NAME

       Bio::Tools::Run::ERPIN - Wrapper for local execution of the ERPIN suite of programs.

SYNOPSIS

         #run

         my @params = (
                     trset => 'BL.erpin',
                     region => [1, 10],
                     # Set up search strategy this way...
                     strategy => [ 'umask'   => [1, 2],
                                   'umask'   => [1, 2, 3, 4],
                                   'umask'   => [1, 2, 3, 4, 5, 6],
                                   'nomask',
                                   'cutoff'  => [0, 10, 15, 20]
                                   ]
                     # or use a simple string...
                     #strategy => '-umask 4 -add 5 -nomask -cutoff 0 10 15',
                     pcw => 100
                    );

         my $factory = Bio::Tools::Run::ERPIN->new(-program =>'erpin',
                                                       @params);

         # Pass the factory a Bio::Seq object or a file name
         # Returns a Bio::SearchIO object

         #my $search = $factory->run("B_sub.fas");
         my $search = $factory->run($seq);
         my @feat;
         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

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::RNAMotif->new(@params)
        Function: creates a new RNAMotif factory
        Returns:  Bio::Tools::Run::RNAMotif
        Args    : list of parameters
                  -tempfile        => set tempfile flag (default 0)
                  -outfile_name    => set file to send output to (default none)

   program_name
        Title   : program_name
        Usage   : $factory>program_name()
        Function: holds the program name
        Returns:  string
        Args    : None

   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
        Example :
        Returns : float or undef
        Args    : none

   run
        Title   :  run
        Usage   :  $obj->run($seqFile)
        Function:  Runs ERPIN programs and returns Bio::SearchIO
        Returns :
        Args    :  Must pass Bio::PrimarySeqI's or file names

   tempfile
        Title   : tempfile
        Usage   : $obj->tempfile(1)
        Function: Set tempfile flag.  When set, writes output to a tempfile; this
                  is overridden by outfile_name() if set
        Returns : Boolean setting (or undef if not set)
        Args    : [OPTIONAL] Boolean

   _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 : writes passed Seq objects to tempfile, to be used as input
                  for program
        Args    :