Question

我在50个文件夹中都有counts.txt文件，每个文件都与一个样本相关。 counts.txt中有两列：第一列是字符串，另一列是数字。我试图通过它们制作一个嵌套的字典。目标是将counts.txt和文件夹的第一列用作字典的键，并将counts.txt中的第二列用作值。不幸的是，我想在文件夹上循环浏览以使其具有适当形状的文件夹列表无法正常工作，并且会遇到问题！

import os
from natsort import natsorted
path1 = "/home/ali/Desktop/SAMPLES/"


data_ali={}
samples_name=natsorted(os.listdir(path1))


data_ali = {}

samples_name=natsorted(os.listdir(path1))
for i in samples_name:    
    with open(path1+i[0:]+"/counts.txt","rt") as fin:    
        for l in fin.readlines():    
            l=l.strip().split()    
            if l[0][:4]=='ENSG':    
                gene=l[0]    
                data_ali[gene]={}       
                reads=int(l[1])    
                data_ali[gene][samples_name]=reads
print(data_ali)




i expect the output like this: 
'ENSG00000120659': {
    'Sample_1-Leish_011_v2': 14,
    'Sample_2-leish_011_v3': 7,
    'Sample_3-leish_012_v2': 6,
    'Sample_4-leish_012_v3': 1,
    'Sample_5-leish_015_v2': 9,
    'Sample_6-leish_015_v3': 3,
    'Sample_7-leish_016_v2': 4,
    'Sample_8-leish_016_v3': 8,
    'Sample_9-leish_017_v2': 8,
    'Sample_10-leish_017_v3': 2,
    'Sample_11-leish_018_v2': 4,
    'Sample_12-leish_018_v3': 4,
    'Sample_13-leish_019_v2': 7,
    'Sample_14-leish_019_v3': 4,
    'Sample_15-leish_021_v2': 12,
    'Sample_16-leish_021_v3': 5,
    'Sample_17-leish_022_v2': 4,
    'Sample_18-leish_022_v3': 2,
    'Sample_19-leish_023_v2': 9,
    'Sample_20-leish_023_v3': 6,
    'Sample_21-leish_024_v2': 22,
    'Sample_22-leish_024_v3': 10,
    'Sample_23-leish026_v2': 9,
    'Sample_24-leish026_v3': 5,
    'Sample_25-leish027_v2': 4,
    'Sample_26-leish027_v3': 1,
    'Sample_27-leish028_v2': 7,
    'Sample_28-leish028_v3': 5,
    'Sample_29-leish032_v2': 8,
    'Sample_30-leish032_v3': 2
     }

Answer 1

尝试一下：

        if l[0][:4] == 'ENSG':
            gene = l[0]
            reads = int(l[1])
            data_ali.setdefault(gene, {})[i] = reads

两个重要更改：

您的代码data_ali[gene]={}总是清除以前的内容，而是制作了一个新的空字典。 setdefault仅在键gene不存在的情况下创建字典。
第二个键应该是i，而不是列表samples_name。

完整代码清除：

import os
from natsort import natsorted

root = "/home/ali/Desktop/SAMPLES/"

data_ali = {}

for sample_name in natsorted(os.listdir(root)):
    with open(os.path.join(root, sample_name, "counts.txt"), "r") as fin:
        for line in fin.readlines():
            gene, reads = line.split()
            reads = int(reads)
            if gene.startswith('ENSG'):
                data_ali.setdefault(gene, {})[sample_name] = reads

print(data_ali)

创建嵌套字典以遍历我的文本文件和文件夹以创建多个关键字典

1 个答案: