def __init__(
self, input, output=None, diags=None, maxhours=None, maxmb=None, clwstrict=False, quiet=True, clw=False
):
self._itemp = None
self._otemp = None
self.maxhours = maxhours
self.clwstrict = clwstrict
self.clw = clw
self.quiet = quiet
self.maxmb = maxmb
if isinstance(input, str):
assert os.path.exists(input), "Can't find file %s" % input
self.input = input
elif isinstance(input, list):
from tempfile import NamedTemporaryFile
from Bio.SeqIO.FastaIO import FastaWriter
self._itemp = NamedTemporaryFile()
self.input = self._itemp.name
writer = FastaWriter(self._itemp, wrap=0)
writer.write_records(input)
self._itemp.flush()
else:
raise Exception("Unknown input type", input)
if isinstance(output, str):
self.output = output
elif output == None:
self._otemp = NamedTemporaryFile()
self.output = self._otemp.name
def __init__(self, input, output=None, identity=0.8, length=0.8):
self._itemp=None
self._otemp=None
self.identity=identity
self.length=length
if isinstance(input, str):
assert(os.path.exists(input))
self.input = input
elif isinstance(input, list):
from tempfile import NamedTemporaryFile
from Bio.SeqIO.FastaIO import FastaWriter
self._itemp = NamedTemporaryFile()
self.input = self._itemp.name
writer = FastaWriter(self._itemp,wrap=0)
writer.write_records(input)
self._itemp.flush()
else:
raise Exception("Unknown input type",input)
if isinstance(output, str):
self.output = output
elif output==None:
self._otemp = NamedTemporaryFile()
self.output = self
