goatools

library1.6.5pypypi✓ verified 79d ago

A Python library to find enrichment of Gene Ontology (GO) terms among a set of genes. It provides tools for GO term enrichment analysis (Fisher's exact test, GOEA), GO term association, and visualization of GO hierarchies. Current version 1.6.4, released June 2024. Regular updates every few months.

data ai-ml

pip install goatools

github ↗package ↗

INSTALL

IMPORT

SIG · GOATOOLS

goatools

datapythonv1.6.5

Install

26.3s avg

Import

—

Disk

595MB

Pass rate

9/ 10

Env Coverage9 / 10

glibc

3.9–3.13

musl

3.9–3.13

Install & Compatibility

Where this runs

tested against v1.6.5 · 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

✓ —

✓ 36.8s

py 3.11

✓ —

✓ 35.7s

py 3.12

✓ 0.1s

✓ 40.8s

py 3.13

✓ 0.1s

✓ 39s

py 3.9

✕ build_error

✓ 31.5s

595MB installed

● package 595MB

Code

Verified usage

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

GOEnrichmentStudy

✓ from goatools.goea.go_enrichment_ns import GOEnrichmentStudy

✗ from goatools import GOEnrichmentStudy

Basic workflow: load GO DAG, load associations, run enrichment study.

from goatools import GOEnrichmentStudy from goatools.obo_parser import GODag from goatools.associations import read_associations # Download go-basic.obo from http://geneontology.org/ontology/go-basic.obo obodag = GODag('go-basic.obo') # Load gene-to-GO associations (tab-separated: gene_id\tGO_id) assoc = read_associations('gene2go.tsv', obodag, no_top=True) # List of gene IDs of interest (e.g., from RNA-seq) gene_list = ['GENE1', 'GENE2', 'GENE3'] # Background population (e.g., all genes in genome) population = list(assoc.keys()) # Run enrichment goea = GOEnrichmentStudy(population, assoc, obodag, propagate_count=True, alpha=0.05) results = goea.run_study(gene_list) print(results[:5])

Debug

Known issues

gotchaThe `GODag` expects a local OBO file. Many users forget to download go-basic.obo first. Use `goatools.obo_parser.GODag('http://purl.obolibrary.org/obo/go/go-basic.obo')` to fetch remotely only if you have stable internet; but for reproducibility, download locally.

fix

Download go-basic.obo from http://geneontology.org/ontology/go-basic.obo and pass local path.

affects: all

gotchaThe `associations` file must be tab-separated with two columns: gene_id and GO_id. Extra columns or non-tab separators cause silent errors.

fix

Ensure exactly two columns: gene_symbol\tGO:0000000.

affects: all

deprecatedThe function `goatools.evidence._evidence_filter` was removed in v1.0. Use `goatools.associations` instead.

fix

Use `from goatools.associations import read_associations`.

affects: >=1.0

gotchaEnrichment results may have many rows with the same p-value due to propagation. Use `propagate_count=True` to avoid spurious significance.

fix

Set `propagate_count=True` in GOEnrichmentStudy constructor.

affects: all

Upgrade

Version history

1.6.5latest on PyPI · released May 12, 2026

Audit

Dependencies

pandasrequiredData manipulation for gene lists and results

numpyrequiredNumerical computations

scipyrequiredStatistical tests (Fisher's exact test)

Agent activity

35 hits · last 30 days

node

OpenAI (training)

Resources

githubhttp://github.com/tanghaibao/goatools ↗

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