已知genebank号 批处理获取gene ID和序列信息

处理一个公开数据集，发现多个genebank号对应1个gene ID，所以写了个脚本在NCBI接口批处理了一下。同时为了避免被封，添加了sleep，不知道是否好用，结过是几万的数据依然很流畅~~

####### 通过 genebank的BC号获取ID和序列信息 #######
from Bio import Entrez
from Bio import SeqIO
import time
import random
import csv
from itertools import islice

def get_gene_id(genebank_accession):

    Entrez.email = "*****@gmail.com"
    M = random.randint(0, 3)
    time.sleep(M)
    # 使用Entrez获取GenBank记录
    handle = Entrez.efetch(db="nucleotide", id=genebank_accession, rettype="gb", retmode="text")
    record = SeqIO.read(handle, "genbank")
    handle.close()
    
    # 获取基因ID
    gene_id = None
    protein_sequence = None
    for feature in record.features:
        if feature.type == "gene":
            gene_id = feature.qualifiers["gene"][0]
        if feature.type == "CDS":
            protein_sequence = feature.qualifiers["translation"][0] 
            break
    
    return gene_id, protein_sequence if protein_sequence is not None else "N/A"

file_path = 'genebank.csv'

with open(file_path, 'r') as infile, open('genseq.csv', 'a', newline='', encoding='gbk') as outfile:
    reader = csv.reader(infile)
    writer = csv.writer(outfile)
    # writer.writerow(['GeneBank Accession', 'Gene ID', 'Protein Sequence'])  # 写入 CSV 文件的表头
    next(reader)  # 跳过 CSV 文件的表头
    for row in islice(reader, 1000, 4000):  # 仅处理前1000-4000行数据
        genebank_accession = row[0]  # 假设GeneBank存取号是行的第一个字段
        try:
            gene_id, protein_sequence = get_gene_id(genebank_accession)
            print("genebank_accession",genebank_accession)
            print("Gene ID:", gene_id)
            print("Protein Sequence:", protein_sequence)
        except Exception as e:
            print(f"Failed to retrieve data for GeneBank Accession {genebank_accession}: {e}")
            gene_id = "N/A"
            protein_sequence = "N/A"
        
        writer.writerow([genebank_accession, gene_id, protein_sequence])

print("############")