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Zhongwei Li
277
skills/gene-database/scripts/fetch_gene_data.py
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277
skills/gene-database/scripts/fetch_gene_data.py
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#!/usr/bin/env python3
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"""
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Fetch gene data from NCBI using the Datasets API.
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This script provides access to the NCBI Datasets API for retrieving
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comprehensive gene information including metadata and sequences.
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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 urllib.parse
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import urllib.request
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from typing import Optional, Dict, Any, List
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DATASETS_API_BASE = "https://api.ncbi.nlm.nih.gov/datasets/v2alpha/gene"
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def get_taxon_id(taxon_name: str) -> Optional[str]:
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"""
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Convert taxon name to NCBI taxon ID.
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Args:
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taxon_name: Common or scientific name (e.g., "human", "Homo sapiens")
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Returns:
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Taxon ID as string, or None if not found
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"""
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# Common mappings
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common_taxa = {
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'human': '9606',
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'homo sapiens': '9606',
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'mouse': '10090',
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'mus musculus': '10090',
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'rat': '10116',
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'rattus norvegicus': '10116',
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'zebrafish': '7955',
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'danio rerio': '7955',
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'fruit fly': '7227',
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'drosophila melanogaster': '7227',
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'c. elegans': '6239',
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'caenorhabditis elegans': '6239',
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'yeast': '4932',
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'saccharomyces cerevisiae': '4932',
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'arabidopsis': '3702',
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'arabidopsis thaliana': '3702',
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'e. coli': '562',
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'escherichia coli': '562',
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}
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taxon_lower = taxon_name.lower().strip()
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return common_taxa.get(taxon_lower)
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def fetch_gene_by_id(gene_id: str, api_key: Optional[str] = None) -> Dict[str, Any]:
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"""
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Fetch gene data by Gene ID.
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Args:
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gene_id: NCBI Gene ID
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api_key: Optional NCBI API key
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Returns:
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Gene data as dictionary
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"""
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url = f"{DATASETS_API_BASE}/id/{gene_id}"
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headers = {}
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if api_key:
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headers['api-key'] = api_key
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try:
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req = urllib.request.Request(url, headers=headers)
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with urllib.request.urlopen(req) as response:
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return json.loads(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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if e.code == 404:
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print(f"Gene ID {gene_id} not found", 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 fetch_gene_by_symbol(symbol: str, taxon: str, api_key: Optional[str] = None) -> Dict[str, Any]:
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"""
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Fetch gene data by gene symbol and taxon.
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Args:
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symbol: Gene symbol (e.g., "BRCA1")
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taxon: Organism name or taxon ID
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api_key: Optional NCBI API key
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Returns:
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Gene data as dictionary
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"""
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# Convert taxon name to ID if needed
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taxon_id = get_taxon_id(taxon)
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if not taxon_id:
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# Try to use as-is (might already be a taxon ID)
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taxon_id = taxon
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url = f"{DATASETS_API_BASE}/symbol/{symbol}/taxon/{taxon_id}"
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headers = {}
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if api_key:
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headers['api-key'] = api_key
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try:
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req = urllib.request.Request(url, headers=headers)
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with urllib.request.urlopen(req) as response:
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return json.loads(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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if e.code == 404:
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print(f"Gene symbol '{symbol}' not found for taxon {taxon}", 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 fetch_multiple_genes(gene_ids: List[str], api_key: Optional[str] = None) -> Dict[str, Any]:
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"""
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Fetch data for multiple genes by ID.
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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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Combined gene data as dictionary
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"""
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# For multiple genes, use POST request
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url = f"{DATASETS_API_BASE}/id"
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data = json.dumps({"gene_ids": gene_ids}).encode('utf-8')
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headers = {'Content-Type': 'application/json'}
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if api_key:
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headers['api-key'] = api_key
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try:
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req = urllib.request.Request(url, data=data, headers=headers, method='POST')
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with urllib.request.urlopen(req) as response:
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return json.loads(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 display_gene_info(data: Dict[str, Any], verbose: bool = False) -> None:
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"""
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Display gene information in human-readable format.
