tinyhgvs

tinyhgvs is a lightweight HGVS parsing Python library backed by a core parser and structured data and error model implemented in Rust.

Installation

tinyhgvs can be installed directly from PyPI:

pip install tinyhgvs

Quick start

• A splicing-site substitution crossing an exon/intron boundary:

from tinyhgvs import parse_hgvs

variant = parse_hgvs("NM_004006.2:c.357+1G>A")
print(variant.reference.primary.id)
print(variant.coordinate_system.value)
print(variant.description.location.start.coordinate)
print(variant.description.location.start.offset)

• An exact repeat is parsed into a structured repeat edit:

from tinyhgvs import parse_hgvs

variant = parse_hgvs("NC_000014.8:g.123CAG[23]")
print(variant.description.location.start.coordinate)
print(variant.description.edit.blocks[0].unit)
print(variant.description.edit.blocks[0].count)

• A protein frameshift variant:

from tinyhgvs import parse_hgvs

variant = parse_hgvs("NP_0123456.1:p.Arg97ProfsTer23")
print(variant.description.effect.edit.to_residue)
print(variant.description.effect.edit.stop.ordinal)

• Known but unsupported HGVS syntax raises TinyHGVSError with a diagnostic code:

from tinyhgvs import TinyHGVSError, parse_hgvs

try:
    parse_hgvs("NP_003997.1:p.Val7=/del")
except TinyHGVSError as error:
    print(error.code)

Documentation

Please refer to official documents for details about both Python and Rust APIs:

• Python API and project docs
• Rust API docs

Citation

If you use tinyhgvs in your project, please kindly cite the github repository.

License

tinyhgvs is licensed under the MIT license.