The updated code according to the developer's advice, to fit eukaryotic plastid screening

[Andyargueasae]

Hi Ben and singleM team,

After talking with Ben several times I reformed the code of my branch, to change the code mainly in condense.py to solve the issue with:

1. error in writing information to otu when prokaryotic taxa are considered as off-targets (in my context, which deals with plastid/eukaryotic sequences);
2. target_domain detection in genus-wise EM that causes zero-division errors.

Now, feel free to review it, and feel free to notify me/deny my pull request.

Cheers
Andy

[Andyargueasae]

I have fixed the condense.py and the trials using default metapackage and my custom plastid metapackage are successful.

[wwood]

@codex review

[Andyargueasae]

Resolved the above issues and the trials for both metapackages are now passed.

[chatgpt-codex-connector]

Codex Review: Didn't find any major issues. Hooray!

Reviewed commit: a8bd6a40d4

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