Provided by: libbio-perl-run-perl_1.7.3-9_all 
NAME
Bio::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 $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 optional outfile_name, returns
# Bio::SearchIO
# 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,
# --merge option allows two alignments generated
# from the same CM to be merged.
# output to outfile_name, returns Bio::AlignIO
$factory->cmscore(); # scores set cov. model against Bio::PrimarySeqI,
# output to outfile_name/STDOUT.
$factory->cmbuild($aln); # builds covariance model based on alignment
# CM to outfile_name or model_file (one is required
# here), output to STDOUT.
$factory->cmemit(); # emits sequence from specified cov. model;
# set one if no file specified. output to
# outfile_name, returns Bio::SeqIO or (if -a is set)
# Bio::AlignIO
$factory->cmcalibrate($file); # calibrates specified cov. model; output to
# STDOUT
$factory->cmstat($file); # summary stats for cov. model; set one if no file
# specified; output to STDOUT
# 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, cmcalibrate, cmalign, cmemit, cmbuild, cmscore, and cmstat. cmsearch will return
a Bio::SearchIO, cmemit a Bio::SeqIO/AlignIO, and cmalign a Bio::AlignIO. All others send
output to STDOUT. Optionally, any program's output can be redirected to outfile_name.
We HIGHLY suggest upgrading to Infernal 1.0. In that spirit, this wrapper now supports
parameters for Infernal 1.0 only; for wrapping older versions of Infernal we suggest using
the version of Bio::Tools::Run::Infernal that came with previous versions of BioPerl-run.
NOTE: Due to conflicts in the way Infernal parameters are now formatted vs. subroutine
naming in Perl (specifically the inclusion of hyphens) and due to the very large number of
parameters available, setting and resetting parameters via set_parameters() and
reset_parameters() is required. All valid parameters can be set, but only ones valid for
the executable set via program()/program_name() are used for calling the executables, the
others are silently ignored.
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::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)
Status : Unstable (may delegate to program_name, which is the interface method)
program_name
Title : program_name
Usage : $factory>program_name()
Function: holds the program name
Returns: string
Args : None
model_file
Title : model_file
Usage : $obj->model_file()
Function: Set the model file 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 : None; set model_file() to use a specific model
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 name
cmscore
Title : cmscore
Usage : $obj->cmscore($seq)
Function: Runs Infernal cmscore and saves output
Returns : None
Args : None; set model_file() to use a specific model
cmcalibrate
Title : cmcalibrate
Usage : $obj->cmcalibrate('file')
Function: Runs Infernal calibrate on specified CM
Returns : None
Args : None; set model_file() to use a specific model
cmstat
Title : cmstat
Usage : $obj->cmstat($seq)
Function: Runs Infernal cmstat and saves output
Returns : None
Args : None; set model_file() to use a specific model
Bio::ParameterBaseI-specific methods
These methods are part of the Bio::ParameterBaseI interface
set_parameters
Title : set_parameters
Usage : $pobj->set_parameters(%params);
Function: sets the parameters listed in the hash or array
Returns : None
Args : [optional] hash or array of parameter/values. These can optionally
be hash or array references
Note : This only sets parameters; to set methods use the method name
reset_parameters
Title : reset_parameters
Usage : resets values
Function: resets parameters to either undef or value in passed hash
Returns : none
Args : [optional] hash of parameter-value pairs
validate_parameters
Title : validate_parameters
Usage : $pobj->validate_parameters(1);
Function: sets a flag indicating whether to validate parameters via
set_parameters() or reset_parameters()
Returns : Bool
Args : [optional] value evaluating to True/False
Note : Optionally implemented method; up to the implementation on whether
to automatically validate parameters or optionally do so
parameters_changed
Title : parameters_changed
Usage : if ($pobj->parameters_changed) {...}
Function: Returns boolean true (1) if parameters have changed
Returns : Boolean (0 or 1)
Args : None
Note : This module does not run state checks, so this always returns True
available_parameters
Title : available_parameters
Usage : @params = $pobj->available_parameters()
Function: Returns a list of the available parameters
Returns : Array of parameters
Args : [optional] name of executable being used; defaults to returning all
available parameters
get_parameters
Title : get_parameters
Usage : %params = $pobj->get_parameters;
Function: Returns list of set key-value pairs, parameter => value
Returns : List of key-value pairs
Args : [optional]
'full' - this option returns everything associated with the parameter
as an array ref value; that is, not just the value but also
the value, type, and prefix. Default is value only.
'valid'- same a 'full', but only returns the grouping valid for the
currently set executable
to_* methods
All to_* methods are implementation-specific
to_exe_string
Title : to_exe_string
Usage : $string = $pobj->to_exe_string;
Function: Returns string (command line string in this case)
Returns : String
Args :
_writeSeqFile
Title : _writeSeqFile
Usage : obj->_writeSeqFile($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 :