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HMS Warspite

代码测试

#!/usr/bin/python
# -*- coding: utf-8 -*-


import os#载入os标准库
from Bio.Blast import NCBIXML#载入biopython的xml文件解析第三方库



def get_fasta_xml(path):#寻找符合fasta_xml文件
    xml_list = []
    fasta_list = []
    for root, directory, files in os.walk(path):
        for fasta_name in files:
            name, _ = os.path.splitext(fasta_name)
            if fasta_name.endswith('.fasta'):
                fasta_list.append(name)
    for root, directory, files in os.walk(path):
        for file_name in files:
            name, _ = os.path.splitext(file_name)
            if name in fasta_list and file_name.endswith('xml'):
                xml_list.append(file_name)
    return xml_list


E_VALUE_THRESH = float(input("输入E值："))#E值的确定


def analysis_xml(xml_list):#利用NCBIXML的xml解析器分析文件信息
    for filename in xml_list:
        result_handle = open(filename)
        blast_record = NCBIXML.read(result_handle)
        for alignment in blast_record.alignments:
            for hsp in alignment.hsps:
                if hsp.expect < E_VALUE_THRESH:#E值比较
                    print('****' + filename + '****')
                    print('****Alignment****')
                    print('sequence:', alignment.title)
                    print('length:', alignment.length)
                    print('e_value:', hsp.expect)
                    print(hsp.query[0:75] + '...')#预览序列长度
                    print(hsp.match[0:75] + '...')#预览序列长度
                    print(hsp.sbjct[0:75] + '...')#预览序列长度
                    print('\n')


if __name__ == '__main__':
    analysis_xml(get_fasta_xml(".\\"))