MAINT: Removed "overall-mapping-stats.txt" from CARDGeneAnnotationDirectoryFormat

[VinzentRisch]

This PR fixes #28 and #30

• Removed "overall-mapping-stats.txt" from CARDGeneAnnotationDirectoryFormat.
• Changed the input of visualize-annotation-stats to only accept CARDAlleleAnnotation because the stats file is now only included in the CARDAlleleAnnotationDirectoryFormat.
• Changed CARDAlleleAnnotation to SampleData[CARDAlleleAnnotation] in the input plugin_setup of visualize-annotation-stats.
• Changed annotate-reads-card so that "overall-mapping-stats.txt" only gets moved to the CARDAlleleAnnotation artifact.

To test annotate-reads-card action, download test files and run this (takes about 3 mins):

qiime amr annotate-reads-card --i-reads 25mb_reads.qza --i-card-db card_db.qza --output-dir test_q2_amr_29 --p-threads 2

To test visualize-annotation-stats run this:

qiime amr visualize-annotation-stats --i-amr-reads-annotation test_q2_amr_29/amr_allele_annotation.qza --o-visualization test_q2_amr_29/amr_allele_annotation_stats.qzv

[codecov-commenter]

Codecov Report

Attention: 2 lines in your changes are missing coverage. Please review.

Comparison is base (898241c) 66.70% compared to head (c7102bf) 66.58%.

Files	Patch %	Lines
q2_amr/card/reads.py	0.00%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #29      +/-   ##
==========================================
- Coverage   66.70%   66.58%   -0.13%     
==========================================
  Files          13       13              
  Lines         835      832       -3     
==========================================
- Hits          557      554       -3     
  Misses        278      278              

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[VinzentRisch]

Hi Santiago :) This is again a very small one with no new functionality.
I added the test data to download and the command to run. Everything should run quickly without any problems.

[Sann5]

Coolioou, I'll check it out :).

[Sann5]

In your second bullet point of the PR message you say

Changed the input of visualize-annotation-stats to only accept CARDAlleleAnnotation because the stats file is now only included in the CARDGeneAnnotationDirectoryFormat.

Do you mean?

Changed the input of visualize-annotation-stats to only accept CARDAlleleAnnotation because the stats file is now only included in the CARDAlleleAnnotationDirectoryFormat.

[Sann5]

• ✅ I all looks good to me!
• ✅ All test pass locally.
• ✅ annotate-reads-card and visualize-annotation-stats run without problems. I did not inspect the outputs to make sure that made sense (not that I could either), but I guess you did this :)
• ❓Im just curious about one thing. How come you decided to set "amr_reads_annotation": SampleData[CARDAlleleAnnotation] and not "amr_reads_annotation": CARDAlleleAnnotation. I'm not an expert on Semantic Types so It's not so obvious why one would choose one over the other. Also apparently you already had CARDAlleleAnnotation registered as a type of SampleData before this PR so I am confused why you didn't use it before.

[VinzentRisch]

Thank you! 👍
Thanks for pointing that out, I did mean CARDAlleleAnnotationDirectoryFormat. :)

And it should have been SampleData[CARDAlleleAnnotation] from the start. That was a bug, visualize-annotation-stats did not work some time before this fix.
So you can't choose the one or the other.