python - 如何将单个 CSV 文件分割成多个按字段分组的较小文件并删除最终 CSV 中的列？

Question

尽管我认为这听起来像是一个重复的问题，但我还没有找到解决方案。嗯，我有一个很大的 .csv 文件，如下所示:

prot_hit_num,prot_acc,prot_desc,pep_res_before,pep_seq,pep_res_after,ident,country
1,gi|21909,21 kDa seed protein [Theobroma cacao],A,ANSPV,L,F40,EB
1,gi|21909,21 kDa seed protein [Theobroma cacao],A,ANSPVL,D,F40,EB
1,gi|21909,21 kDa seed protein [Theobroma cacao],L,SSISGAGGGGLA,L,F40,EB
1,gi|21909,21 kDa seed protein [Theobroma cacao],D,NYDNSAGKW,W,F40,EB
....

目的是根据最后两列(“ident”和“country”)将此 .csv 文件分割成多个较小的 .csv 文件。

我使用了之前的答案中的代码post如下:

csv_contents = []
with open(outfile_path4, 'rb') as fin:
  dict_reader = csv.DictReader(fin)   # default delimiter is comma
  fieldnames = dict_reader.fieldnames # save for writing
  for line in dict_reader:            # read in all of your data
    csv_contents.append(line)         # gather data into a list (of dicts)

# input to itertools.groupby must be sorted by the grouping value 
sorted_csv_contents = sorted(csv_contents, key=op.itemgetter('prot_desc','ident','country'))


for groupkey, groupdata in it.groupby(sorted_csv_contents, 
                                  key=op.itemgetter('prot_desc','ident','country')):

  with open(outfile_path5+'slice_{:s}.csv'.format(groupkey), 'wb') as fou:
    dict_writer = csv.DictWriter(fou, fieldnames=fieldnames)    
    dict_writer.writerows(groupdata)

但是，我需要我的输出 .csv 仅包含“pep_seq”列，所需的输出如下:

pep_seq    
ANSPV
ANSPVL
SSISGAGGGGLA
NYDNSAGKW

我能做什么？

Answer 1

您的代码几乎是正确的，只需要正确设置fieldsnames并设置extraaction='ignore'即可。这告诉 DictWriter 仅写入您指定的字段:

import itertools   
import operator    
import csv

outfile_path4 = 'input.csv'    
outfile_path5 = r'my_output_folder\output.csv'
csv_contents = []

with open(outfile_path4, 'rb') as fin:
    dict_reader = csv.DictReader(fin)   # default delimiter is comma
    fieldnames = dict_reader.fieldnames # save for writing

    for line in dict_reader:            # read in all of your data
        csv_contents.append(line)         # gather data into a list (of dicts)

group = ['prot_desc','ident','country']
# input to itertools.groupby must be sorted by the grouping value 
sorted_csv_contents = sorted(csv_contents, key=operator.itemgetter(*group))

for groupkey, groupdata in itertools.groupby(sorted_csv_contents, key=operator.itemgetter(*group)):
    with open(outfile_path5+'slice_{:s}.csv'.format(groupkey), 'wb') as fou:
        dict_writer = csv.DictWriter(fou, fieldnames=['pep_seq'], extrasaction='ignore')    
        dict_writer.writeheader()
        dict_writer.writerows(groupdata) 

这将为您提供一个输出 csv 文件，其中包含:

pep_seq
ANSPV
ANSPVL
SSISGAGGGGLA
NYDNSAGKW