RG::Reprof::Reprof - protein secondary structure and accessibility
predictor
See module commented source for further details.
- 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',
... ] ).
Original version by Peter Hoenigschmid
<hoenigschmid@rostlab.org> and Burkhard Rost.
Some perl module work and documentation by Laszlo Kajan
<lkajan@rostlab.org>.