We are currently utilizing Biopython's BLAST wrapper, Bio.Blast.Applications.NcbiblastnCommandline, which has been deprecated in the latest Biopython release with plans for removal in the future.
This deprecation is currently indicated by the following warning:
/home/user1/micall/venv/lib/python3.10/site-packages/Bio/Application/__init__.py:40: BiopythonDeprecationWarning: The
Bio.Application modules and modules relying on it have been deprecated.
Due to the ongoing maintenance burden of keeping command line application
wrappers up to date, we have decided to deprecate and eventually remove these
modules.
We instead now recommend building your command line and invoking it directly
with the subprocess module.
warnings.warn(
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
There are only two instances of this deprecated API in MiCall, and the transition to a direct subprocess call should be straightforward.
We are currently utilizing Biopython's BLAST wrapper,
Bio.Blast.Applications.NcbiblastnCommandline, which has been deprecated in the latest Biopython release with plans for removal in the future.This deprecation is currently indicated by the following warning:
There are only two instances of this deprecated API in MiCall, and the transition to a direct subprocess call should be straightforward.