biotite.application.viennarna.RNAalifoldApp¶

class biotite.application.viennarna.RNAalifoldApp(alignment, temperature=37, bin_path='RNAalifold')[source]¶

Bases: LocalApp

Predict the consensus secondary structure from a ribonucleic acid alignment using ViennaRNA’s RNAalifold software.

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

Internally this creates a Popen instance, which handles the execution.

Parameters

alignmentAlignment: An alignment of RNA sequences.
temperatureint, optional: The temperature (°C) to be assumed for the energy parameters.
bin_pathstr, optional: Path of the RNAalifold binary.

add_additional_options(options)¶

Add additional options for the command line program. These options are put before the arguments automatically determined by the respective LocalApp subclass.

This method is focused on advanced users, who have knowledge on the available options of the command line program and the options already used by the LocalApp subclasses. Ignoring the already used options may result in conflicting CLI arguments and potential unexpected results. It is recommended to use this method only, when the respective LocalApp subclass does not provide a method to set the desired option.

Parameters

optionslist of str: A list of strings representing the command line options.

Notes

In order to see which options the command line execution used, try the get_command() method.

Examples

>>> seq1 = ProteinSequence("BIQTITE")
>>> seq2 = ProteinSequence("TITANITE")
>>> seq3 = ProteinSequence("BISMITE")
>>> seq4 = ProteinSequence("IQLITE")
>>> # Run application without additional arguments
>>> app = ClustalOmegaApp([seq1, seq2, seq3, seq4])
>>> app.start()
>>> app.join()
>>> print(app.get_command())
clustalo --in ...fa --out ...fa --force --output-order=tree-order --seqtype Protein --guidetree-out ...tree
>>> # Run application with additional argument
>>> app = ClustalOmegaApp([seq1, seq2, seq3, seq4])
>>> app.add_additional_options(["--full"])
>>> app.start()
>>> app.join()
>>> print(app.get_command())
clustalo --full --in ...fa --out ...fa --force --output-order=tree-order --seqtype Protein --guidetree-out ...tree

cancel()¶: Cancel the application when in RUNNING or FINISHED state.

clean_up()¶

Do clean up work after the application terminates.

PROTECTED: Optionally override when inheriting.

static compute_secondary_structure(alignment, bin_path='RNAalifold')¶

Predict the secondary structure of a ribonucleic acid sequence using ViennaRNA’s RNAalifold software.

This is a convenience function, that wraps the RNAalifoldApp execution.

Parameters

alignmentAlignment: An alignment of RNA sequences.
bin_pathstr, optional: Path of the RNAalifold binary.

Returns

dotbracketstr: The secondary structure in dot bracket notation.
free_energyfloat: The free energy.
covariance_energyfloat: The energy of the covariance term.

evaluate()¶

Evaluate application results. Called in join().

PROTECTED: Override when inheriting.

get_app_state()¶

Get the current app state.

Returns

app_stateAppState: The current app state.

get_base_pairs(sequence_index=None)¶

Get the base pairs from the suggested secondary structure.

Parameters

sequence_indexint, optional: By default, the base pairs point to positions in the alignment. If sequence_index is set, the returned base pairs point to positions in the given sequence, instead. The sequence is specified as index in the alignment. For example, if the alignment comprises three sequences, sequence_index is in range 0-2.

Returns

base_pairsndarray, shape=(n,2): Each row corresponds to the positions of the bases in the alignment. If sequence_index is set, the positions correspond to the given sequence.

get_command()¶

Get the executed command.

Cannot be called until the application has been started.

Returns

commandstr: The executed command.

Examples

>>> seq1 = ProteinSequence("BIQTITE")
>>> seq2 = ProteinSequence("TITANITE")
>>> seq3 = ProteinSequence("BISMITE")
>>> seq4 = ProteinSequence("IQLITE")
>>> app = ClustalOmegaApp([seq1, seq2, seq3, seq4])
>>> app.start()
>>> print(app.get_command())
clustalo --in ...fa --out ...fa --force --output-order=tree-order --seqtype Protein --guidetree-out ...tree

get_consensus_sequence_string()¶

Get the consensus sequence.

As the consensus may contain gaps, the sequence is returned as string.

Returns

consensusstr: The consensus sequence.

get_covariance_energy()¶

Get the energy of the artificial covariance term (kcal/mol) of the suggested consensus secondary structure.

Returns

covariance_energyfloat: The energy of the covariance term.