varcode

library6.0.0pypypi✓ verified 85d ago

Varcode is a Python library for variant annotation, providing tools to annotate genomic variants with predicted coding effects, such as amino acid changes, splice sites, and more. Current version is 6.0.0, requiring Python ≥3.9. It is part of the OpenVax project and follows a regular release cycle.

devops

pip install varcode

github ↗homepage ↗

INSTALL

IMPORT

SIG · VARCODE

varcode

devopspythonv6.0.0

harness data pending

Install & Compatibility

Where this runs

No compatibility data collected yet for this library.

Code

Verified usage

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

Variant

✓ from varcode import Variant

✗ import varcode; varcode.Variant

Direct import is more straightforward.

VariantCollection

✓ from varcode import VariantCollection

ProteinSequence

✓ from varcode import ProteinSequence

A minimal example: create a single variant and retrieve its predicted coding effect and protein change.

from varcode import Variant from pyensembl import EnsemblRelease # Load reference genome (first time downloads data) ensembl = EnsemblRelease(75) # Create a variant: chromosome, position, ref, alt variant = Variant('1', 123456, 'A', 'T', ensembl=ensembl) # Annotate the variant effect = variant.effect() print(effect) # Get predicted protein change protein_change = variant.protein_change() print(protein_change)

Debug

Known issues

breakingVarcode v6.0.0 dropped support for Python 2.7 and Python 3.5-3.8. Requires Python >=3.9.

fix

Upgrade Python to 3.9 or later. If stuck on older Python, use varcode <=5.0.x.

affects: >=6.0.0

deprecatedThe `Variant.effect()` method may return complex effect objects; prefer using `variant.effect().short_description` for a simple string.

fix

Use `str(variant.effect())` or `variant.effect().short_description` instead of relying on the default __repr__.

affects: all

gotchaGenome data is downloaded automatically by PyEnsembl the first time you use a release. This can be slow and requires internet. For offline use, pre-download with `pyensembl install --release <number>`.

fix

Run `pyensembl install --release 75` (or your desired release) offline.

affects: all

gotchaVariant positions are 1-based. Using 0-based coordinates from other tools (e.g., BED) will produce incorrect annotations.

fix

Always use 1-based positions as per VCF convention.

affects: all

breakingThe `annotate` module and `VariantAnnotationResult` class were removed or refactored in v6.0.0. Code using `from varcode.annotate import ...` will break.

fix

Use `Variant.effect()` and `Variant.protein_change()` directly. Replace `VariantAnnotationResult` with `VariantEffect`.

affects: >=6.0.0

Errors

Common errors & fixes

ImportError: No module named pyensembl

PyEnsembl is not installed, or the environment is missing the dependency.

fix

Install pyensembl: `pip install pyensembl`

ValueError: Genome release 75 not found. Please install it using: pyensembl install --release 75

The required Ensembl release data has not been downloaded.

fix

Run `pyensembl install --release 75` (or the release you need) in your terminal.

AttributeError: 'Variant' object has no attribute 'effect'

The varcode version is too old (<5.0) or the import path is wrong (e.g., using varcode.Variant instead of direct import).

fix

Update varcode: `pip install --upgrade varcode`. Use `from varcode import Variant`.

Upgrade

Version history

6.0.0latest on PyPI · released May 26, 2026

Audit

Dependencies

pyensemblrequiredRequired for genome assemblies and gene annotations.

pandasrequiredUsed for data manipulation and output.

numpyrequiredUsed for numerical operations.

pyvcfoptionalFor reading VCF files (optional but common).

Agent activity

5 hits · last 30 days

node

Amazon

Resources

githubhttps://github.com/openvax/varcode ↗

homepagehttps://github.com/openvax/varcode ↗