[英]how to parse a file and write to an output file in python
我是python的新手。 我正在尝试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,但是将它们写入输出文件时遇到了麻烦。
这是原始测试文件:
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(尽管我知道我的代码还不完整)
Pld5 GO:0003824:GO:0008152
Exo1 GO:0003677:GO:0003824:GO:0004518:GO:0006281
谢谢
Upendra
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()
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
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