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ENH: Added new action create-feature-table #20

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@VinzentRisch VinzentRisch commented Jan 29, 2025

closes #19

  • Adds new action that creates a FeatureTable[Frequency] from a GenomeData[AMRFinderPlusAnnotations] artifact.
  • The feature table shows the abundance of genes per contig.
  • It creates one table per artifact.
  • It reads in all tables as data frames with the columns ["Contig id", "Gene symbol", "Start", "Stop", "Strand"].
  • Next all duplicated rows are dropped. This is done because there can be multiple entries for the same hit that have different values only in the column "Accession of closest sequence" and "Name of closest sequence". These duplicated entries do not mean multiple hits in the same contig and have to be removed. Example: amr_annotations.tsv.zip
  • Error handling for cases if annotations without positional information is passed (when running with only protein input), or if empty mutation files are passed.

Test data:
amr_annot_contigs_0017.qza.zip

@VinzentRisch VinzentRisch requested a review from misialq January 30, 2025 10:23
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Hey @VinzentRisch, this all looks good! I have talked to our favourite tester, though, and I am getting a feeling that it perhaps would really make sense to integrate that functionality directly into the action which produces the original annotation tables since most likely people would be interested in looking at those directly. What do you think?

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ENH: Add new action for contigs x genes table
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