WIP: Case study report automation

[awasyn]

Cases study report automation with MolEvolvR

• https://github.com/JRaviLab/MolEvolvR/issues/27
• https://github.com/JRaviLab/MolEvolvR/issues/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?

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

Checklist

Please ensure that all boxes are checked before indicating that this pull request is ready for review.

• [ ] I have read and followed the CONTRIBUTING.md guidelines.
• [ ] I have searched for existing content to ensure this is not a duplicate.
• [ ] I have performed a self-review of these additions (including spelling, grammar, and related).
• [ ] I have added comments to my code to help provide understanding.
• [ ] I have added a test which covers the code changes found within this PR.
• [ ] I have deleted all non-relevant text in this pull request template.
• [ ] Reviewer assignment: Tag a relevant team member to review and approve the changes.

[awasyn]

@awasyn, were these changes (& these) pulled from main? If not, stylistic changes such as trailing spaces & indentation can be addressed later (post-merge).

okay thanks. I wanted to ease review by updating back to only the changed lines. my editor added spaces during save.