protein-variant-nomenclature-parser 0.5.0

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, e.g.: BRAF V600E, BRAFV600E, BRAFᵛ⁶⁰⁰ᵉ
  • Range of amino acid substitutions: BRAFVK600_601>E
• 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
• Pure python with zero dependencies and no dependency on an internet connection

Usage

For parsing:

from protein_variant_nomenclature_parser.parser import parse

mutation_string = "BRAF V600E"
parsed_components = parse(mutation_string)

print(parsed_components)

ProteinVariant(gene='BRAF', ref='V', position=NumberOrRange(start=600, end=None), alt='E')

For validation:

from protein_variant_nomenclature_parser.parser import parse
from protein_variant_nomenclature_parser.parser import InvalidProteinVariantError


mutation_string = "INVALID V600E"

try:
    parse(mutation_string)
except InvalidProteinVariantError:
    print(f"{mutation_string} is not valid")

Supported Nomenclature

The parser supports all HUGO gene names.

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

The parser supports situations where the variant has no space between the gene name in the substitution, which unfortunately comes up sometimes.

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.