python - 查找文本列表并在匹配字段处替换

Question

好吧，我承认标题对于我的问题来说是含糊的，我无法以更容易理解的方式表达它。我是编程新手，我的技术术语仍在发展中。

我有两个文件，文件 A 如下所示:

CHROM   POS ID  AGM12   AGM14   AGM15   AGM18 ..
1   14930   rs150145850     0/0 1/1 0/0  0/0 ..
1   14933   rs138566748 0/0 0/0 0/0  0/0 ..
1   63671   rs116440577 0/1 0/0 0/0  0/0 ..
2   808922  rs6594027   0/0 0/0 0/0  0/1 ..
2   753474  rs2073814   1/0 0/0 0/1  0/0 ..
3   753405  rs61770173  0/0 1/1 0/0  1/0 ..
...
...
...

文件B看起来像:

CHROM   POS rsID    Sample_ID
1   14930   rs150145850 AGM15
2   808922  rs6594027   AGM18
3   753405  rs61770173  AGM12
...
...
...

我希望使用文件B中的POS字段信息(第2列)来替换文件A中相应Sample_ID中的内容由NA。

例如:输出应如下所示

CHROM   POS ID  AGM12   AGM14   AGM15   AGM18
1   14930   rs150145850     0/0 1/1 NA   0/0
1   14933   rs138566748 0/0 0/0 0/0  0/0
1   63671   rs116440577 0/1 0/0 0/0  0/0
2   808922  rs6594027   0/0 0/0 0/0  NA
2   753474  rs2073814   1/0 0/0 0/1  0/0
3   753405  rs61770173  NA  1/1 0/0  1/0

如何在 Python 或 Unix 中执行此操作？

Answer 1

这是一个使用 csv 的版本模块(我假设您的列是制表符分隔的)。

import csv
import collections

a = 'path/to/a'
b = 'path/to/b'
output = 'output/path'

pos = collections.defaultdict(list)

with open(b) as csvin:
    reader = csv.DictReader(csvin, delimiter='\t')
    for line in reader:
        pos[line['POS']].append(line['Sample_ID'])

with open(a) as csvin, open(output, 'wb') as csvout:
    reader = csv.DictReader(csvin, delimiter='\t')
    writer = csv.DictWriter(csvout, fieldnames=reader.fieldnames, delimiter='\t')
    writer.writeheader()
    for line in reader:
        fields = pos.get(line['POS'], [])
        for field in fields:
            line[field] = 'NA'
        writer.writerow(line)