pybiomart

library0.2.0pypypi✓ verified 86d ago

A simple pythonic interface to BioMart, providing easy querying of biological databases (e.g., Ensembl, HGNC) and retrieval of gene annotations, transcripts, etc. Current version 0.2.0 is stable but low activity; no breaking changes since release.

devops

pip install pybiomart

github ↗homepage ↗

INSTALL

IMPORT

SIG · PYBIOMART

pybiomart

devopspythonv0.2.0

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.

Dataset

✓ from pybiomart import Dataset

Query Ensembl for human gene IDs and gene names.

from pybiomart import Dataset dataset = Dataset(name='hsapiens_gene_ensembl', host='http://www.ensembl.org') results = dataset.query(attributes=['ensembl_gene_id', 'external_gene_name']) print(results.head())

Debug

Known issues

gotchaDataset name and host are case-sensitive; common mistake is 'hsapiens_gene_Ensembl' (capital E) which fails silently.

fix

Use exact case as in BioMart: e.g., 'hsapiens_gene_ensembl' and host 'http://www.ensembl.org' (note: http, not https).

affects: all

gotchaThe default host uses http, which may cause SSL errors or redirects in some environments; using https may break the API.

fix

Explicitly set host='http://www.ensembl.org' to avoid connection issues.

affects: all

gotchaQuerying with many attributes or large result sets can be slow; no pagination support.

fix

Limit attributes to necessary ones and consider splitting large queries.

affects: all

Errors

Common errors & fixes

requests.exceptions.ConnectionError: HTTPSConnectionPool

Using https host instead of http; pybiomart backend may not support https.

fix

Use host='http://www.ensembl.org' (note: http, no 's').

ValueError: Dataset name not found

Incorrect dataset name or host (e.g., typo, wrong case, or host not pointing to a valid BioMart registry).

fix

Check exact dataset name from BioMart website (e.g., 'hsapiens_gene_ensembl') and host (e.g., 'http://www.ensembl.org').

AttributeError: 'Dataset' object has no attribute 'query'

Often due to import error: importing 'pybiomart' directly instead of 'Dataset' class.

fix

Use from pybiomart import Dataset

Upgrade

Version history

0.2.0latest on PyPI · released May 10, 2017

Audit

Dependencies

pandasrequiredRequired for returning query results as DataFrames

requestsrequiredHTTP library for API calls

Agent activity

2 hits · last 30 days

node

Resources

githubhttps://github.com/jrderuiter/pybiomart ↗

homepagehttps://github.com/jrderuiter/pybiomart ↗