biostars 169723

answer.py

from pyfaidx import Fasta

file_1 = {}
with open('file1.txt', 'r') as ids:
  for line in ids:
    key, value = line.strip().split('\t')
    file_1[key] = value
    
file_2 = Fasta('file2.fa', key_function=lambda key: file_1[key])

with open('file3.fa', 'w') as renamed:
  for entry in file_2:
    print(entry.name, file=renamed)
    for line in entry:
      print(line, file=renamed)