hgvs

library1.5.7pypypi✓ verified 84d ago

HGVS (Human Genome Variation Society) nomenclature parser, formatter, validator, and mapper. Version 1.5.7 supports Python >=3.10. Released irregularly, with recent focus on selenocysteine support and bug fixes.

data serialization

pip install hgvs

github ↗package ↗homepage ↗

INSTALL

IMPORT

SIG · HGVS

hgvs

datapythonv1.5.7

Install

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Import

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Disk

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Pass rate

0/ 10

Env Coverage0 / 10

glibc

3.9–3.13

musl

3.9–3.13

Install & Compatibility

Where this runs

tested against v? · pip install

Install × environment matrix

Each cell = how many times install + import succeeded across repeated harness runs. Partial = flaky.
glibc = Debian/Ubuntu slim · musl = Alpine Linux

musl

py 3.10–3.95 runs

build_error

glibc

py 3.10–3.95 runs

build_error

Code

Verified usage

Verified import paths — ran on the pinned version, not inferred.

parser

✓ import hgvs.parser

variantmapper

✓ import hgvs.variantmapper

SequenceVariant

✓ from hgvs.sequencevariant import SequenceVariant

✗ import hgvs.SequenceVariant

SequenceVariant is in a submodule, not top-level.

Parse an HGVS variant string using the default parser.

import hgvs.parser import hgvs.dataproviders.uta # Initialize parser hp = hgvs.parser.Parser() # Parse an HGVS variant string var = hp.parse_hgvs_variant('NM_000551.3:c.101T>A') print(var) # SequenceVariant(...) # For mapping, need a data provider (e.g., UTA) # hdp = hgvs.dataproviders.uta.connect() # vm = hgvs.variantmapper.VariantMapper(hdp) # t_vm = vm.c_to_t(var) # print(t_vm)

Debug

Known issues

deprecatedhgvs.dataproviders.uta.connect() uses an environment-based connection string; UTA_DB_URL must be set.

fix

Set environment variable UTA_DB_URL or use hgvs.dataproviders.uta.connect(url='postgresql://...')

affects: >=1.5.0

breakingIn version 1.5.7, selenocysteine support changed protein translation for variants in selenocysteine-encoding transcripts (UGA codon). Existing code relying on prior behavior may produce different protein HGVS strings.

fix

Review and update expected protein variant strings for transcripts with selenocysteine.

affects: >=1.5.7

gotchahgvs requires a sequence data provider (e.g., UTA or seqrepo) for mapping operations. Without one, c_to_t, etc. will fail.

fix

Ensure a data provider is configured via environment variables or explicitly passed.

affects: all

gotchaUTA database credentials may be URL-encoded; decoding is fixed in 1.5.8rc1, but 1.5.7 may fail if UTA_DB_URL contains percent-encoded characters.

fix

Upgrade to 1.5.8rc1 or pass raw (non-encoded) credentials.

affects: 1.5.0 - 1.5.7

Errors

Common errors & fixes

AttributeError: 'UTA_postgresql' object has no attribute '_pool'

Outdated psycopg2 or missing pool module; fixed in 1.5.5.

fix

Upgrade hgvs to >=1.5.5 or install psycopg2-binary.

ValueError: Could not find a data provider; set UTA_DB_URL or provide connection

No database connection configured.

fix

Set environment variable UTA_DB_URL or pass url to hgvs.dataproviders.uta.connect().

hgvs.exceptions.HGVSParseError: Expected '>' at position ...

Malformed variant string (e.g., missing allele after '>').

fix

Verify the variant string conforms to HGVS syntax; e.g., 'NM_000551.3:c.101T>A'.

Upgrade

Version history

1.5.7latest on PyPI · released Mar 17, 2026

Audit

Dependencies

bioutilsrequiredRequired for sequence utilities

parsleyrequiredRequired for grammar parsing

psycopg2-binaryoptionalRequired for UTA database connection

seqrepooptionalRequired for local sequence retrieval

Agent activity

12 hits · last 30 days

node

Resources

githubhttps://github.com/biocommons/hgvs ↗

packagehttps://pypi.org/project/hgvs/ ↗

homepagehttps://hgvs.readthedocs.io ↗