Question

我正在尝试从没有重复的CSV创建字典。 CSV文件包含：样品名称（s1，s2等）基因名称，样品1突变的影响，样品2突变的影响。这是CSV文件的两行示例：

s1, s2, gene1, MODERATE, HIGH
s3, s4, gene2, HIGH, MODERATE

我的目标是获得有关特定基因突变的样本数量的摘要，然后得出该突变是否对HIGH产生影响的总结。

例如：

gene12  7   ['s1', 's3', 's4', 's10 [HIGH]', 's17', 's19', 's24 [HIGH]']
gene20  2   ['s10 [HIGH]', 's21']

当前我的代码如下：

import os
import sys

path = ("path/to/csv")
open_csv = open(path+"csvfile", "r")
read_csv = open_csv.read().splitlines()
gene_dict = {}
for line in read_csv:
    split_lines = line.split(", ")
    gene = split_lines[2]
    sample1 = split_lines[0]
    sample2 = split_lines[1]
    impact1 = split_lines[3]
    impact2 = split_lines[4]
    for i in range(0, len(read_csv):
        if gene in gene_dict:
            if impact1 == "HIGH":
                gene_dict[gene].append(sample1+" [HIGH]")
            if impact2 == "HIGH":
                gene_dict[gene].append(sample2+" [HIGH]")
            else:
                gene_dict[gene].append(sample1)
                gene_dict[gene].append(sample2)
        else:
            gene_dict[gene] = [sample1]

final_dict = {a:list(set(b)) for a, b in gene_dict.items()}

for key, value in final_dict.items():
    genename = key
    num_samples = len([item for item in value if item])
    samples = value     
    print(genename,num_samples,samples)

我的脚本可以正常工作，除了我得到重复的样本。我的意思是，如果样本中的基因具有高影响突变，那么最终摘要将两次列出样本。以下是我的意思的示例：

gene12  8   ['s1', 's3', 's4', 's10 [HIGH]', 's17', 's19', 's24', 's24 [HIGH]']
gene20  3   ['s10', 's10 [HIGH]', 's21']

这可能是我创建导致重复的字典的方式，但我无法弄清楚。您会看到，对于gene12，s24被列出两次，从而消除了计数。对于带有s10的gene20也是如此。样品被列出两次，一次是正确的具有高影响突变，另一次是没有高影响突变。但是，s24仅在gene12中具有HIGH影响突变，而s10仅在gene20中具有HIGH影响突变。我希望这是有道理的。我可以澄清是否需要。预先感谢您提供的所有帮助！

Answer 1

好像您的内循环for i in range(0, len(read_csv):正在复制并添加无用的匹配。另外，if / if / else结构和添加[HIGH]的标记看起来也很损坏。

更正的版本：

import os
import sys

path = ("path/to/csv")
open_csv = open(path+"csvfile", "r")
read_csv = open_csv.read().splitlines()
gene_dict = {}
for line in read_csv:
    split_lines = line.split(", ")
    gene = split_lines[2]
    sample1 = split_lines[0]
    sample2 = split_lines[1]
    impact1 = split_lines[3]
    impact2 = split_lines[4]
    if impact1 == "HIGH":
        sample1 = sample1 + " [HIGH]"
    if impact2 == "HIGH":
        sample2 = sample2 + " [HIGH]"

    if gene in gene_dict:
        gene_dict[gene].append(sample1)
        gene_dict[gene].append(sample2)
    else:
        gene_dict[gene] = [sample1, sample2]

final_dict = {a:list(set(b)) for a, b in gene_dict.items()}

for key, value in final_dict.items():
    genename = key
    num_samples = len([item for item in value if item])
    samples = value     
    print(genename,num_samples,samples)

对于我尝试的几个示例，这看起来是一致的。

Answer 2

我会创建一个像这样的类：

class Sample:
    def __init__(self, name, level="low",):
        self.level = level
        self.name = name

    def __eq__(self, equal):
        if equal.name == self.name:
            return True
        return False

类似的东西（无法测试）：

import os
import sys

path = ("path/to/csv")
open_csv = open(path+"csvfile", "r")
read_csv = open_csv.read().splitlines()
gene_dict = {}
for line in read_csv:
    split_lines = line.split(", ")
    gene = split_lines[2]
    sample1 = Sample(split_lines[0])
    sample2 = Sample(split_lines[1])
    impact1 = split_lines[3]
    impact2 = split_lines[4]
    for i in range(0, len(read_csv):
        if gene in gene_dict:
            if not sample1 in gene_dict[gene]:
                if impact1 == "HIGH":
                    sample1.level = impact1
                    gene_dict[gene].append(sample1)

                else:
                    gene_dict[gene].append(sample1)

            if not sample2 in gene_dict[gene]:
                if impact2 == "HIGH":
                    sample2.level = impact2
                    gene_dict[gene].append(sample2)
                else:
                    gene_dict[gene].append(sample2)
        else:
            gene_dict[gene] = [sample1]

创建没有重复的字典

2 个答案: