BUG: Changed read_in_txt helper function to use unique column as index for allele mapping data

[VinzentRisch]

This PR was created to fix #26.

• Added new map_type parameter to read_in_txt.
• If map_type is set to "allele" the column Reference Sequence is used as the index for the count tables. Reference Sequence values are unique and this solves the issue with the biom table format. Only downside is that the unique identifiers are quite long and not very readable (eg. Prevalence_Sequence_ID:97743|ID:1437|Name:AcrF|ARO:3000502) instead of just AcrF
• If map_type is set to "gene" the behaviour is as before and the column ARO Term is used as the index.

Set up an environment

CONDA_SUBDIR=osx-64 mamba create -yn q2-amr \
  -c conda-forge -c bioconda -c qiime2 -c defaults \
  -c https://packages.qiime2.org/qiime2/2023.9/shotgun/released/ \
  qiime2 q2cli q2templates q2-types q2-types-genomics rgi

conda activate q2-amr
conda config --env --set subdir osx-64

pip install --no-deps --force-reinstall \
  git+https://github.com/misialq/rgi.git@py38-fix \
  git+https://github.com/bokulich-lab/q2-amr.git

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/27/head:pr-27
git checkout pr-27
pip install -e .

2. Download test files reads.qza and card_db.qza

3. Test it out!
   Takes about 10 min.

qiime amr annotate-reads-card --i-reads 25mb_reads.qza --i-card-db card_db.qza --output-dir test_27 --p-threads 2 --p-include-wildcard

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (c179878) 93.35% compared to head (2efc691) 93.37%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #27      +/-   ##
==========================================
+ Coverage   93.35%   93.37%   +0.01%     
==========================================
  Files          18       18              
  Lines        1054     1056       +2     
==========================================
+ Hits          984      986       +2     
  Misses         70       70              

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[misialq]

Hey @ChristosMatzoros, could you please check this one out? Thanks!

[ChristosMatzoros]

Thank you for putting this together @VinzentRisch. I executed both the old and new code and achieved the expected results. You did an excellent job introducing the unique identifier for allele mappings, effectively preventing duplicate IDs in the biom table. I consider this to be the most straightforward and clean solution. Regarding the size of the unique identifiers, I believe they do not detract from readability; quite the opposite, they may provide important information to the user. Everything seems ok from my side!

[VinzentRisch]

Hi @misialq, @ChristosMatzoros just reviewed and approved my changes, but i still can't merge the PR.
I think it is because @ChristosMatzoros lacks the needed permissions to approve my changes.
Can you give @ChristosMatzoros these permissions?

[misialq]

Hey @VinzentRisch, sorry about that - I fixed the permissions and you should be able to merge now (after updating). 🚀