import re import sys file = open(sys.argv[1], 'r') # HERE: variable 'comment' is a pattern for a comment line in FASTA format comment = re.compile(.....) line = file.readline() seq = [] while line: line = line.replace('\n', '') # HERE: search pattern in line m = comment....... if m : print ''.join(seq) seq = [] else: seq.append(line) line = file.readline()