def test_ceba_bovin(self): # ../psCoils.py -f ./ferritin.fasta -l F > ./ferritin.Coils weight = "un" wlambda = 0.5 win = 21 modeprofile = False seqs = readFasta("tests/ceba_bovin.fasta") modefasta = True labels = "F" params = Params(weight, win) output = StringIO.StringIO() for name in seqs.keys(): seqr = SeqRecord(seqs[name], id=name) seqr = pred_coil(seqr, params) printCoil(seqr, labels, io=output) bench_output = open("tests/ceba_bovin.Coils").read() self.assertEqual(output.getvalue(), bench_output)
def run(self, seqr, **kwargs): #TODO: manage kwargs weight='un' win=21 params=Params(weight,win) return pred_coil(seqr, params)