import io FASTA='''\ >Rosetta_Example_1 THERECANBENOSPACE >Rosetta_Example_2 THERECANBESEVERAL LINESBUTTHEYALLMUST BECONCATENATED''' infile = io.StringIO(FASTA) def fasta_parse(infile): key = '' for line in infile: if line.startswith('>'): if key: yield key, val key, val = line[1:].rstrip().split()[0], '' elif key: val += line.rstrip() if key: yield key, val print('\n'.join('%s: %s' % keyval for keyval in fasta_parse(infile)))