ENH: New action to annotate FeatureData[MAG] or GenomeData[Proteins] with optional GenomeData[Loci]

[VinzentRisch]

solves #89

• Adds new action that can annotate FeatureData[MAG] or GenomeData[Proteins] with optional GenomeData[Loci].
• MAGs can be predicted with the moshpit action predict-genes-prodigal and then a combined analysis can be run with annotate-feature-data-amrfinderplus
• refactoriong in pluginsetup

Set up an environment

https://github.com/bokulich-lab/q2-amr?tab=readme-ov-file#installation

Run it locally

1. First, clone the repo and checkout the PR branch:

git clone https://github.com/bokulich-lab/q2-amr.git
cd q2-amr
git fetch origin pull/90/head:pr-90
git checkout pr-90
pip install -e .

2. Download test files
   PR-90.zip

3. Test it out!

qiime amr fetch-amrfinderplus-db --o-amrfinderplus-db amrfinderplus-db.qza --verbose
qiime amr annotate-feature-data-amrfinderplus --i-amrfinderplus-db amrfinderplus-db.qza --i-mags feature_data_mags.qza --i-proteins proteins.qza --i-loci loci.qza --p-organism "Escherichia" --p-plus --p-curated-ident --output-dir output_combined --verbose
qiime amr annotate-feature-data-amrfinderplus --i-amrfinderplus-db amrfinderplus-db.qza --i-mags feature_data_mags.qza --p-organism "Escherichia" --p-plus --p-curated-ident --output-dir output_mags --verbose
qiime amr annotate-feature-data-amrfinderplus --i-amrfinderplus-db amrfinderplus-db.qza --i-proteins proteins.qza --p-organism "Escherichia" --p-plus --p-curated-ident --output-dir output_proteins --verbose