RG::Reprof(3pm) 					User Contributed Perl Documentation					   RG::Reprof(3pm)

NAME

       RG::Reprof::Reprof - protein secondary structure and accessibility predictor

SYNOPSIS

       use RG::Reprof::Reprof;

DESCRIPTION

       See module commented source for further details.

   Methods
       OBJ RG::Reprof::Reprof->new( model_dir => PATH )
	   Default model_dir: /tmp/lkajan/root/share/reprof.

	   Returns new instance of RG::Reprof::Reprof.

       int $OBJ->run( input_file => PATH, out_file => PATH, mutation_file => PATH, specific_models => hashref, output_func => coderef )
	   out_file may be a directory.
	   mutation_file may be undefined.
	   specific_models may be undefined.
	       This is a hash of model and feature files with 'model_name' keys like:

		{
		  'fub_model' => '/path/to/model_file',
		  'fub_features' => '/path/to/features_file'
		}

	       Check the module source for the list for model names.

	   void output_func( out_file, sec_pred, acc_pred, sequence ) - function to call when output is ready.
	       If undefined, the built-in write_output() function is called that prints results to one or more files.  The following positional
	       parameters are passed to this function:

	       out_file
		   Output file name.

	       sec_pred
		   Secondary structure prediction, see source for details.

	       acc_pred
		   Accessibility prediction, see source for details.

	       sequence
		   Reference to array of residues of input sequence (e.g. [ 'M', 'A', 'G', ... ] ).

AUTHOR

       Original version by Peter Hoenigschmid <hoenigschmid@rostlab.org> and Burkhard Rost.

       Some perl module work and documentation by Laszlo Kajan <lkajan@rostlab.org>.

SEE ALSO

       <http://rostlab.org/>

perl v5.14.2							    2012-01-13							   RG::Reprof(3pm)