RNAmediator.Tweaks.RNAtweaks.cmd_rnafold

RNAmediator.Tweaks.RNAtweaks.cmd_rnafold(sequence: str, window: int, span: int, region: int = 30, temperature: float = 37, constype: str = 'hard', consval: str = '', constraint: Iterable[Tuple[str, int, int]] = None, FoldOut: FoldOutput = None) → PLFoldOutput

command line wrapper for RNAplfold

Parameters:

  • sequence (str) – string representation of the sequence either RNA or DNA

  • window (int) – RNAplfold window option

  • span (int) – RNAplfold span option

  • region (int, optional) – RNAplfold region (u) option (default is 30)

  • temperature (float) – RNAplfold temperature setting

  • constype (str) – Type of constraint to apply, can be [‘hard’(Default), ‘soft’(not implemented yet), ‘mutate’]

  • consval (str) – Value for constraint to apply, ignored when constype is ‘hard’

  • constraint (Iterable[Tuple[str, int, int]], optional) –

    Constraints as Tuple in format (paired(p)/unpaired(u), start, end) (default is None)

    !!Warning!! ZERO BASED !!Warning!!

    FoldOut: FoldOutput, optional

    FoldOutput object to work on

Returns:

FoldOutput object

Return type:

FoldOutput