查找两个文本文件的差异

Question

我有两个超过 100000 行的单独文件 A 和 B。现在我需要比较每一行以查找它们是否在 A 中但不在 B 中。两个文件都是文本格式。

文件A：

>Q63544|9
----------------------MDVFKKGFSIAREGVVGAVEKTKQGVTEAAEKTKEGVMY
>Q63544|51
KTKQGVTEAAEKTKEGVMYVGTKTKGERGTSVTSVAEKTKEQANAVSEAVVSSVNTVATKT
>Q63544|54
QGVTEAAEKTKEGVMYVGTKTKGERGTSVTSVAEKTKEQANAVSEAVVSSVNTVATKTVEE
>Q63544|67
VMYVGTKTKGERGTSVTSVAEKTKEQANAVSEAVVSSVNTVATKTVEEAENIVVTTGVVRK
>Q63544|72
TKTKGERGTSVTSVAEKTKEQANAVSEAVVSSVNTVATKTVEEAENIVVTTGVVRKEDLEP
>Q63544|73
KTKGERGTSVTSVAEKTKEQANAVSEAVVSSVNTVATKTVEEAENIVVTTGVVRKEDLEPP

文件 B:

>Q63544|51
KTKQGVTEAAEKTKEGVMYVGTKTKGERGTSVTSVAEKTKEQANAVSEAVVSSVNTVATKT
>Q63544|54
QGVTEAAEKTKEGVMYVGTKTKGERGTSVTSVAEKTKEQANAVSEAVVSSVNTVATKTVEE
>Q63544|67
VMYVGTKTKGERGTSVTSVAEKTKEQANAVSEAVVSSVNTVATKTVEEAENIVVTTGVVRK
>Q63544|73
KTKGERGTSVTSVAEKTKEQANAVSEAVVSSVNTVATKTVEEAENIVVTTGVVRKEDLEPP

我需要：A-B

>Q63544|9
----------------------MDVFKKGFSIAREGVVGAVEKTKQGVTEAAEKTKEGVMY 
>Q63544|72
TKTKGERGTSVTSVAEKTKEQANAVSEAVVSSVNTVATKTVEEAENIVVTTGVVRKEDLEP

如有任何帮助或建议，我们将不胜感激。

Answer 1

你可以试试regular expression

import re

# here I am taking as text but u can read the file like text_1 = open('file_1.txt').read()
text_1 = """>Q63544|9
----------------------MDVFKKGFSIAREGVVGAVEKTKQGVTEAAEKTKEGVMY
>Q63544|51
KTKQGVTEAAEKTKEGVMYVGTKTKGERGTSVTSVAEKTKEQANAVSEAVVSSVNTVATKT
>Q63544|54
QGVTEAAEKTKEGVMYVGTKTKGERGTSVTSVAEKTKEQANAVSEAVVSSVNTVATKTVEE
>Q63544|67
VMYVGTKTKGERGTSVTSVAEKTKEQANAVSEAVVSSVNTVATKTVEEAENIVVTTGVVRK
>Q63544|72
TKTKGERGTSVTSVAEKTKEQANAVSEAVVSSVNTVATKTVEEAENIVVTTGVVRKEDLEP
>Q63544|73
KTKGERGTSVTSVAEKTKEQANAVSEAVVSSVNTVATKTVEEAENIVVTTGVVRKEDLEPP"""

text_2 = """>Q63544|51
KTKQGVTEAAEKTKEGVMYVGTKTKGERGTSVTSVAEKTKEQANAVSEAVVSSVNTVATKT
>Q63544|54
QGVTEAAEKTKEGVMYVGTKTKGERGTSVTSVAEKTKEQANAVSEAVVSSVNTVATKTVEE
>Q63544|67
VMYVGTKTKGERGTSVTSVAEKTKEQANAVSEAVVSSVNTVATKTVEEAENIVVTTGVVRK
>Q63544|73
KTKGERGTSVTSVAEKTKEQANAVSEAVVSSVNTVATKTVEEAENIVVTTGVVRKEDLEPP
"""

protein_1 = {i[0]:i[1] for i in re.findall(r'^>Q63544|(\d+)\n(.*)', text_1, re.MULTILINE) if len(i[0])>0}
protein_2 = {i[0]:i[1] for i in re.findall(r'^>Q63544|(\d+)\n(.*)', text_2, re.MULTILINE) if len(i[0])>0}

dissimilar_protein = {i:protein_1[i] for i in protein_1 if i not in protein_2}

print(list(dissimilar_protein.values()))

['----------------------MDVFKKGFSIAREGVVGAVEKTKQGVTEAAEKTKEGVMY', 'TKTKGERGTSVTSVAEKTKEQANAVSEAVVSSVNTVATKTVEEAENIVVTTGVVRKEDLEP']

或者如果您想要特定格式

output = [f'>Q63544|{i}\n{j}' for i,j in dissimilar_protein.items()]
for i in output:
    print(i)

>Q63544|9
----------------------MDVFKKGFSIAREGVVGAVEKTKQGVTEAAEKTKEGVMY
>Q63544|72
TKTKGERGTSVTSVAEKTKEQANAVSEAVVSSVNTVATKTVEEAENIVVTTGVVRKEDLEP

NOTR：我假设所有蛋白质编号都以 Q63544

开头

查找两个文本文件的差异

Find differences of two text files

python

string

bioinformatics

sequence

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