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https://github.com/K-Dense-AI/claude-scientific-skills.git
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Add more scientific skills
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Timothy Kassis
293
scientific-packages/biopython/scripts/ncbi_entrez.py
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293
scientific-packages/biopython/scripts/ncbi_entrez.py
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#!/usr/bin/env python3
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"""
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NCBI Entrez database access using BioPython.
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This script demonstrates:
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- Searching NCBI databases
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- Downloading sequences by accession
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- Retrieving PubMed articles
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- Batch downloading with WebEnv
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- Proper error handling and rate limiting
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"""
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import time
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from Bio import Entrez, SeqIO
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# IMPORTANT: Always set your email
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Entrez.email = "your.email@example.com" # Change this!
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def search_nucleotide(query, max_results=10):
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"""Search NCBI nucleotide database."""
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print(f"Searching nucleotide database for: {query}")
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print("-" * 60)
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handle = Entrez.esearch(db="nucleotide", term=query, retmax=max_results)
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record = Entrez.read(handle)
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handle.close()
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print(f"Found {record['Count']} total matches")
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print(f"Returning top {len(record['IdList'])} IDs:")
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print(record["IdList"])
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print()
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return record["IdList"]
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def fetch_sequence_by_accession(accession):
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"""Download a sequence by accession number."""
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print(f"Fetching sequence: {accession}")
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try:
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handle = Entrez.efetch(
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db="nucleotide", id=accession, rettype="gb", retmode="text"
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)
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record = SeqIO.read(handle, "genbank")
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handle.close()
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print(f"Successfully retrieved: {record.id}")
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print(f"Description: {record.description}")
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print(f"Length: {len(record.seq)} bp")
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print(f"Organism: {record.annotations.get('organism', 'Unknown')}")
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print()
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return record
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except Exception as e:
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print(f"Error fetching {accession}: {e}")
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return None
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def fetch_multiple_sequences(id_list, output_file="downloaded_sequences.fasta"):
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"""Download multiple sequences and save to file."""
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print(f"Fetching {len(id_list)} sequences...")
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try:
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# For >200 IDs, efetch automatically uses POST
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handle = Entrez.efetch(
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db="nucleotide", id=id_list, rettype="fasta", retmode="text"
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)
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# Parse and save
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records = list(SeqIO.parse(handle, "fasta"))
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handle.close()
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SeqIO.write(records, output_file, "fasta")
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print(f"Successfully downloaded {len(records)} sequences to {output_file}")
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print()
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return records
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except Exception as e:
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print(f"Error fetching sequences: {e}")
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return []
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def search_and_download(query, output_file, max_results=100):
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"""Complete workflow: search and download sequences."""
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print(f"Searching and downloading: {query}")
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print("=" * 60)
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# Search
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handle = Entrez.esearch(db="nucleotide", term=query, retmax=max_results)
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record = Entrez.read(handle)
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handle.close()
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id_list = record["IdList"]
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print(f"Found {len(id_list)} sequences")
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if not id_list:
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print("No results found")
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return
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# Download in batches to be polite
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batch_size = 100
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all_records = []
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for start in range(0, len(id_list), batch_size):
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end = min(start + batch_size, len(id_list))
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batch_ids = id_list[start:end]
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print(f"Downloading batch {start // batch_size + 1} ({len(batch_ids)} sequences)...")
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handle = Entrez.efetch(
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db="nucleotide", id=batch_ids, rettype="fasta", retmode="text"
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)
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batch_records = list(SeqIO.parse(handle, "fasta"))
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handle.close()
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all_records.extend(batch_records)
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# Be polite - wait between requests
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time.sleep(0.5)
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# Save all records
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SeqIO.write(all_records, output_file, "fasta")
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print(f"Downloaded {len(all_records)} sequences to {output_file}")
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print()
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def use_history_for_large_queries(query, max_results=1000):
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"""Use NCBI History server for large queries."""
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print("Using NCBI History server for large query")
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print("-" * 60)
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# Search with history
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search_handle = Entrez.esearch(
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db="nucleotide", term=query, retmax=max_results, usehistory="y"
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)
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search_results = Entrez.read(search_handle)
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search_handle.close()
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count = int(search_results["Count"])
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webenv = search_results["WebEnv"]
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query_key = search_results["QueryKey"]
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print(f"Found {count} total sequences")
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print(f"WebEnv: {webenv[:20]}...")
