Question

即使我是python的新手，我也无法理解我是如何解决这个问题/采取正确的方法。因此，任何帮助，链接到有用的教程都会受到高度赞赏，因为我不时会做这种事情。

我有一个CSV文件，我需要重新格式化/修改一下。

我需要存储基因所在的样本量。

输入文件：

AHCTF1: Sample1, Sample2, Sample4
AHCTF1: Sample2, Sample7, Sample12
AHCTF1: Sample5, Sample6, Sample7

结果：

 AHCTF1 in 7 samples (Sample1, Sample2, Sample4, Sample5, Sample6, Sample7, Sample12)

代码：

f = open("/CSV-sorted.csv")
gene_prev = ""

hit_list = []

csv_f = csv.reader(f)

for lines in csv_f:

    #time.sleep(0.1)
    gene = lines[0]
    sample = lines[11].split(",")
    repeat = lines[8]

    for samples in sample:
        hit_list.append(samples)

    if gene == gene_prev:

        for samples in sample:

            hit_list.append(samples)

        print gene
        print hit_list
        print set(hit_list)
        print "samples:", len(set(hit_list))


    hit_list = []

    gene_prev = gene

因此，简而言之，我想将每个基因的命中结合起来，并从中删除重复。

也许字典可以做到这一点：将ave基因作为关键并将样本添加为值？

发现这个 - 相似/有用：How can I combine dictionaries with the same keys in python?

Answer 1

删除重复项的标准方法是转换为set。

但是我觉得你读文件的方式有些不对劲。第一个问题：它不是csv文件（前两个字段之间有冒号）。

gene = lines[0]
sample = lines[11].split(",")
repeat = lines[8]

应该做什么？

如果我写这篇文章，我会将“：”替换为另一个“，”。因此，通过此修改并使用集合字典，您的代码将类似于：

# Read in csv file and convert to list of list of entries. Use with so that 
# the file is automatically closed when we are done with it
csvlines = []
with open("CSV-sorted.csv") as f:
    for line in f:
        # Use strip() to clean up trailing whitespace, use split() to split
        # on commas.
        a = [entry.strip() for entry in line.split(',')]
        csvlines.append(a)

# I'll print it here so you can see what it looks like:
print(csvlines)



# Next up: converting our list of lists to a dict of sets.

# Create empty dict
sample_dict = {}

# Fill in the dict
for line in csvlines:
    gene = line[0] # gene is first entry
    samples = set(line[1:]) # rest of the entries are samples

    # If this gene is in the dict already then join the two sets of samples
    if gene in sample_dict:
        sample_dict[gene] = sample_dict[gene].union(samples)

    # otherwise just put it in
    else:
        sample_dict[gene] = samples


# Now you can print the dictionary:
print(sample_dict)

输出结果为：

[['AHCTF1', 'Sample1', 'Sample2', 'Sample4'], ['AHCTF1', 'Sample2', 'Sample7', 'Sample12'], ['AHCTF1', 'Sample5', 'Sample6', 'Sample7']]
{'AHCTF1': {'Sample12', 'Sample1', 'Sample2', 'Sample5', 'Sample4', 'Sample7', 'Sample6'}}

第二行是你的字典。

Python列表，csv，删除重复

1 个答案: