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Zhongwei Li
251
skills/gene-database/scripts/query_gene.py
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251
skills/gene-database/scripts/query_gene.py
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#!/usr/bin/env python3
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"""
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Query NCBI Gene database using E-utilities.
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This script provides access to ESearch, ESummary, and EFetch functions
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for searching and retrieving gene information.
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"""
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import argparse
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import json
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import sys
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import time
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import urllib.parse
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import urllib.request
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from typing import Optional, Dict, List, Any
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from xml.etree import ElementTree as ET
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BASE_URL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/"
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DB = "gene"
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def esearch(query: str, retmax: int = 20, api_key: Optional[str] = None) -> List[str]:
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"""
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Search NCBI Gene database and return list of Gene IDs.
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Args:
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query: Search query (e.g., "BRCA1[gene] AND human[organism]")
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retmax: Maximum number of results to return
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api_key: Optional NCBI API key for higher rate limits
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Returns:
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List of Gene IDs as strings
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"""
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params = {
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'db': DB,
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'term': query,
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'retmax': retmax,
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'retmode': 'json'
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}
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if api_key:
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params['api_key'] = api_key
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url = f"{BASE_URL}esearch.fcgi?{urllib.parse.urlencode(params)}"
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try:
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with urllib.request.urlopen(url) as response:
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data = json.loads(response.read().decode())
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if 'esearchresult' in data and 'idlist' in data['esearchresult']:
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return data['esearchresult']['idlist']
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else:
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print(f"Error: Unexpected response format", file=sys.stderr)
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return []
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except urllib.error.HTTPError as e:
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print(f"HTTP Error {e.code}: {e.reason}", file=sys.stderr)
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return []
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except Exception as e:
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print(f"Error: {e}", file=sys.stderr)
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return []
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def esummary(gene_ids: List[str], api_key: Optional[str] = None) -> Dict[str, Any]:
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"""
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Get document summaries for Gene IDs.
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Args:
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gene_ids: List of Gene IDs
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api_key: Optional NCBI API key
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Returns:
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Dictionary of gene summaries
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"""
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params = {
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'db': DB,
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'id': ','.join(gene_ids),
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'retmode': 'json'
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}
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if api_key:
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params['api_key'] = api_key
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url = f"{BASE_URL}esummary.fcgi?{urllib.parse.urlencode(params)}"
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try:
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with urllib.request.urlopen(url) as response:
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data = json.loads(response.read().decode())
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return data
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except urllib.error.HTTPError as e:
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print(f"HTTP Error {e.code}: {e.reason}", file=sys.stderr)
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return {}
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except Exception as e:
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print(f"Error: {e}", file=sys.stderr)
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return {}
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def efetch(gene_ids: List[str], retmode: str = 'xml', api_key: Optional[str] = None) -> str:
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"""
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Fetch full gene records.
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Args:
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gene_ids: List of Gene IDs
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retmode: Return format ('xml', 'text', 'asn.1')
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api_key: Optional NCBI API key
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Returns:
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Gene records as string in requested format
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"""
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params = {
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'db': DB,
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'id': ','.join(gene_ids),
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'retmode': retmode
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}
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if api_key:
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params['api_key'] = api_key
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url = f"{BASE_URL}efetch.fcgi?{urllib.parse.urlencode(params)}"
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try:
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with urllib.request.urlopen(url) as response:
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return response.read().decode()
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except urllib.error.HTTPError as e:
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print(f"HTTP Error {e.code}: {e.reason}", file=sys.stderr)
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return ""
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except Exception as e:
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print(f"Error: {e}", file=sys.stderr)
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return ""
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def search_and_summarize(query: str, organism: Optional[str] = None,
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max_results: int = 20, api_key: Optional[str] = None) -> None:
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"""
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Search for genes and display summaries.
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Args:
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query: Gene search query
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organism: Optional organism filter
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max_results: Maximum number of results
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api_key: Optional NCBI API key
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"""
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# Add organism filter if provided
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if organism:
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if '[organism]' not in query.lower():
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query = f"{query} AND {organism}[organism]"
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print(f"Searching for: {query}")
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print("-" * 80)
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# Search for gene IDs
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gene_ids = esearch(query, retmax=max_results, api_key=api_key)
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if not gene_ids:
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print("No results found.")
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return
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print(f"Found {len(gene_ids)} gene(s)")
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print()
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# Get summaries
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summaries = esummary(gene_ids, api_key=api_key)
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if 'result' in summaries:
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for gene_id in gene_ids:
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if gene_id in summaries['result']:
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gene = summaries['result'][gene_id]
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print(f"Gene ID: {gene_id}")
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print(f" Symbol: {gene.get('name', 'N/A')}")
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print(f" Description: {gene.get('description', 'N/A')}")
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print(f" Organism: {gene.get('organism', {}).get('scientificname', 'N/A')}")
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print(f" Chromosome: {gene.get('chromosome', 'N/A')}")
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print(f" Map Location: {gene.get('maplocation', 'N/A')}")
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print(f" Type: {gene.get('geneticsource', 'N/A')}")
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print()
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# Respect rate limits
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time.sleep(0.34) # ~3 requests per second
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def fetch_by_id(gene_ids: List[str], output_format: str = 'json',
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api_key: Optional[str] = None) -> None:
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"""
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Fetch and display gene information by ID.
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Args:
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gene_ids: List of Gene IDs
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output_format: Output format ('json', 'xml', 'text')
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api_key: Optional NCBI API key
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"""
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if output_format == 'json':
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# Get summaries in JSON format
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summaries = esummary(gene_ids, api_key=api_key)
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print(json.dumps(summaries, indent=2))
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else:
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# Fetch full records
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data = efetch(gene_ids, retmode=output_format, api_key=api_key)
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print(data)
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# Respect rate limits
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time.sleep(0.34)
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def main():
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parser = argparse.ArgumentParser(
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description='Query NCBI Gene database using E-utilities',
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formatter_class=argparse.RawDescriptionHelpFormatter,
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epilog="""
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Examples:
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# Search for gene by symbol
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%(prog)s --search "BRCA1" --organism "human"
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# Fetch gene by ID
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%(prog)s --id 672 --format json
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# Complex search query
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%(prog)s --search "insulin[gene] AND diabetes[disease]"
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# Multiple gene IDs
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%(prog)s --id 672,7157,5594
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"""
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)
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parser.add_argument('--search', '-s', help='Search query')
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parser.add_argument('--organism', '-o', help='Organism filter')
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parser.add_argument('--id', '-i', help='Gene ID(s), comma-separated')
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parser.add_argument('--format', '-f', default='json',
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choices=['json', 'xml', 'text'],
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help='Output format (default: json)')
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parser.add_argument('--max-results', '-m', type=int, default=20,
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help='Maximum number of search results (default: 20)')
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parser.add_argument('--api-key', '-k', help='NCBI API key for higher rate limits')
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args = parser.parse_args()
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if not args.search and not args.id:
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parser.error("Either --search or --id must be provided")
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if args.id:
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# Fetch by ID
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gene_ids = [id.strip() for id in args.id.split(',')]
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fetch_by_id(gene_ids, output_format=args.format, api_key=args.api_key)
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else:
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# Search and summarize
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search_and_summarize(args.search, organism=args.organism,
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max_results=args.max_results, api_key=args.api_key)
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if __name__ == '__main__':
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main()
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