ENH: Added actions that can partition annotation artifacts from reads and MAGs.

[VinzentRisch]

This PR closes #53

• Added partition-reads-gene-annotations, partition-reads-allele-annotations and partition-mags-annotations actions.
• These actions can partition artifacts of type SampleData[CARDAnnotation], SampleData[CARDAlleleAnnotation] and SampleData[CARDAnnotation] into a collection of a specified number of partitions with the same type.
• These actions are needed to enable parallelisation of the kmer query functions that will be added ENH: Add new action that predicts the origin of detected ARGs. #21.

Set up an environment for intel

mamba create -yn q2-amr \
  -c conda-forge -c bioconda -c qiime2 -c defaults \
  -c https://packages.qiime2.org/qiime2/2024.2/shotgun/released/ \
  qiime2 q2cli q2templates q2-types rgi

conda activate q2-amr

pip install --no-deps --force-reinstall \
  git+https://github.com/misialq/rgi.git@py38-fix \

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/54/head:pr-54
git checkout pr-54
pip install -e .

2. Download test files
   PR-54.zip

3. Test it out!

qiime amr partition-mags-annotations --i-annotations PR-54/amr_annotations.qza --p-num-partitions 13 --o-partitioned-annotations PR-54/partition_mags --verbose
qiime amr partition-reads-allele-annotations --i-annotations PR-54/amr_allele_annotation.qza --p-num-partitions 3 --o-partitioned-annotations PR-54/partition_reads-allele --verbose
qiime amr partition-reads-gene-annotations --i-annotations PR-54/amr_gene_annotation.qza --p-num-partitions 2 --o-partitioned-annotations PR-54/partition_reads-gene --verbose

4. Check if partitioned artifacts from allele annotations and gene annotations are of type SampleData[CARDGeneAnnotation % Properties('kma')]

[VinzentRisch]

Hi @misialq
Can you have a look at the partitioning actions for the annotation formats?
Its very similar to the function you wrote for the MAGs.

[VinzentRisch]

Hey @misialq
My CI is failing here
https://github.com/bokulich-lab/q2-amr/actions/runs/8081580912/job/22080505032?pr=54#step:8:116
is this something i have to resolve or is this a problem because there was a new release of qiime?

[misialq]

Hey @VinzentRisch, on the CI: it seems like the conda channel for the 2024.5 distro does not exist yet so I'd say it's related to the new release.

[VinzentRisch]

Good Morning @misialq
Could you give this a look?

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 94.29%. Comparing base (0ff2501) to head (75c8438).

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #54      +/-   ##
==========================================
+ Coverage   93.89%   94.29%   +0.40%     
==========================================
  Files          20       20              
  Lines        1393     1491      +98     
==========================================
+ Hits         1308     1406      +98     
  Misses         85       85              

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[misialq]

Hey @VinzentRisch, see some suggestions below.

[misialq]

Hey @VinzentRisch, some more suggestions floating your way - mostly about readability.

[misialq]

Hey @VinzentRisch, I think this looks pretty good now! I just had a little realization - see below. This is the last comment on this one, promise!

[misialq]

Great work, thanks @VinzentRisch! Merge away 🚀

[VinzentRisch]

Perfect!
But I cant merge because there is still this expected Ci check for macos latest
Can you merge it for me?

[misialq]

Oh, yeah, sure thing!