从NCBI下载基因序列，NCBI下载基因序列,[Python]代码Py

从NCBI下载基因序列，NCBI下载基因序列,[Python]代码Py

[Python]代码

Python语言: 从NCBI下载基因序列#!/usr/bin/env python# -*- coding:utf-8 -*-'''读取文件（每行一个ID）中的GeneID，下载其序列，并保存到文件中'''__file__    = 'download_gene.py'__date__    = '2008-10-30'__version__ = '0.1'__author__  = 'Wubin Qu <[email protected]> @CZlab @BMI @CHINA'__blog__    = 'http://quwubin.blogspot.com'__license__ = 'GPL v3 License'from Bio import Entrezdef read_id(file_name):    '''从文件中读取GeneID'''    id_array = []    fh = open(file_name, 'r')    lines = fh.readlines()    for line in lines:        id = line.strip()        id_array.append(id)    fh.close()    id_array = ','.join(id_array)    return id_arraydef download_seq (id_array):    '''根据GeneID下载相应格式的序列'''    result_handle = Entrez.efetch(db="nucleotide", rettype="genbank",  id=id_array)    result = result_handle.read()    return resultdef write_to_file(file_out_name, content):    '''将序列写入文件中 '''    fh = open(file_out_name, 'w')    fh.write(content)    fh.close()def main():    '''主控制程序'''    file_name = 'id_list.txt'    file_out_name = 'sequences.txt'    id_array = read_id(file_name)    result = download_seq(id_array)    write_to_file(file_out_name, result)if __name__ == '__main__':    main()