WIP: Case study report automation

[awasyn]

Cases study report automation with MolEvolvR

• Automate case study creation | starting with rmd report #27
• [FEAT] Generate case study report Rmd/Qmd #102

This commit introduces a series of scripts and supporting code for automating case study reports via the MolEvolvR analysis pipeline. The added scripts enable end-to-end processing of pathogen and/or drug data from CARD data in FASTA format, automating key tasks like sequence retrieval, alignment, and protein annotation. Currently, the pipeline supports only the "full" analysis option,
Specifically, the following capabilities have been implemented:

• BLAST and InterProScan Integration:

  • BLAST: Utilizes NCBI’s online BLAST API to retrieve sequence alignment results.
  • InterProScan: Supports local execution with dependencies on the command-line version of InterProScan. Future work will include developing an InterProScan API wrapper (iprscanr) for more accessible remote processing, reducing local resource demands.

This approach is based on the MolEvolvR webapp pipeline , with portions of code directly adapted from MolEvolvR scripts. The original authorship has been retained to acknowledge the foundational work and provide proper attribution.

Current dependencies not inlcuded in this commit :

• lineage_lookup.txt, cln_lookup_tbl.tsv data files
• blast+ for local sequence alignments
• InterProScan (local installation)

To-Do:

• Clean scripts and post-analysis report generation
• Add a wrapper for the InterProScan API to reduce local resource constraints
• Extend support for additional analysis options ("da" "dblasts", "phylo")
• Extend support for other formats ("msa", "accnum", "ipr" )

@jananiravi @the-mayer @falquaddoomi

What kind of change(s) are included?

• Feature (adds or updates new capabilities)
• Enhancement (adds functionality).

Checklist

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