🧬 Codon Translator

A lightweight command-line tool to translate RNA (or DNA) sequences into their corresponding amino acid chains.

A small, zero-dependency Python CLI that takes a raw nucleotide sequence, splits it into codons, and translates each one to its amino acid using the standard genetic code, with output as full names, three-letter abbreviations, or single-letter FASTA-style codes.

📝 I wrote about the design decisions here

Install

Clone the repository directly:

git clone https://github.com/eben-vranken/codon-translator.git
cd codon-translator

Usage

Pass an RNA sequence as a positional argument:

python codon-translator.py AUGAAAUAA

If your sequence is DNA rather than RNA, add -d to convert T→U before translating:

python codon-translator.py -d ATGAAATAA

Output Formats

By default, amino acids are printed by their full name. Use -s for three-letter abbreviations, or -f for single-letter FASTA-style codes:

python codon-translator.py -s AUGAAAUAA
python codon-translator.py -f AUGAAAUAA

File Input & Output

Translate directly from a FASTA file with -i, and write the result to a file with -o:

python codon-translator.py -d -f -i data/synthetic_zika.fasta -o protein.txt

Configuration Matrix

Argument	Option / Choices	Default	Description
sequence	Positional sequence string	Required if -i not set	The raw RNA (or DNA, with -d) sequence to translate.
-i, --input	File path	Required if sequence not set	Read the sequence from a FASTA file instead of the command line.
-o, --output	File path	None (prints to stdout)	Write the translated output to a file.
-d, --dna	Flag	False	Treat the input as DNA and convert T→U before translating.
-s, --short	Flag	False	Output amino acids as three-letter abbreviations (e.g. Met).
-f, --fasta	Flag	False	Output amino acids as single-letter FASTA codes (e.g. M).

Feature Set

• Standard Genetic Code: Full 64-codon lookup table, including all three stop codons.
• DNA or RNA Input: Accepts RNA natively, or DNA via the -d flag.
• Multiple Output Formats: Full amino acid names, three-letter abbreviations, or single-letter FASTA codes.
• FASTA File Support: Reads multi-line FASTA records directly with -i, skipping header lines automatically.

License

MIT