ENH: Removed AMRFinderPlusAnnotation type

[VinzentRisch]

solves #94

• Removed AMRFinderPlusAnnotation. Now there are SampleData[AMRFinderPlusAnnotations] and FeatureData[AMRFinderPlusAnnotations] that both use the same type and dir format.
• Renamed files in fir format from "mutations" to "all_mutations".

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/95/head:pr-95
git checkout pr-95
pip install -e .

Download test data:
PR-94.zip

2. Test it out!

qiime tools import --input-path sample_data --output-path amr_annotations.qza --type "SampleData[AMRFinderPlusAnnotations]"
qiime tools import --input-path feature_data --output-path amr_annotation.qza --type "FeatureData[AMRFinderPlusAnnotations]"

2. Download test files
   PR-88.zip

3. Test it out!

qiime amr fetch-amrfinderplus-db --o-amrfinderplus-db amrfinderplus_db.qza --verbose
qiime amr annotate-sample-data-amrfinderplus --i-sequences test_mags.qza --output-dir output_mags --i-amrfinderplus-db amrfinderplus_db.qza --p-plus --p-curated-ident --p-organism "Escherichia" --p-report-all-equal --p-coverage-min 0.4 --p-translation-table "11" --verbose
qiime amr annotate-sample-data-amrfinderplus --i-sequences test_contigs.qza --output-dir output_contigs --i-amrfinderplus-db amrfinderplus_db.qza --p-plus --p-curated-ident --p-organism "Escherichia" --p-report-all-equal --p-coverage-min 0.4 --p-translation-table "11" --verbose

[ChristosMatzoros]

Hey @VinzentRisch,

Are the changes in annotate_sample_data_amrfinderplus part of this PR? If yes can you give me the commands to test it?

[VinzentRisch]

Yes they belong there. Although a bit hacky that they are there but didn't want a whole other PR for 3 name changes.
I added a second folder and second sets of commands to test sample data annotate function.
Thanks!

[ChristosMatzoros]

Hey @VinzentRisch,

It passed all the tests, it works as expecrted and the code looks good. Thanks for the extra commands.