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🚀 QuickStart Guide - FastaAAExtractor

Welcome! This guide shows you how to extract protein sequences from many genomes in just a few minutes—no bioinformatics expertise required!

What Does This Tool Do?

  • Finds genes in your bacterial genomes using coordinate tables
  • Translates DNA to protein (amino acid) sequences
  • Saves each protein as a FASTA file, ready for BLAST, alignment, etc.

Installation

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

Your First Extraction (Batch Mode)

Step 1: Place all your genome files (.fasta or .fa) in one folder, and all coordinate files (.tsv) in another folder. Make sure filenames match:

  • AP018572.2.fasta → AP018572.2.tsv
  • CP029242.fasta → CP029242.tsv

Step 2: Run the tool:

fasta_aa_extractor --genome-dir path/to/genomes/ --coords-dir path/to/coords/ --genes "acrA,acrB,tolC" --parallel --output-dir results/

Step 3: Check your results in the output folder. You'll see files like:

  • AP018572.2_acrA.faa
  • AP018572.2_acrB.faa
  • CP029242_tolC.faa

Common Use Cases

  • Extract all resistance genes from 100+ genomes in one go
  • Use a gene list file: --genes @genes.txt
  • Works on Windows, Mac, Linux

Troubleshooting

  • No output? Check that genome and coordinate filenames match exactly
  • Missing genes? Make sure gene names in your coordinate files match what you requested
  • Need help? Run fasta_aa_extractor --help or ask on GitHub

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