value
my @params = (hmmfb => 1,
thresh => 20);
my $factory = Bio::Tools::Run::Infernal->new(@params);
# run cmalign|cmbuild|cmsearch|cmscore|cmemit directly as a wrapper method
# this resets the program flag if previously set
$factory->cmsearch(@seqs); # searches Bio::PrimarySeqI's based on set cov. model
# saves output to outfile()/tempfile
# only values which are allowed for a program are set, so one can use the same
# wrapper for the following...
$factory->cmalign(@seqs); # aligns Bio::PrimarySeqI's to a set cov. model
# saves output to outfile()/tempfile
$factory->cmscore(@seqs); # scores set cov. model against Bio::PrimarySeqI's,
# saves output to outfile()/tempfile/STDERR.
$factory->cmbuild($aln); # builds covariance model based on alignment
# saves CM to model(), output to outfile()/tempfile/STDERR.
$factory->cmemit($file); # emits sequence from specified cov. model;
# set one if no file specified
# run based on the setting of the program parameter
my $factory = Bio::Tools::Run::Infernal->new(-program => 'cmsearch',
@params);
my $search = $factory->run($seq);
# using cmsearch returns a Bio::SearchIO object
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";
}
}
}
DESCRIPTION
Wrapper module for Sean Eddy's Infernal suite of programs. The current
implementation runs cmsearch, cmalign, cmemit, cmbuild, and cmscore.
The only current BioPerl object returned is for cmsearch (as shown in
the SYNOPSIS); all others are sent to either the designated outfile, a
tempfile, or STDOUT.
Since the Infernal suite is under constant development, consider this
wrapper as highly experimental. It will only actively support the
latest Infernal release (now at v. 0.81, used to build Rfam 8.0) until
a 1.0 Infernal release is made.
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::Infernal->new(@params)
Function: creates a new Infernal factory
Returns: Bio::Tools::Run::Infernal wrapper
Args : list of parameters
program
Title : program
Usage : $obj->program()
Function: Set the program called when run() is used. Synonym of
program_name()
Returns : String (program name)
Args : String (program name)
program_name
Title : program_name
Usage : $factory>program_name()
Function: holds the program name
Returns: string
Args : None
model
Title : model
Usage : $obj->model()
Function: Set the model used when run() is called.
Returns : String (file location of covariance model)
Args : String (file location of covariance model)
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 (uses cmsearch)
Example :
Returns : float or undef
Args : none
run
Title : run
Usage : $obj->run($seqFile)
Function: Runs Infernal and returns Bio::SearchIO
Returns : A Bio::SearchIO
Args : A Bio::PrimarySeqI or file name
Specific program interface methods
cmsearch
Title : cmsearch
Usage : $obj->cmsearch($seqFile)
Function: Runs Infernal cmsearch and returns Bio::SearchIO
Returns : A Bio::SearchIO
Args : Bio::PrimarySeqI or file name
cmalign
Title : cmalign
Usage : $obj->cmalign($seqFile)
Function: Runs Infernal cmalign and returns Bio::AlignIO
Returns : A Bio::AlignIO
Args : Bio::PrimarySeqI or file name
cmemit
Title : cmemit
Usage : $obj->cmemit($modelfile)
Function: Runs Infernal cmemit and returns Bio::AlignIO
Returns : A Bio::AlignIO
Args : [optional] File name containing covariance model
(will use model() if not passed)
cmbuild
Title : cmbuild
Usage : $obj->cmbuild($alignment)
Function: Runs Infernal cmbuild and saves covariance model
Returns : 1 on success (no object for covariance models)
Args : Bio::AlignIO with structural information (such as from Stockholm
format source) or alignment file
cmscore
Title : cmscore
Usage : $obj->cmscore($seq)
Function: Runs Infernal cmscore and saves output
Returns : None
Args : Bio::PrimarySeqI or file
_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 :
Args :
_writeAlignFile
Title : _writeAlignFile
Usage : obj->_writeAlignFile($seq)
Function: Internal(not to be used directly)
Returns :
Args :
perl v5.14.1 2011-07-21 Bio::Tools::Run::Infernal(3)
