RG::Reprof3pm

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', ... ] ).