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Bio::Tools::Run::Infernal.3pm

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 @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    :