application subpackage

Beyond Biotite - The application subpackage

Although you can achieve a lot with Biotite, there are still a lot of things which are not implemented in this Python package. But wait, this is what the biotite.application package is for: It contains interfaces for popular external software. This ranges from locally installed software to external tools running on web servers. The usage of these interfaces is seamless: Rather than writing input files and reading output files, you simply put in your Python objects (e.g. instances of Sequence or AtomArray) and the interface returns Python objects (e.g. an Alignment object).

Note

Note that in order to use an interface in biotite.application the corresponding software must be installed or the web server must be reachable, respectively. These programs are not shipped with the Biotite package.

The base class for all interfaces is the Application class. Each Application can be started by calling Application.start(). The results are collected with Application.join().

from biotite.sequence import ProteinSequence
from biotite.application.muscle import MuscleApp

app = MuscleApp([ProteinSequence("BIQTITE"), ProteinSequence("IQLITE")])
app.start()
# The application is running in the background
app.join()

The lines between start() and join() can be used to run any other code while the application is running in the background, including starting another Application in parallel.

The following chapters will give you an overview of the different applications interfaced in the biotite.application subpackage.