GeneTicker

A small utility for calculating codon frequencies from GenBank (GBFF) files.

This project parses CDS features from GenBank flat files, counts codon occurrences, maps codons to amino acids (including marking start/stop codons), and produces tabular frequency reports that can be exported to several formats or printed to the console.

Features

• Parse GenBank (.gbff) files using Biopython
• Count codons across CDS features and compute frequency (percentage)
• Mark special codons as START or STOP when applicable
• Export results to .csv, .tsv, .json, .pickle, .xlsx, .xml, and columnar formats (feather/parquet/orc) if dependencies are available
• Simple CLI entry points and programmatic API

Quickstart

1. Install GeneTicker:

Install a specific version by changing v0.1.0 to a specific tag version found on github.

pip install git+https://github.com/exTerEX/[email protected]

If you want to install optional dependencies (all, excel, hadoop, arrow, parquet, orc)

pip install GeneTicker[all]@git+https://github.com/exTerEX/GeneTicker

or

pip install GeneTicker[all]@git+https://github.com/exTerEX/[email protected]

2. Example usage:

Command-line interface (CLI):

gtick -o output.csv path/to/input.gbff

Callable:

from pathlib import Path
from GeneTicker.core import run_codon_analysis

df = run_codon_analysis(Path('path/to/input.gbff'))

Output a Pandas DataFrame with columns:

• Amino Acid: Amino acid IUPAC one letter codes
• Codon: Nucleic acid three letter codes
• Count: Number of specific codon
• Freq. (%): Frequency of total codon count
• Special Type: Indicate special role (START, STOP, etc.)

Notes and dependencies

• Biopython is required to parse GenBank files (Bio package).
• Optional packages like pyarrow, fastparquet, or lxml are required to export to some formats (parquet/feather/orc/xml).

License

This repository is provided as-is. See pyproject.toml for package metadata.