Eskape case studies

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Description

What kind of change(s) are included?

• Feature (adds or updates new capabilities)
• Bug fix (fixes an issue).
• Enhancement (adds functionality).
• Breaking change (these changes would cause existing functionality to not work as expected).

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  @jananiravi @the-mayer

[jananiravi]

Assigned this to @AbhirupaGhosh (primary) and @epbrenner @the-mayer (secondary).

Abhirupa/Evan/David, along with the script, could you also check if this is the right file format we want to use? Thanks!

[AbhirupaGhosh]

Refer to this comment for guidance.

Title: Process CARD Data, Map Short Names, and Run MolEvolveR

• Download CARD Data: Retrieve the latest CARD dataset. (DOWNLOAD)
• Open ARO_index.tsv: Parse the file (in R).
• Map CARD Short Name: Map the CARD Short Name column to shortname_antibiotics.tsv and shortname_pathogens.tsv. The CARD Short Name values follow the format pathogen_gene or pathogen_gene_drug.
• Sort and Group the data by pathogens and antibiotics.
• Filter Favorite Bug-Drug or Bug for further analysis.
• Download FASTA Sequences for the list of protein accessions filtered. (use Entrez)
• Run MolEvolvR: Run the protein sequences through the MolEvolvR tool for evolutionary analysis.