bio-grumpy

library1.1.4pypypi✓ verified 80d ago

Grumpy is a Python library for genomic manipulation, reimplemented in Rust for performance. It provides tools for working with VCF, FASTA, and GenBank files, including slicing, filtering, and reverse complement operations. Current version is 1.1.4, supporting Python >=3.8, <3.13. Release cadence is irregular, with several bug fix releases in 2024-2025.

data

pip install bio-grumpy

github ↗package ↗

INSTALL

IMPORT

SIG · BIO-GRUMPY

bio-grumpy

datapythonv1.1.4

Install

2.0s avg

Import

—

Disk

19MB

Pass rate

8/ 10

Env Coverage8 / 10

glibc

3.9–3.13

musl

3.9–3.13

Install & Compatibility

Where this runs

tested against v1.1.4 · pip install

no network on importno background threads

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

glibc

py 3.10

✓ —

✓ 1.8s

py 3.11

✓ —

✓ 2s

py 3.12

✓ —

✓ 2.2s

py 3.13

✕ build_error

py 3.9

✓ —

✓ 2s

19MB installed

● package 19MB

Code

Verified usage

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

grumpy

✓ from grumpy import grumpy

✗ from grumpy import Grumpy

Genome

✓ from grumpy import Genome

VCFFile

✓ from grumpy import VCFFile

Basic usage: create a Grumpy object from a GenBank file, extract a sequence slice, and demonstrate VCF filtering. Requires Python 3.8+ and a GenBank file.

from grumpy import Grumpy from pathlib import Path # Initialize with a GenBank file grumpy = Grumpy(Path('example.gb')) # Get sequence slice seq = grumpy.get_sequence(100, 200) print(seq) # Check if VCF filter works vcf_path = Path('input.vcf') filtered = grumpy.filter_vcf(vcf_path, min_quality=30) print(len(filtered))

grumpy --version

Debug

Known issues

breakingPython 3.13 not supported: requires Python <3.13.0a0, so cannot install on Python 3.13+.

fix

Use Python 3.8 to 3.12.

affects: >=1.0.0

gotchaWindows wheels removed starting from v1.1.0: library only available on Linux and macOS. Attempting pip install on Windows may fail or require building from source.

fix

Use Linux or macOS, or run in a Docker container. For advanced users, compile from source with Rust toolchain.

affects: >=1.1.0

gotchaGenBank location parsing changed in v1.1.0, which may break existing code that relied on older parsing behavior.

fix

Review GenBank files for non-standard locations. If reproducibility is critical, pin to v1.0.1.

affects: >=1.1.0

gotchaVCF null calls handling changed in v0.2.6: filter behavior differs. Ensure VCF filtering logic accounts for null calls.

fix

Upgrade to >=0.2.6 and adapt any VCF filtering scripts that depend on null call behaviour.

affects: <0.2.6

Upgrade

Version history

1.1.4latest on PyPI · released Mar 12, 2026

Audit

Dependencies

No dependency data recorded yet.

Agent activity

17 hits · last 30 days

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OpenAI (training)

Resources

githubhttps://github.com/oxfordmmm/grumpy ↗

packagehttps://pypi.org/project/bio-grumpy/ ↗