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)
