`biotite.application_v2`#

A redesigned subpackage that provides interfaces for external software.

In contrast to biotite.application, an Application is a reusable, stateless handle to the wrapped software. A run is launched by calling the respective method (e.g. align()) with all required parameters, which returns a Future. The actual result is obtained by calling Future.result().

Content#

`Application`	Subclasses of this base class represent wrappers around external runnable software.
`CLIArgument`	A positional command line argument.
`CLIFlag`	A valueless command line flag.
`CLIOption`	A key-value command line option.
`CancelledError`	The Future was cancelled.
`CommandSetup`	The specification of a single command line run.
`CompositeFuture`	A future combining the results of multiple futures.
`Future`	A handle to an application run that may still be in progress.
`LocalApp`	The base class for all locally installed command line applications.
`LocalProcessFuture`	A `Future` backed by a locally running `Popen` process.
`MSAInput`	The sequences and substitution matrix prepared for an MSA run.
`PostprocessFuture`	A future applying a function to the result of another future.
`VersionError`	Indicate that the version of the wrapped software is not supported.
`command`	Turn a `LocalApp` method into a runnable command.
`resolve_gap_penalty`	Split a gap penalty into a gap opening and gap extension penalty.

Subpackages#

`biotite.application_v2.autodock`	A subpackage for static ligand docking with Autodock.
`biotite.application_v2.dssp`	A subpackage for protein secondary structure assignment using DSSP.
`biotite.application_v2.sra`	A subpackage for fetching sequencing data from the NCBI sequence read archive (SRA) using sra-tools.
`biotite.application_v2.muscle`	A subpackage for multiple sequence alignments using MUSCLE.
`biotite.application_v2.mmseqs`	Interfaces to the MMseqs2 and Foldseek command line programs.
`biotite.application_v2.tantan`	A subpackage for masking sequence regions using the `tantan` software.
`biotite.application_v2.mafft`	A subpackage for multiple sequence alignments using MAFFT.
`biotite.application_v2.clustalo`	A subpackage for multiple sequence alignments using Clustal-Omega.
`biotite.application_v2.viennarna`	A subpackage that provides interfaces to the ViennaRNA software package.