def save_load(hmm):
f = tempfile.TemporaryFile('w+r')
hmmfile.write(hmm, f)
f.seek(0)
parser = hmmfile.HMMParser()
hmmout = parser.read(f)[0]
f.close()
return hmmout
def test_build(self):
#Should be case insensitive
hmm = hmmfile.HMM(alphabet='DnA')
#build the HMM
for i in build_data:
hmm.addState(**i)
hmm.clean()
#there are the correct number of states
self.assertEqual(len(hmm.states), len(build_data),
"{} states built - should be {}".format(len(hmm.states),
len(build_data)))
s = StringIO()
hmmfile.write(hmm, s)
s.seek(0)
hmm2 = hmmfile.read(s)[0]
for o in hmmfile.OPTIONS:
if hasattr(hmm, o):
self.assertEqual(getattr(hmm, o), getattr(hmm2, o))
def r(l):
ret = []
for i in l:
if type(i) == float:
ret.append(round(i,5))
else:
ret.append(i)
return ret
for i,(e,g) in enumerate(zip(hmm.states, hmm2.states)):
msg = "State {}: {} != {}"
self.assertEqual(r(e.me), g.me, msg.format(i,e.me,g.me))
self.assertEqual(r(e.ie), g.ie, msg.format(i,e.ie,g.ie))
self.assertEqual(r(e.tr), g.tr, msg.format(i,e.tr,g.tr))
self.assertEqual(e.map,g.map, msg.format(i,e.map,g.map))
self.assertEqual(e.rf, g.rf, msg.format(i,e.rf,g.rf))
self.assertEqual(e.cs, g.cs, msg.format(i,e.cs,g.cs))
def update_models():
"""Recalculate the HMM models"""
print "Extracting C-Termini..."
ct = extract.get_c_terminus(extract.extract(localization=None))
print "Done. Got {} tails".format(len(ct))
(E, Ep, DYW) = utils.get_tail_consensus()
print "E"
j = HMMER.jackhmmer(E,ct)
j.hmms[-1].name = 'E'
hmmfile.write(j.hmms[-1], os.path.join(utils.HMMDir, 'E.hmm'))
print "E+"
j = HMMER.jackhmmer(Ep,ct)
j.hmms[-1].name = 'E+'
hmmfile.write(j.hmms[-1], os.path.join(utils.HMMDir, 'E+.hmm'))
print "DYW"
j = HMMER.jackhmmer(DYW,ct)
j.hmms[-1].name = 'DYW'
hmmfile.write(j.hmms[-1], os.path.join(utils.HMMDir, 'DYW.hmm'))