#!/usr/bin/env python3
"""
UniProt REST API Client
A Python client for interacting with the UniProt REST API.
Provides helper functions for common operations including search,
retrieval, ID mapping, and streaming.
Usage examples:
# Search for proteins
results = search_proteins("insulin AND organism_name:human", format="json")
# Get a single protein
protein = get_protein("P12345", format="fasta")
# Map IDs
mapped = map_ids(["P12345", "P04637"], from_db="UniProtKB_AC-ID", to_db="PDB")
# Stream large results
for batch in stream_results("taxonomy_id:9606 AND reviewed:true", format="fasta"):
process(batch)
"""
import requests
import time
import json
from typing import List, Dict, Optional, Generator
from urllib.parse import urlencode
BASE_URL = "https://rest.uniprot.org"
POLLING_INTERVAL = 3 # seconds
def search_proteins(query: str, format: str = "json",
fields: Optional[List[str]] = None,
size: int = 25) -> Dict:
"""
Search UniProt database with a query.
Args:
query: Search query (e.g., "insulin AND organism_name:human")
format: Response format (json, tsv, xlsx, xml, fasta, txt, rdf)
fields: List of fields to return (e.g., ["accession", "gene_names", "organism_name"])
size: Number of results per page (default 25, max 500)
Returns:
Response data in requested format
"""
endpoint = f"{BASE_URL}/uniprotkb/search"
params = {
"query": query,
"format": format,
"size": size
}
if fields:
params["fields"] = ",".join(fields)
response = requests.get(endpoint, params=params)
response.raise_for_status()
if format == "json":
return response.json()
else:
return response.text
def get_protein(accession: str, format: str = "json") -> str:
"""
Retrieve a single protein entry by accession number.
Args:
accession: UniProt accession number (e.g., "P12345")
format: Response format (json, txt, xml, fasta, gff, rdf)
Returns:
Protein data in requested format
"""
endpoint = f"{BASE_URL}/uniprotkb/{accession}.{format}"
response = requests.get(endpoint)
response.raise_for_status()
if format == "json":
return response.json()
else:
return response.text
def batch_retrieve(accessions: List[str], format: str = "json",
fields: Optional[List[str]] = None) -> str:
"""
Retrieve multiple protein entries efficiently.
Args:
accessions: List of UniProt accession numbers
format: Response format
fields: List of fields to return
Returns:
Combined results in requested format
"""
query = " OR ".join([f"accession:{acc}" for acc in accessions])
return search_proteins(query, format=format, fields=fields, size=len(accessions))
def stream_results(query: str, format: str = "fasta",
fields: Optional[List[str]] = None,
chunk_size: int = 8192) -> Generator[str, None, None]:
"""
Stream large result sets without pagination.
Args:
query: Search query
format: Response format
fields: List of fields to return
chunk_size: Size of chunks to yield
Yields:
Chunks of response data
"""
endpoint = f"{BASE_URL}/uniprotkb/stream"
params = {
"query": query,
"format": format
}
if fields:
params["fields"] = ",".join(fields)
response = requests.get(endpoint, params=params, stream=True)
response.raise_for_status()
for chunk in response.iter_content(chunk_size=chunk_size, decode_unicode=True):
if chunk:
yield chunk
def map_ids(ids: List[str], from_db: str, to_db: str,
format: str = "json") -> Dict:
"""
Map protein identifiers between different database systems.
Args:
ids: List of identifiers to map (max 100,000)
from_db: Source database (e.g., "UniProtKB_AC-ID", "Gene_Name")
to_db: Target database (e.g., "PDB", "Ensembl", "RefSeq_Protein")
format: Response format
Returns:
Mapping results
Note:
- Maximum 100,000 IDs per job
- Results stored for 7 days
- See id_mapping_databases.md for all supported databases
"""
if len(ids) > 100000:
raise ValueError("Maximum 100,000 IDs allowed per mapping job")
# Step 1: Submit job
submit_endpoint = f"{BASE_URL}/idmapping/run"
data = {
"from": from_db,
"to": to_db,
"ids": ",".join(ids)
}
response = requests.post(submit_endpoint, data=data)
response.raise_for_status()
job_id = response.json()["jobId"]
# Step 2: Poll for completion
status_endpoint = f"{BASE_URL}/idmapping/status/{job_id}"
while True:
response = requests.get(status_endpoint)
response.raise_for_status()
status = response.json()
if "results" in status or "failedIds" in status:
break
time.sleep(POLLING_INTERVAL)
# Step 3: Retrieve results
results_endpoint = f"{BASE_URL}/idmapping/results/{job_id}"
params = {"format": format}
response = requests.get(results_endpoint, params=params)
response.raise_for_status()
if format == "json":
return response.json()
else:
return response.text
def get_available_fields() -> List[Dict]:
"""
Get list of all available fields for queries.
Returns:
List of field definitions with names and descriptions
"""
endpoint = f"{BASE_URL}/configure/uniprotkb/result-fields"
response = requests.get(endpoint)
response.raise_for_status()
return response.json()
def get_id_mapping_databases() -> Dict:
"""
Get list of all supported databases for ID mapping.
Returns:
Dictionary of database groups and their supported databases
"""
endpoint = f"{BASE_URL}/configure/idmapping/fields"
response = requests.get(endpoint)
response.raise_for_status()
return response.json()
# Example usage
if __name__ == "__main__":
# Example 1: Search for human insulin proteins
print("Searching for human insulin proteins...")
results = search_proteins(
"insulin AND organism_name:human AND reviewed:true",
format="json",
fields=["accession", "id", "gene_names", "protein_name"],
size=5
)
print(json.dumps(results, indent=2))
# Example 2: Get a specific protein in FASTA format
print("\nRetrieving protein P01308 (human insulin)...")
protein = get_protein("P01308", format="fasta")
print(protein)
# Example 3: Map UniProt IDs to PDB IDs
print("\nMapping UniProt IDs to PDB...")
mapping = map_ids(
["P01308", "P04637"],
from_db="UniProtKB_AC-ID",
to_db="PDB"
)
print(json.dumps(mapping, indent=2))