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)
