/ 
BioPerl-Run-1.007003
River stage one • 2 direct dependents • 2 total dependents
/ Bio::Tools::Run::Infernal

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    :