biostars 165335

answer.py

from pyfaidx import Fasta

name_map = {}
with open('newnames.txt') as newnames:
  next(newnames)  # remove header
  for line in newnames:
    old, new = line.rstrip().split()
    name_map[old] = new
  
with open('seqnew.fa', 'w') as new_fasta:
  # replace the fasta sequence names for lookup
  fasta = Fasta('seq.fa', key_function = lambda x: name_map[x])
  for seq in fasta:
    new_fasta.write(seq.name + '/n')
    for line in seq:
      new_fasta.write(line + '/n')