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" )

Update:

Hi, below are the complete instructions for running the case study report generation on Windows and Ubuntu, including how to install and use the getCaseStudyReport function for automating the case study:

Setup Instructions

Windows

1. Install BLAST:

• Download from NCBI BLAST+ and follow the instructions to install and add it to your PATH.
• Verify:
  blastn -version

2. Install CD-HIT:

• Download binaries from CD-HIT GitHub Releases and extract the files.
• Add the folder containing cd-hit.exe to your PATH.
• Verify:
  cd-hit -h

3. Install MolEvolvR:

install.packages("devtools")
devtools::install_github("awasyn/MolEvolvR", ref = "case_study", dependencies = TRUE)

Ubuntu

1. Install BLAST:

sudo apt-get update
sudo apt-get install ncbi-blast+ -y

2. Install CD-HIT:
   sudo apt-get install cd-hit -y
3. Install MolEvolvR:

install.packages("devtools")
devtools::install_github("awasyn/MolEvolvR", ref = "case_study", dependencies = TRUE)

Next add this support data.

# create common_data folder inside the MolEvolvR library
common_data_path <- file.path(.libPaths()[1], "MolEvolvR", "common_data")

dir.create(common_data_path, showWarnings = FALSE)

# download data
download.file("https://drive.google.com/uc?id=1qN3NGUahVZmRniedy_2ijMKaY_TBrwOz", 
              destfile = file.path(common_data_path, "cln_lookup_tbl.tsv"))

download.file("https://drive.google.com/uc?id=1h_CjURK5laxT7Prhm_U2IqRYlCf6WwKJ", 
              destfile = file.path(common_data_path, "lineage_lookup.txt"))

Try out the case study

Once everything is set up, you can test the automation by running the following in R/RStudio:

library(MolEvolvR)
getCaseStudyReport(pathogen = "Acinetobacter baumannii", drug = "Beta-lactams")

This will generate and open a detailed case study report. 🚀
The output files are in the parent directory of the current directory where the function is called.

@jananiravi @the-mayer @falquaddoomi

What kind of change(s) are included?

• Feature (adds or updates new capabilities)
• 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.

[jananiravi]

@awasyn, thanks again for putting together this PR. I haven't gone through all the files & functions line-by-line, but I started noting some high-level comments first that might help with a more careful review by our team.

1. It might help if this PR focuses on new function definitions and MolEvolvR/CARD calls. When possible, call existing functions directly from R/ or use the downloaded github package calls. @the-mayer may advise one way or another.
2. Use current function names post batch renaming (recently merged PRs). The current list is here: https://jravilab.github.io/MolEvolvR/reference/index.html. This is another reason to avoid redefining functions.
3. Avoid stylistic changes or minor formatting changes, incl. stripping tail-end white spaces as part of commits to keep content and style-based commits and PRs separate.

Please help us by pointing to new functions/functionalities so we can focus our code review there.
MolEvolvR: @the-mayer @falquaddoomi @epbrenner
CARD/amR: @AbhirupaGhosh @epbrenner

Thanks a ton once again, for your concerted effort on this mega issue!

[jananiravi]

@the-mayer, make sure this switch causes no errors?

[jananiravi]

@the-mayer, do we prefer curly curly or is this switch going to be consistent with the rest of our code? @awasyn, is there any particular reason for this switch? Did it ({{}}) throw a warning or error?

[awasyn]

Yes, it threw an error. eg column <- "DomArch" is passed as string but earlier in the code there was a column <- sym(column) which change "DomArch" to a symbol i.e "DomArch" and the code tries to find column name in dataframe as "DomArch" which doesn't exist.

[jananiravi]

I see. {{column}} should work similar to sym(column). So not sure what's going on. @the-mayer?

[jananiravi]

Distinguish from https://jravilab.github.io/MolEvolvR/reference/mapAcc2Name.html

[jananiravi]

same as https://jravilab.github.io/MolEvolvR/reference/createRepresentativeAccNum.html?

Avoid function duplication, please.

[falquaddoomi]

First off, I commend you for taking on a difficult task and completing it!

I'm still in the process of reviewing your PR, but I thought I'd submit what comments I had so far so you can act on them. I'll likely do a second review a bit later on, when I get a chance to run it and investigate your changes further.

[jananiravi]

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

[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.