ValueError: invalid mode (expected 'global' or 'local'

[wangzc66]

NEAT/neat/read_simulator/utils/read.py

Line 413 in 82649c1

aligner2.mode = "fogsaa"

ValueError: invalid mode (expected 'global' or 'local'

There is a dependency issue with the Bioconda version of the software. The latest version of Biopython cannot be installed, which has caused this problem.

[keshav-gandhi]

Hello! Would you be able to provide us with more information about how you installed NEAT?

[wangzc66]

There is no fogsaa mode in Biopython versions 1.79.*.

[keshav-gandhi]

Hello! I will look into this further.

In the meantime, this form of installation should be more stable:

(base) $ conda env create -f environment.yml
(base) $ conda activate neat
(neat) $ poetry install
(neat) $ neat --help # tests that NEAT has installed correctly

[joshfactorial]

At this point, I would try to manually install biopython 1.8+ to ensure you have the correct version.

[keshav-gandhi]

Hello @wangzc66,

We are working on a fix as described in /issues/257.

[keshav-gandhi]

The issue has been resolved (#257).