Find differences of two protein sequence files

Question

I have two separate files A and B of more than 100000 records of protein sequences. Now I need to find the sequences that are in A but not in B. Both files are in text format. Each ID and Sequence is separated by new line character. I tried making pandas data frame and finding the difference but couldn't make it work.

File A:

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

File B:

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

What I need: A-B

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

Any help or suggestion would be appreciated.

Answer 1

You can do this very easily using python sets as follows:

with open("file_a.txt", "r") as f:
    data_a = f.read().splitlines()

with open("file_b.txt", "r") as f:
    data_b = f.read().splitlines()

set(data_a) - set(data_b)

# {'----------------------MDVFKKGFSIAREGVVGAVEKTKQGVTEAAEKTKEGVMY',
#  '>Q63544|72',
#  '>Q63544|9',
#  'TKTKGERGTSVTSVAEKTKEQANAVSEAVVSSVNTVATKTVEEAENIVVTTGVVRKEDLEP'}