MyGene.Info Python Client

3.2.2 · active · verified Sat Apr 11

mygene is an easy-to-use Python wrapper to access MyGene.Info services, which provide simple-to-use REST web services to query/retrieve gene annotation data. It is currently at version 3.2.2 and is actively maintained, with releases tied to updates in the underlying MyGene.info API and its `biothings_client` dependency.

Warnings

breaking The `mygene` package became a thin wrapper around `biothings_client` since v3.1.0. While the `mygene.MyGeneInfo()` interface is maintained, the underlying MyGene.info v3 API introduced changes to data structures for fields like `refseq`, `accession`, `ensembl`, and `exons`. Also, the default behavior for 'dotfield' notation changed, requiring explicit `dotfield=1` for the old behavior.
Fix: Review the MyGene.info v3 API migration guide if your application relies on specific data structures or 'dotfield' behavior for annotation fields. Update your code to handle the new JSON structure or explicitly request 'dotfield=1' if needed.
deprecated The `findgenes()` method was deprecated in version 2.0.0. It is kept as an alias for `querymany()` for backward compatibility, but `querymany()` should be used instead for new code.
Fix: Replace calls to `mg.findgenes(...)` with `mg.querymany(...)`. The arguments are generally compatible.
gotcha When querying with Ensembl gene IDs that include a version postfix (e.g., 'ENSG00000000003.14'), the `getgene()` method might not return results. The postfix should be removed.
Fix: Strip the version postfix (e.g., '.14') from Ensembl gene IDs before passing them to `mg.getgene()`.
gotcha In MyGene.info API v2 (and by extension older `mygene` client versions), the 'filter' parameter was used for specifying returned fields. This parameter was replaced by 'fields' in MyGene.info API v2, though 'filter' was kept for back-compatibility in the client. Users should use 'fields' for clarity and future compatibility.
Fix: Always use the `fields` parameter instead of `filter` when calling `query()` or `querymany()` to specify desired return fields.
gotcha While the `mygene` client defaults to the latest MyGene.info API (v3), older API versions (e.g., v2) can still be accessed by explicitly setting `mg.url`. However, data from older API versions are no longer updated.
Fix: Ensure you are using the default API endpoint unless you have a specific reason to access an older, unmaintained version. Do not rely on data from `mg.url='http://mygene.info/v2'` for up-to-date information.

Install

pip install mygene Install stable version

Imports

MyGeneInfo
```
from mygene import MyGeneInfo
```
While 'mygene' internally uses 'biothings_client', the primary public interface for 'mygene' users remains 'mygene.MyGeneInfo()' for consistency and direct library usage.

Quickstart

Initialize the MyGeneInfo client and perform basic queries for gene annotation data, demonstrating retrieval of single gene information and searching by symbol with field filtering.

import mygene

mg = mygene.MyGeneInfo()

# Get information for a single gene (Entrez ID for CDK2)
gene_info = mg.getgene(1017)
print(f"Gene Symbol: {gene_info.get('symbol')}, Name: {gene_info.get('name')}")

# Query for genes by symbol, returning only specific fields
query_results = mg.query('CDK2', fields='symbol,name,taxid', species='human', size=2)
for hit in query_results.get('hits', []):
    print(f"Query Hit: {hit.get('symbol')} ({hit.get('taxid')}) - {hit.get('name')}")

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