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/>
