sgd-rest

Saccharomyces Genome Database (SGD) REST API wrapper. Refer to the SGD REST page for information about API usage and terms of service.

Installation

pip install sgd-rest --upgrade

Quick start

Get GO (gene ontology) details for gene ARO1.

import sgd

aro1 = sgd.gene("ARO1")
aro1.go_details.json()

# >>> [{'id': 9761727, 'annotation_type': 'computational', 'date_created': '2024-10-14', 'qualifier': 'enables', 'locus': {'display_name': 'ARO1', 'link': '/locus/S000002534', 'id': 1284912, 'format_name': 'YDR127W'}, 'go': {'display_name': 'lyase activity', 'link': '/go/GO:0016829', 'go_id': 'GO:0016829', 'go_aspect': 'molecular function', 'id': 291052}, ...]

Background

Easily navigate the SGD REST API with Python.

Classes

Instantiate the SGD class prior to working with subclasses:

import sgd

aro1 = sgd.gene("ARO1")

Subclasses

Use the endpoints attribute to display subclasses of a class:

import sgd

print(sgd.gene.endpoints)

Use a subclass to retrieve the endpoint's response. This library utilizes the requests library, returning a requests.models.Response instance. Use this instance to define how the REST API content should be processed.

For example, for gene ARO1, get GO details as JSON and literature details as text:

import sgd

aro1 = sgd.gene("ARO1")
aro1.go_details.json()
aro1.literature_details.text

Advanced

Just like a subclass returns a requests.models.Response instance, the user can pass keyword arguments directly to the requests.get method during class instantiation. For example, you can add a header to prevent server-side caching and parse the locus details response as text:

import sgd

go_0000001 = sgd.go("GO:0000001", headers={"Cache-Control": "no-cache", "Pragma": "no-cache"})
go_0000001.locus_details.text

Additional attributes

• url: Gets the endpoint's URL. Available for all classes.
• locus_id: Gets the endpoint's locus ID. Avaialble for locus and gene classes.

import sgd

tor2 = sgd.gene("TOR2")

# 1 
print(tor2.url)
# >>> 'https://www.yeastgenome.org/backend/locus/S000001686'

# 2
print(tor2.locus_id)
# >>> 'S000001686'

Exceptions

• InvalidGene: An invalid gene was queried.

import sgd
from sgd.exceptions import InvalidGene

try:
    bad_gene = sgd.gene("BadGene")
except InvalidGene:
    print("Whoops, an invalid gene was queried.")

Contribute

• Issues Tracker
• Source Code

Support

If you are having issues or would like to propose a new feature, please use the issues tracker.

License

This project is licensed under the MIT license.