How to read a list of gene pairs and write a fasta file for each line

I'm new to bioinformatics and would really aprecciated some help!

I have a big multi-fasta file (genes.faa), like this:

>gene1_A
MCTGTRNKIIRTCDNCRKRKIKCDRKRPAC
>gene2_A
MCTGTRNKIIRTCDNCRKRKIKCDRKRPAC
>gene3_B
MCTGTRNKIIRTCDNCRKRKIKCDRKRPAC
>gene4_B
MCTGTRNKIIRTCDNCRKRKIKCDRKRPAC
(...)

And a list of gene pairs (gene.pairs.txt), with two genes per line separeted by a tab:

gene13_A \t gene33_B
gene2_A \t gene48_B
gene56_A \t gene2_B

And I needed a way to read the list of gene pairs and create a fasta file for each line of the list of gene pairs. So, in this case, I would have 3 fasta files (the name of the output fasta files is not important), like this:

fasta1

>gene13_A
MCTGTRNKIIRTCDNCRKRKIKCDRKRPAC
>gene33_B
MCTGTRNKIIRTCDNCRKRKIKCDRKRPAC

fasta2

>gene2_A 
MCTGTRNKIIRTCDNCRKRKIKCDRKRPAC
>gene48_B
MCTGTRNKIIRTCDNCRKRKIKCDRKRPAC

fasta3

>gene56_A 
MCTGTRNKIIRTCDNCRKRKIKCDRKRPAC
>gene2_B
MCTGTRNKIIRTCDNCRKRKIKCDRKRPAC

I tried to write a script in python but I couldn't find a way to read the list in a loop and write a fasta file for each line.
Thank you so much in advance for any help!

My attempt, sure there are faster better ways to accomplish it, it makes me wonder if there could be a way to skip the creation of the big dictionary : sequences = { i.id : i for i in SeqIO.parse('big_fasta_2.fa', 'fasta')}.

I am using the Biopython library to parse the fasta file and to write them https://biopython.org/ , https://github.com/biopython/biopython; anyway:

input 'big_fasta_2.fa' :

>gene1_A
MCTGTRNKIIRTCDNCRKRKIKCDRKRPAC
>gene2_A
MCTGTRNKIIRTCDNCRKRKIKCDRKRPAC
>gene2_B
MCTGTRNKIIRTCDNCRKRKIKCDRKRPAC
>gene3_B
MCTGTRNKIIRTCDNCRKRKIKCDRKRPAC
>gene4_B
MCTGTRNKIIRTCDNCRKRKIKCDRKRPAC
>gene13_A
MCTGTRNKIIRTCDNCRKRKIKCDRKRPAA
>gene33_B
MCTGTRNKIIRTCDNCRKRKIKCDRKRPAY
>gene48_B
MCTGTRNKIIRTCDNCRKRKIKCDRKRPAW
>gene56_A
MCTGTRNKIIRTCDNCRKRKIKCDRKRPAP

input "gene_pairs_3.txt":

gene13_A	gene33_B
gene1344_A	gene33_B
gene2_A	gene48_B
gene23333_A	gene48_B
gene56_A	gene2_B

code :

from Bio import SeqIO,  __version__

print('Biopython version : ', __version__)


sequences = { i.id : i for i in SeqIO.parse('big_fasta_2.fa', 'fasta')}

print(sequences)


file = open("gene_pairs_3.txt","r")


cnt = 1
for line in file:
    
    
    a, b  =  line.split()
    print('++++++++++++')
    print('pairs N° : ', cnt)
    print(a)
    print(b)
    
    if a in sequences:
        print('ok A')
        print(sequences[a])
        
        if b in sequences:
            print('ok B')
            print(sequences[b])
            
            SeqIO.write([sequences[a],sequences[b]] , 'Fasta'+str(cnt)+'.fa' , 'fasta')
            
            print('\nwritten file : ' ,'Fasta'+str(cnt)+'.fa' )
            
            cnt += 1
        else:
            
            print('No B')
    
    else:
        print('No A')
        continue
    
    print('-----------\n')

Have a look at the output files and see if they are what you expected.

This code works. I have tested on the following files:

Input FASTA file:

>gene1_A
MCTGTRNKIIRTCDNCRKRKIKCDRKRPA1
>gene2_A
MCTGTRNKIIRTCDNCRKRKIKCDRKRPA2
>gene3_B
MCTGTRNKIIRTCDNCRKRKIKCDRKRPA3
>gene4_B
MCTGTRNKIIRTCDNCRKRKIKCDRKRPA4

Gene List file:

gene1_A	gene3_B
gene2_A	gene4_B

Code:

from Bio import SeqIO

my_gene_file   = open('genelist.txt','r')
my_fasta_file  = open('input.fasta','r')

my_list=[]
for line in my_gene_file:
    line = line.strip(' \n')
    gene_id1, gene_id2 = line.split('\t')   
    gene_tuple = (gene_id1, gene_id2)
    my_list.append(gene_tuple)

my_dict={}
for seq_record in SeqIO.parse(my_fasta_file, "fasta"):   
    my_dict[seq_record.id] = seq_record.seq

for item in my_list:
    if item[0] in my_dict and item[1] in my_dict:
        output_file_name=(f'{item[0]}_{item[1]}.fasta')
        f = open(output_file_name, "w")
        f.write(f'>{item[0]}\n{my_dict[item[0]]}\n>{item[1]}\n{my_dict[item[1]]}')

It outputs files with fasta record ids in the filenames.