RNAmediator.ConstraintFold.fold

RNAmediator.ConstraintFold.fold(run_settings, outdir, window, span, temp, constrain, conslength, procs, save=None, pattern=None, queue=None, configurer=None, level=None)

fold prepares and submits sequences to be folded constrained and unconstrained

Parameters:

  • run_settings (Dict[str, SequenceSettings] RNAmediator run settings dictionary using fasta ids as keys and Sequence Settings as values) –

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

  • window (int Size of window to fold) –

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

  • temp (int) – Temperature to fold at

  • constrain (str The file location of constrain file) –

  • conslength (int Length of the constraint, only used if constrain is sliding) –

  • procs (int Number of processes to run in parallel) –

  • save (str) – If not STDOUT will be saved to file

  • pattern (str String pattern for gene of interest) –

  • queue (multiprocessing_queue Logging process queue) –

  • configurer (multiprocessing_config for Logging processes) –

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

Return type:

Call to constrain_seq