def __init__(self, input, output=None): self._itemp=None self.output = output if isinstance(input, str): assert(os.path.exists(input)) self.input = input elif isinstance(input, list): from tempfile import NamedTemporaryFile from Bio.AlignIO.PhylipIO import PhylipWriter self._itemp = NamedTemporaryFile() self.input = self._itemp.name writer = PhylipWriter(self._itemp) writer.write_alignment(input) self._itemp.flush() else: raise Exception("Unknown input type",input)