def test_annotation(self):
#load the hmm
hmm = hmmfile.read('tests/data/valid.hmm')
s1 = SeqIO.read('tests/data/PPR10.gb', 'genbank')
s1.features = []
s2 = SeqIO.read('tests/data/PPR10.gb', 'genbank')
s2.features = []
s2.seq = s2.seq.reverse_complement()
h1 = HMMER.hmmsearch(hmm, s1)
h2 = HMMER.hmmsearch(hmm, s2)
h1.annotate(s1)
h2.annotate(s2)
for (f1, f2) in zip(s1.features, s2.features):
self.assertEqual(str(f1.extract(s1.seq)), str(f2.extract(s2.seq)))
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 get_tail_models(): return (hmmfile.read(os.path.join(HMMDir, 'E.hmm'))[0], hmmfile.read(os.path.join(HMMDir, 'E+.hmm'))[0], hmmfile.read(os.path.join(HMMDir, 'DYW.hmm'))[0])
def loadmodels():
"""Load all the models from a file"""
modelfiles = [ os.path.join(HMMDir, "PPR_{}.hmm".format(i)) for i in
range(4)]
return [hmmfile.read(f)[0] for f in modelfiles]
def loadmodels():
"""Load all the models from a file"""
modelfiles = [
os.path.join(HMMDir, "PPR_{}.hmm".format(i)) for i in range(4)
]
return [hmmfile.read(f)[0] for f in modelfiles]
def get_tail_models():
return (hmmfile.read(os.path.join(HMMDir, 'E.hmm'))[0],
hmmfile.read(os.path.join(HMMDir, 'E+.hmm'))[0],
hmmfile.read(os.path.join(HMMDir, 'DYW.hmm'))[0])
