🧬 FastAAExtractor

FastAAExtractor is a simple, fast tool for extracting amino acid sequences from bacterial genomes using coordinate tables.

Features

• Easy batch processing: just point to your genome and coordinate folders
• Automatic matching: genome and coordinate files are paired by name
• Parallel extraction for speed
• Flexible gene selection
• Works on Windows, Mac, Linux

Quick Start

1. Install

pip install -r requirements.txt
pip install -e .

2. Extract from a folder of genomes

fasta_aa_extractor --genome-dir input/genomes/ --coords-dir input/coords/ --genes "acrA,acrB,tolC" --parallel --max-workers 8 --output-dir results/

• --genome-dir: folder with .fasta or .fa files
• --coords-dir: folder with .tsv files (named to match genomes)
• --genes: comma-separated list or @genes.txt file
• --parallel: enables fast parallel processing
• --max-workers: number of parallel jobs (default: 4)
• --output-dir: where to save results

3. Output

• Creates one .faa file per genome-gene pair: GenomeName_GeneName.faa
• Standard FASTA format, ready for BLAST, alignment, etc.

Example

fasta_aa_extractor --genome-dir input/ --coords-dir input/ --genes "acrA,acrB" --parallel --output-dir proteins/

Need help?

• See QUICKSTART.md for more details
• For advanced options, run: fasta_aa_extractor --help

---

Simple. Fast. No CSVs. Just point and extract!