PlexApp

class biotite.application_v2.viennarna.PlexApp(path: PathLike[str] | str = 'RNAplex')

Bases: LocalApp

A handle to ViennaRNA’s RNAplex software.

Parameters:

pathstr, optional

Path of the RNAplex binary.

Examples

>>> target = NucleotideSequence("AAAAAAAGGGGGGGGGGAAAAAAA")
>>> query = NucleotideSequence("CCCCCCCCCC")
>>> results = PlexApp().run(target, query).result()
>>> print(results[0].dot_bracket)
.((((((((((.&))))))))))
>>> print(results[0].spans)
[(6, 18), (0, 10)]
>>> print(results[0].base_pairs())
[[ 0  7  1  9]
 [ 0  8  1  8]
 [ 0  9  1  7]
 [ 0 10  1  6]
 [ 0 11  1  5]
 [ 0 12  1  4]
 [ 0 13  1  3]
 [ 0 14  1  2]
 [ 0 15  1  1]
 [ 0 16  1  0]]

run(target: NucleotideSequence, query: NucleotideSequence, temperature: float = 37, **kwargs: Any) → CommandSetup[list[CofoldedRNA]]

Find hybridization sites of a query in a target.

Parameters:

targetNucleotideSequence

The (usually long) target RNA strand.

queryNucleotideSequence

The (usually short) query RNA strand.

temperaturefloat, optional

The temperature (°C) to be assumed for the energy parameters.

**kwargs

Additional command line options.

Returns:

futureFuture of list of CofoldedRNA

A handle to the running computation. In each CofoldedRNA the first strand is the target and the second the query. Only the interacting parts are covered by the structure, as given by CofoldedRNA.spans.