`AlifoldApp`#

class biotite.application_v2.viennarna.AlifoldApp(path: PathLike[str] | str = 'RNAalifold')[source]#

Bases: LocalApp

A handle to ViennaRNA’s RNAalifold software.

In contrast to FoldApp, the energy function includes a term that includes coevolution information extracted from an alignment in addition to the physical free energy term.

Parameters:

pathstr, optional: Path of the RNAalifold binary.

Examples

>>> matrix = SubstitutionMatrix.std_nucleotide_matrix()
>>> alignment = align_multiple(
...     [
...         NucleotideSequence("GGGGAAAACCCC"),
...         NucleotideSequence("GGGGAAAAACCCC"),
...         NucleotideSequence("GGGGGAAAACCCCC"),
...         NucleotideSequence("GGGAAAACCC"),
...     ],
...     matrix,
...     terminal_penalty=False,
... )[0]
>>> print(alignment)
-GGGGAAAACCCC-
-GGGGAAAAACCCC
GGGGGAAAACCCCC
--GGGAAAACCC--
>>> result = AlifoldApp().run(alignment).result()
>>> print(result.dot_bracket)
.((((....)))).
>>> print(result.free_energy, result.covariance_energy)
-4.47 0.31
>>> print(result.base_pairs())
[[ 1 12]
 [ 2 11]
 [ 3 10]
 [ 4  9]]
>>> print(result.base_pairs_of(0))
[[ 0 11]
 [ 1 10]
 [ 2  9]
 [ 3  8]]

run(alignment: Alignment, temperature: float = 37, pairs: Any = None, paired: Any = None, unpaired: Any = None, downstream: Any = None, upstream: Any = None, enforce: bool = False, **kwargs: Any) → CommandSetup[FoldedAlignment]#

Predict the consensus secondary structure of an alignment.

Constraints of known paired or unpaired bases can be added to the folding algorithm via pairs, paired, unpaired, downstream and upstream.

Parameters:

alignmentAlignment: An alignment of RNA sequences.
temperaturefloat, optional: The temperature (°C) to be assumed for the energy parameters.
pairsndarray, shape=(n,2), dtype=int, optional: Positions of constrained base pairs.
pairedndarray, shape=(n,), dtype=int or dtype=bool, optional: Positions of bases that are paired with any other base.
unpairedndarray, shape=(n,), dtype=int or dtype=bool, optional: Positions of bases that are unpaired.
downstreamndarray, shape=(n,), dtype=int or dtype=bool, optional: Positions of bases that are paired with any downstream base.
upstreamndarray, shape=(n,), dtype=int or dtype=bool, optional: Positions of bases that are paired with any upstream base.
enforcebool, optional: If set to true, the given constraints are enforced, i.e. the respective base pairs must form. By default, a constraint only forbids the formation of a base pair that would conflict with this constraint.
**kwargs: Additional command line options.

Returns:

futureFuture of FoldedAlignment: A handle to the running computation.

AlifoldApp#

`AlifoldApp`#