Question

我是python的新手。我试图解析文件以提取某些列并写入输出文件。我能够解析并提取所需的列，但无法将它们写入输出文件。

以下是原始测试文件：

EGW05759        Pld5    I79_005987      GO_function: GO:0003824 - catalytic activity [Evidence IEA]; GO_process: GO:0008152 - metabolic process [Evidence IEA]                                  
EGW05760        Exo1    I79_005988      GO_function: GO:0003677 - DNA binding [Evidence IEA]; GO_function: GO:0003824 - catalytic activity [Evidence IEA]; GO_function: GO:0004518 - nuclease activity [Evidence IEA]; GO_process: GO:0006281 - DNA repair [Evidence IEA]

这是我的python代码

f = open('test_parsing.txt', 'rU')
f1 = open('test_parsing_out.txt', 'a')
for line in f:
   match = re.search('\w+\s+(\w+)\s+\w+\s+\w+\:', line)
   match1 = re.findall('GO:\d+', line)
   f1.write(match.group(1), match1)
f1.close()

基本上我希望输出看起来像这样（虽然我知道我的代码并不完整，但

Pld5 GO:0003824:GO:0008152
Exo1 GO:0003677:GO:0003824:GO:0004518:GO:0006281

由于

众议员

Answer 1

f = open('test_parsing.txt', 'rU')
f1 = open('test_parsing_out.txt', 'a')
for line in f:
    match = re.search('\w+\s+(\w+)\s+\w+\s+\w+\:', line)
    match1 = re.findall('GO:\d+', line)
    f1.write('%s %s \n'%(match.group(1), ''.join(match1)))
f1.close()

Answer 2

使用csv模块：

import csv, re

with open('test_parsing.txt', 'rU') as infile, open('test_parsing_out.txt', 'a') as outfile:
    reader = csv.reader(infile, delimiter="\t")
    for line in reader:
        result = line[1] + " " + ':'.join(re.findall("GO:\d{6}", line[3]))
        outfile.write(result + "\n")

# OUTPUT
Pld5 GO:000382:GO:000815
Exo1 GO:000367:GO:000382:GO:000451:GO:000628

如何在python中解析文件并写入输出文件

2 个答案: