table of contents
RG::Reprof(3pm) | User Contributed Perl Documentation | RG::Reprof(3pm) |
NAME¶
RG::Reprof::Reprof - protein secondary structure and accessibility predictorSYNOPSIS¶
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/>2016-07-14 | perl v5.22.2 |