ENH: New type called AMRFinderPlusDatabase

[VinzentRisch]

solves #80

This new type is used for the storage of the database for the amrfinderplus tool.

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/81/head:pr-81
git checkout pr-81
pip install -e .

2. Download test files
   amrfinderplus_database.zip: https://polybox.ethz.ch/index.php/s/nJmbGpkM1ywS9VW

3. Test it out!

qiime tools import --input-path database --output-path database.qza --type AMRFinderPlusDatabase 

[VinzentRisch]

Hey @misialq
Could you have a look at this? I now created two formats that just validate any binary or text file. Should I add formats for the tab separated files?
I could add new formats for these files that just validates the header:
AMR_DNA-Streptococcus_pneumoniae.tab
changes.txt
database_format_version.txt
fam.tab
taxgroup.tab
version.txt
AMRProt-mutation.tab
AMRProt-susceptible.tab

Those would be 8 new formats so Im not so sure if that even makes sense.

[misialq]

Once you change the directory format as I pointed out above, you can remove most of those test files - they are just polluting the repo.

[VinzentRisch]

I left them there, because if I remove most files, the test would become meaningless.
Only like this it is actually tested if all regex expressions work with the database files.

[misialq]

Why do you think it will become meaningless? Your test should just make sure that the regex is working - for this you don't need all the files for all the species - you could just keep a set of those for, say, two taxa and remove everything else (now that you have the FileCollection in place).

[VinzentRisch]

Hi @misialq could you have another look at this?
I'm not so sure about the path makers. Do they work like this with a regex?

[misialq]

Looks good! 🚀