Bio::Tools::Run::ERPIN(3pm)				User Contributed Perl Documentation			       Bio::Tools::Run::ERPIN(3pm)

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("	", ( $r->query_name,
				      $hit->name,
				      $hsp->hit->start,
				      $hsp->hit->end,
				      $hsp->meta,
				      $hsp->score,
				      )), "
";
	   }
	  }
	 }

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	:

perl v5.12.3							    2011-06-18					       Bio::Tools::Run::ERPIN(3pm)