NCBI BLASTp Wrapper (R) — WIP

Small R pipeline that runs offline BLASTp pairwise alignments for curated pairs of protein sequences.

Project status: early setup / scaffold. Expect breaking changes.

Requirements

• NCBI BLAST+ (tested with 2.12.0+)
• R ≥ 4.0 with package: Biostrings
• (Optional) RStudio

The original scaffold targeted BLAST+ 2.12.0+, R 4.0.3.
See library(Biostrings) in the script for package needs.

Repo layout

.
├─ ncbi\_blastp\_wrap.R # main pipeline
├─ prepare\_input.sh # builds ./data from *.fasta in repo root
├─ transcript\_type\_info.csv # mapping of pairs: name, prin, alt
└─ data/ # example multi-FASTA files

Input expectations

• transcript_type_info.csv with columns:

name	prin	alt
ESRRB_1	ENST00000512784_domains.fasta	ENST00000505752_domains.fasta
ESRRB_2	ENST00000512784_domains.fasta	ENST00000644823_domains.fasta

• ./data/<name>.fasta multi-FASTA files whose sequence headers contain the transcript IDs used above (e.g., >zf-C4_1_ENST00000512784).

Quick start

1. Install BLAST+ and R deps (Biostrings).
2. Prepare data (either):

• Put your multi-FASTA files under ./data, or
• Place *.fasta in repo root and run:

  bash prepare_input.sh

3. Configure ncbi_blastp_wrap.R if needed:

• path_to_domain_files <- "data/" (default)

4. Run:

Rscript ncbi_blastp_wrap.R

What it does (pipeline)

• Splits each multi-FASTA into per-sequence files and tags them as query or subject based on transcript_type_info.csv.

• For each name, finds the matching query/subject pair and runs:

  blastp -query <query.fasta> -subject <subject.fasta> -outfmt 0

• Saves text outputs under ./alignment/ (folder name may appear as alingment/ in early versions).

Outputs

• For each domain/family name, a folder is created containing:

  • alignment/Alignment_<query>_<subject>_out.txt (pairwise BLASTp report, -outfmt 0).

Roadmap / known issues (early stage)

• Define or replace open_input_files(); fix save_metafile() variable names/scope.
• Normalize output folder to alignment/.
• Add argument parsing (input dir, CSV path, outdir, -outfmt).
• Add unit tests and CI for R/BLAST+ presence.
• Example notebook / vignette.

License

TBD.