在python中过滤CSV文件

问题内容：

我已经下载了这个csv文件，该文件创建了基因信息电子表格。重要的是在HLA-*列中有基因信息。如果该基因的分辨率太低，DQB1*03则应删除该行。如果数据分辨率过高（例如）DQB1*03:02:01，则:01需要删除最后的标签。因此，理想情况下，我希望蛋白质处于这种格式DQB1*03:02，以便在之后具有两个分辨率级别DQB1*。我如何告诉python查找这些格式，而忽略存储在其中的数据。例如

if (csvCell is of format DQB1*03:02:01):
   delete the :01 # but do this in a general format
elif (csvCell is of format DQB1*03):
   delete row
else:
   goto next line

更新：我引用的已编辑代码

import csv
import re
import sys

csvdictreader = csv.DictReader(open('mhc.csv','r+b'), delimiter=',')
csvdictwriter = csv.DictWriter(file('mhc_fixed.csv','r+b'), fieldnames=csvdictreader.fieldnames, delimiter=',')
csvdictwriter.writeheader()
targets = [name for name in csvdictreader.fieldnames if name.startswith('HLA-D')]

for rowfields in csvdictreader:
  keep = True
  for field in targets:
    value = rowfields[field]
    if re.match(r'^\w+\*\d\d$', value):
      keep = False
      break # quit processing target fields
    elif re.match(r'^(\w+)\*(\d+):(\d+):(\d+):(\d+)$', value):
      rowfields[field] = re.sub(r'^(\w+)\*(\d+):(\d+):(\d+):(\d+)$',r'\1*\2:\3', value)
    else: # reduce gene resolution if too high
              # by only keeping first two alles if three are present
      rowfields[field] = re.sub(r'^(\w+)\*(\d+):(\d+):(\d+)$',r'\1*\2:\3', value)
  if keep:
     csvdictwriter.writerow(rowfields)

问题答案：

我认为这可以满足您的需求。这不是Peter的回答那么简单，因为它使用Python的csv模块来处理文件。它可能会被重写和简化，只是像他一样将文件视为纯文本，但这应该很容易。

import csv
import re
import sys

csvdictreader = csv.DictReader(sys.stdin, delimiter=',')
csvdictwriter = csv.DictWriter(sys.stdout, fieldnames=csvdictreader.fieldnames, delimiter=',')
csvdictwriter.writeheader()
targets = [name for name in csvdictreader.fieldnames if name.startswith('HLA-')]

for rowfields in csvdictreader:
    keep = True
    for field in targets:
        value = rowfields[field]
        if re.match(r'^DQB1\*\d\d$', value): # gene resolution too low?
            keep = False
            break # quit processing target fields
        else: # reduce gene resolution if too high
              # by only keeping first two alles if three are present
            rowfields[field] = re.sub(r'^DQB1\*(\d\d):(\d\d):(\d\d)$',
                                      r'DQB1*\1:\2', value)
    if keep:
        csvdictwriter.writerow(rowfields)

对我而言，最难的部分是确定您想做什么。

在python中过滤CSV文件

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