protein-variant-nomenclature-parser 0.0.1

An ANTLR based parser for colloquial protein variant nomenclature

Protein Variant Nomenclature Parser

This repository contains a Python library for parsing and validating colloquial protein variant nomenclature strings like BRAF V600E that commonly appear in manuscripts.

Features

• Parse protein variant nomenclature strings in the following formats:
  • Single amino acid substitution: "BRAF V600E", "BRAFV600E", "PTEN R130G", "TP53 R175H"
  • Range of amino acid substitutions: "BRAF V600_601E", "PTEN R130_131A", "TP53 R175_176N"
• Extract the components of the nomenclature string, such as gene name, prefix amino acid, position or range, and suffix amino acid
• Validate whether a given string conforms to the expected format

Supported Nomenclature

The parser supports all HUGO gene names.

The parser supports the following amino acid single letter codes and stop codon (*).

Installation

From PyPI

pip install protein-variant-nomenclature-parser

From Source

To install the library, clone the repository and install it using pip:

git clone https://github.com/yourusername/protein-variant-nomenclature-parser.git
cd protein-variant-nomenclature-parser
make install

Docker container

A docker container is available:

docker pull jeffquinnmsk/protein-variant-nomenclature-parser:latest

License

This project is licensed under the MIT License. See the LICENSE file for more information.