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)