🧫 Protein Amino Acid Counter

A command-line utility to count amino acid frequencies in a protein sequence.

A modular, zero-dependency Python CLI built to analyze protein sequences. It takes a raw sequence or a FASTA file, validates it against the 20-letter amino acid alphabet, tallies how often each amino acid occurs, and reports the result as plain output or a formatted table.

Install

Clone the repository directly:

git clone https://github.com/eben-vranken/protein-aa-counter.git
cd protein-aa-counter

Usage

Pass a raw protein sequence with -s, or a FASTA file with -f. Exactly one of the two is required. The tool counts every amino acid in the sequence and can print the result as a plain list or as a table, with optional full amino acid names.

python amino-acid-counter.py -s MTEYKLVVVGAGGVGKSALTIQ --table --verbose

Short Flags

The same arguments are available in short form:

python amino-acid-counter.py -s MTEYKLVVVGAGGVGKSALTIQ -t -v

FASTA Input

python amino-acid-counter.py -f data/human_protein.fasta -t

Example Output

| Amino         | Count |
-------------------------
| Alanine       | 23    |
| Arginine      | 7     |
| Asparagine    | 10    |
| Aspartic acid | 21    |
| Cysteine      | 13    |
| Glutamic acid | 36    |
| Glutamine     | 13    |
| Glycine       | 15    |
| Histidine     | 8     |
| Isoleucine    | 8     |
| Leucine       | 22    |
| Lysine        | 12    |
| Methionine    | 8     |
| Phenylalanine | 7     |
| Proline       | 14    |
| Serine        | 10    |
| Threonine     | 15    |
| Tryptophan    | 6     |
| Tyrosine      | 6     |
| Valine        | 21    |

Configuration Matrix

Argument	Option / Choices	Default	Description
-s, --sequence	Protein sequence string	None	Raw protein sequence to count (e.g. MTEYK). Required unless -f is used.
-f, --file	File path	None	Path to a FASTA protein file. Required unless -s is used.
-t, --table	Flag	False	Print the frequencies as a formatted table instead of a plain list.
-v, --verbose	Flag	False	Print full amino acid names (e.g. Alanine) instead of single-letter codes.

Feature Set

• Sequence Parsing: Reads a raw sequence directly, or extracts and concatenates the sequence lines from a FASTA file, skipping header lines.
• Input Validation: Rejects any character outside the 20-letter amino acid alphabet and requires exactly one of -s or -f.
• Frequency Counting: Tallies occurrences of all 20 amino acids across the sequence, including ones with zero occurrences.
• Plain Output: Prints each amino acid and its count on its own line.
• Table Rendering: Prints a clean, column-aligned table of counts, with column widths sized to fit the longest label.
• Verbose Labels: Swaps single-letter codes for full amino acid names in either output mode.

License

MIT