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Args:
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data: Gene data dictionary from API
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verbose: Show detailed information
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"""
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if 'genes' not in data:
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print("No gene data found in response")
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return
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for gene in data['genes']:
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gene_info = gene.get('gene', {})
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print(f"Gene ID: {gene_info.get('gene_id', 'N/A')}")
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print(f"Symbol: {gene_info.get('symbol', 'N/A')}")
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print(f"Description: {gene_info.get('description', 'N/A')}")
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if 'tax_name' in gene_info:
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print(f"Organism: {gene_info['tax_name']}")
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if 'chromosomes' in gene_info:
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chromosomes = ', '.join(gene_info['chromosomes'])
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print(f"Chromosome(s): {chromosomes}")
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# Nomenclature
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if 'nomenclature_authority' in gene_info:
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auth = gene_info['nomenclature_authority']
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print(f"Nomenclature: {auth.get('authority', 'N/A')}")
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# Synonyms
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if 'synonyms' in gene_info and gene_info['synonyms']:
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print(f"Synonyms: {', '.join(gene_info['synonyms'])}")
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if verbose:
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# Gene type
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if 'type' in gene_info:
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print(f"Type: {gene_info['type']}")
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# Genomic locations
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if 'genomic_ranges' in gene_info:
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print("\nGenomic Locations:")
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for range_info in gene_info['genomic_ranges']:
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accession = range_info.get('accession_version', 'N/A')
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start = range_info.get('range', [{}])[0].get('begin', 'N/A')
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end = range_info.get('range', [{}])[0].get('end', 'N/A')
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strand = range_info.get('orientation', 'N/A')
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print(f" {accession}: {start}-{end} ({strand})")
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# Transcripts
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if 'transcripts' in gene_info:
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print(f"\nTranscripts: {len(gene_info['transcripts'])}")
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for transcript in gene_info['transcripts'][:5]: # Show first 5
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print(f" {transcript.get('accession_version', 'N/A')}")
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print()
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def main():
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parser = argparse.ArgumentParser(
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description='Fetch gene data from NCBI Datasets API',
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formatter_class=argparse.RawDescriptionHelpFormatter,
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epilog="""
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Examples:
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# Fetch by Gene ID
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%(prog)s --gene-id 672
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# Fetch by gene symbol and organism
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%(prog)s --symbol BRCA1 --taxon human
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# Fetch multiple genes
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%(prog)s --gene-id 672,7157,5594
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# Get JSON output
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%(prog)s --symbol TP53 --taxon "Homo sapiens" --output json
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# Verbose output with details
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%(prog)s --gene-id 672 --verbose
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"""
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)
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parser.add_argument('--gene-id', '-g', help='Gene ID(s), comma-separated')
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parser.add_argument('--symbol', '-s', help='Gene symbol')
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parser.add_argument('--taxon', '-t', help='Organism name or taxon ID (required with --symbol)')
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parser.add_argument('--output', '-o', choices=['pretty', 'json'], default='pretty',
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help='Output format (default: pretty)')
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parser.add_argument('--verbose', '-v', action='store_true',
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help='Show detailed information')
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parser.add_argument('--api-key', '-k', help='NCBI API key')
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args = parser.parse_args()
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if not args.gene_id and not args.symbol:
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parser.error("Either --gene-id or --symbol must be provided")
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if args.symbol and not args.taxon:
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parser.error("--taxon is required when using --symbol")
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# Fetch data
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if args.gene_id:
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gene_ids = [id.strip() for id in args.gene_id.split(',')]
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if len(gene_ids) == 1:
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data = fetch_gene_by_id(gene_ids[0], api_key=args.api_key)
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else:
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data = fetch_multiple_genes(gene_ids, api_key=args.api_key)
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else:
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data = fetch_gene_by_symbol(args.symbol, args.taxon, api_key=args.api_key)
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if not data:
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sys.exit(1)
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# Output
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if args.output == 'json':
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print(json.dumps(data, indent=2))
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else:
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display_gene_info(data, verbose=args.verbose)
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if __name__ == '__main__':
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main()
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