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

Question

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!

Answer 1

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.