Provided by: libbio-perl-run-perl_1.7.2-4_all bug

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    :