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print(f"QueryKey: {query_key}")
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print()
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# Fetch in batches using history
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batch_size = 500
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all_records = []
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for start in range(0, min(count, max_results), batch_size):
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end = min(start + batch_size, max_results)
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print(f"Downloading records {start + 1} to {end}...")
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fetch_handle = Entrez.efetch(
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db="nucleotide",
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rettype="fasta",
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retmode="text",
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retstart=start,
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retmax=batch_size,
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webenv=webenv,
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query_key=query_key,
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)
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batch_records = list(SeqIO.parse(fetch_handle, "fasta"))
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fetch_handle.close()
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all_records.extend(batch_records)
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# Be polite
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time.sleep(0.5)
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print(f"Downloaded {len(all_records)} sequences total")
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return all_records
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def search_pubmed(query, max_results=10):
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"""Search PubMed for articles."""
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print(f"Searching PubMed for: {query}")
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print("-" * 60)
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handle = Entrez.esearch(db="pubmed", term=query, retmax=max_results)
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record = Entrez.read(handle)
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handle.close()
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id_list = record["IdList"]
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print(f"Found {record['Count']} total articles")
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print(f"Returning {len(id_list)} PMIDs:")
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print(id_list)
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print()
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return id_list
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def fetch_pubmed_abstracts(pmid_list):
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"""Fetch PubMed article summaries."""
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print(f"Fetching summaries for {len(pmid_list)} articles...")
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handle = Entrez.efetch(db="pubmed", id=pmid_list, rettype="abstract", retmode="text")
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abstracts = handle.read()
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handle.close()
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print(abstracts[:500]) # Show first 500 characters
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print("...")
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print()
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def get_database_info(database="nucleotide"):
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"""Get information about an NCBI database."""
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print(f"Getting info for database: {database}")
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print("-" * 60)
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handle = Entrez.einfo(db=database)
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record = Entrez.read(handle)
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handle.close()
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db_info = record["DbInfo"]
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print(f"Name: {db_info['DbName']}")
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print(f"Description: {db_info['Description']}")
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print(f"Record count: {db_info['Count']}")
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print(f"Last update: {db_info['LastUpdate']}")
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print()
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def link_databases(db_from, db_to, id_):
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"""Find related records in other databases."""
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print(f"Finding links from {db_from} ID {id_} to {db_to}")
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print("-" * 60)
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handle = Entrez.elink(dbfrom=db_from, db=db_to, id=id_)
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record = Entrez.read(handle)
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handle.close()
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if record[0]["LinkSetDb"]:
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linked_ids = [link["Id"] for link in record[0]["LinkSetDb"][0]["Link"]]
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print(f"Found {len(linked_ids)} linked records")
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print(f"IDs: {linked_ids[:10]}")
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else:
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print("No linked records found")
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print()
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def example_workflow():
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"""Demonstrate complete Entrez workflow."""
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print("=" * 60)
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print("BioPython Entrez Example Workflow")
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print("=" * 60)
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print()
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# Note: These are examples - uncomment to run with your email set
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# # Example 1: Search and get IDs
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# ids = search_nucleotide("Homo sapiens[Organism] AND COX1[Gene]", max_results=5)
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#
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# # Example 2: Fetch a specific sequence
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# fetch_sequence_by_accession("NM_001301717")
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#
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# # Example 3: Complete search and download
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# search_and_download("Escherichia coli[Organism] AND 16S", "ecoli_16s.fasta", max_results=50)
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#
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# # Example 4: PubMed search
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# pmids = search_pubmed("CRISPR[Title] AND 2023[PDAT]", max_results=5)
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# fetch_pubmed_abstracts(pmids[:2])
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#
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# # Example 5: Get database info
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# get_database_info("nucleotide")
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print("Examples are commented out. Uncomment and set your email to run.")
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if __name__ == "__main__":
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example_workflow()
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print()
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print("IMPORTANT: Always set Entrez.email before using these functions!")
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print("NCBI requires an email address for their E-utilities.")
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