使用 python 在两个文件中查找匹配项

Question

我正在分析测序数据，我需要找到它们功能的候选基因很少。

编辑可用的人类数据库后，我想将我的候选基因与数据库进行比较，并输出我的候选基因的功能。

我只有基本的 python 技能，所以我认为这可能会帮助我加快寻找候选基因功能的工作。

所以包含候选基因的文件1看起来像这样

Gene
AQP7
RLIM
SMCO3
COASY
HSPA6

和数据库，file2.csv 看起来像这样：

Gene   function 
PDCD6  Programmed cell death protein 6 
CDC2   Cell division cycle 2, G1 to S and G2 to M, isoform CRA_a 
CDC2   Cell division cycle 2, G1 to S and G2 to M, isoform CRA_a 
CDC2   Cell division cycle 2, G1 to S and G2 to M, isoform CRA_a 
CDC2   Cell division cycle 2, G1 to S and G2 to M, isoform CRA_a

期望的输出

 Gene(from file1) ,function(matching from file2)

我尝试使用此代码：

file1 = 'file1.csv'
file2 = 'file2.csv'
output = 'file3.txt'

with open(file1) as inf:
    match = set(line.strip() for line in inf)

with open(file2) as inf, open(output, 'w') as outf:
    for line in inf:
        if line.split(' ',1)[0] in match:
            outf.write(line)

我只得到空白页。

我试过使用交集函数

with open('file1.csv', 'r') as ref:
    with open('file2.csv','r') as com:
       with open('common_genes_function','w') as output:
           same = set(ref).intersection(com)
                print same

也不工作..

请帮忙，否则我需要手动执行此操作

Answer 1

我建议使用 pandas merge 函数。但是，它需要在 'Gene' 和 'function' 列之间有一个明确的分隔符。在我的示例中，我假设它位于 tab:

import pandas as pd
#open files as pandas datasets
file1 = pd.read_csv(filepath1, sep = '\t')
file2 = pd.read_csv(filepath2, sep = '\t')

#merge files by column 'Gene' using 'inner', so it comes up
#with the intersection of both datasets
file3 = pd.merge(file1, file2, how = 'inner', on = ['Gene'], suffixes = ['1','2'])
file3.to_csv(filepath3, sep = ',')

Answer 2

使用基本 Python，您可以尝试以下操作：

import re

gene_function = {}
with open('file2.csv','r') as input:
    lines = [line.strip() for line in input.readlines()[1:]]
    for line in lines:
        match = re.search("(\w+)\s+(.*)",line)
        gene = match.group(1)
        function = match.group(2)
        if gene not in gene_function:
            gene_function[gene] = function

with open('file1.csv','r') as input:
    genes = [i.strip() for i in input.readlines()[1:]]
    for gene in genes:
        if gene in gene_function:
            print "{}, {}".format(gene, gene_function[gene])

使用 python 在两个文件中查找匹配项

find matches in two file using python

python

match