RNAmediator.ConstraintPLFold.pl_fold

RNAmediator.ConstraintPLFold.pl_fold(window, span, region, temperature, multi, unconstrained, unpaired, paired, save, procs, outdir, run_settings: Dict[str, SequenceSettings], pattern=None, queue=None, configurer=None, level=None)

Run RNAplfold

Parameters:

• window (int Size of window to fold) –

• span (int Maximum base-pair span to be evaluated) –

• region (int -u Option of RNAplfold) –

• temp (float Temperature) –

• multi (int Multiplyer for Window extension) –

• unconstrained (str Infix for ouput files of unconstrained folding) –

• unpaired (str Infix for ouput files of unpaired constraint) –

• paired (str Infix for output files of paired constraint, None will skip paired constraint folding) –

• save (bool Should npy or npy and gz output be saved) –

• procs (int Number of cores to use) –

• outdir (str Location of the Output directory. If it is an empty string os.cwd() is used) –

• run_settings (Dict[str, SequenceSettings] Dictionary with sequence settings per Fasta ID) –

• pattern (str Filter for Gene of Interest (optional)) –

• queue (multiprocessing_queue Logging process queue) –

• configurer (multiprocessing_config for Logging processes) –

• level (logging.level Level for log process) –