/usr/lib/python2.7/dist-packages/csb/test/cases/bio/hmm/__init__.py is in python-csb 1.2.2+dfsg-2ubuntu1.
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from csb.core import Enum, OrderedDict
from csb.bio.hmm import State, Transition, ProfileHMM, HMMLayer, ProfileLength, StateFactory, ProfileHMMSegment
from csb.bio.hmm import StateExistsError, UnobservableStateError, EmissionExistsError
from csb.bio.hmm import HHpredHitList, HHpredHit, ScoreUnits, States, EVDParameters, BACKGROUND
from csb.bio.sequence import ProteinAlphabet
from csb.bio.structure import ProteinResidue
from csb.bio.io import HHProfileParser
def build_hmm():
hmm = ProfileHMM(units=ScoreUnits.Probability)
factory = StateFactory()
background = OrderedDict([ (ProteinAlphabet.ALA, 0.02457563),
(ProteinAlphabet.CYS, 0.00325358),
(ProteinAlphabet.GLU, 0.01718016) ])
emission = dict( (aa, 1.0 / i) for i, aa in enumerate(background, start=1) )
# States
# Start / End
hmm.start = State(States.Start)
hmm.start_insertion = factory.create_insertion(background)
hmm.end = State(States.End)
# L1
match1 = factory.create_match(emission, background)
insertion1 = factory.create_insertion(background)
deletion1 = factory.create_deletion()
states = {States.Match: match1, States.Insertion: insertion1, States.Deletion: deletion1}
layer1 = HMMLayer(1, ProteinResidue(1, ProteinAlphabet.ALA), states)
hmm.layers.append(layer1)
# L2
match2 = factory.create_match(emission, background)
insertion2 = factory.create_insertion(background)
deletion2 = factory.create_deletion()
states = {States.Match: match2, States.Insertion: insertion2, States.Deletion: deletion2}
layer2 = HMMLayer(2, ProteinResidue(2, ProteinAlphabet.CYS), states)
hmm.layers.append(layer2)
# Transitions
# start
hmm.start.transitions.append(Transition(hmm.start, match1, 0.8))
hmm.start.transitions.append(Transition(hmm.start, deletion1, 0.1))
hmm.start.transitions.append(Transition(hmm.start, hmm.start_insertion, 0.1))
hmm.start_insertion.transitions.append(Transition(hmm.start_insertion, hmm.start_insertion, 0.5))
hmm.start_insertion.transitions.append(Transition(hmm.start_insertion, match1, 0.5))
# L1
match1.transitions.append(Transition(match1, match2, 0.8))
match1.transitions.append(Transition(match1, insertion1, 0.1))
match1.transitions.append(Transition(match1, deletion2, 0.1))
insertion1.transitions.append(Transition(insertion1, insertion1, 0.5))
insertion1.transitions.append(Transition(insertion1, match2, 0.5))
deletion1.transitions.append(Transition(deletion1, deletion2, 0.5))
deletion1.transitions.append(Transition(deletion1, match2, 0.5))
# L2
match2.transitions.append(Transition(match2, hmm.end, 0.9))
match2.transitions.append(Transition(match2, insertion2, 0.1))
insertion2.transitions.append(Transition(insertion2, insertion2, 0.5))
insertion2.transitions.append(Transition(insertion2, hmm.end, 0.5))
deletion2.transitions.append(Transition(deletion2, hmm.end, 1.0))
hmm.effective_matches = 10
hmm.version = 1.5
hmm.name = 'name'
hmm.id = 'id'
hmm.family = 'fam'
hmm.length = ProfileLength(2, 2)
return hmm
@test.unit
class TestProfileHMM(test.Case):
def setUp(self):
super(TestProfileHMM, self).setUp()
self.hmm = build_hmm()
self.hmm2 = build_hmm()
self.string = self.config.getContent('test.hhm')
def testName(self):
self.assertEqual(self.hmm.name, 'name')
def testID(self):
self.assertEqual(self.hmm.id, 'id')
def testLayers(self):
self.assertEqual(self.hmm.layers.length, 2)
self.assertTrue(isinstance(self.hmm.layers[1], HMMLayer))
self.assertEqual(set(self.hmm.layers[1]), set([States.Match, States.Insertion, States.Deletion]))
for i in [0, 3]:
self.assertRaises(IndexError, lambda:self.hmm.layers[i])
def testStart(self):
self.assertEqual(self.hmm.start.type, States.Start)
def testStartInsertion(self):
self.assertEqual(self.hmm.start_insertion.type, States.Insertion)
def testEnd(self):
self.assertEqual(self.hmm.end.type, States.End)
def testAllLayers(self):
self.assertEqual(len(self.hmm.all_layers), 3)
def testScoreUnits(self):
self.assertEqual(self.hmm.score_units, ScoreUnits.Probability)
self.hmm2.convert_scores(units=ScoreUnits.LogScales)
self.assertEqual(self.hmm2.score_units, ScoreUnits.LogScales)
def testConvertScores(self):
self.hmm2.convert_scores(units=ScoreUnits.LogScales)
self.assertEqual(self.hmm2.score_units, ScoreUnits.LogScales)
self.assertEqual(self.hmm2.layers[1][States.Match].emission[ProteinAlphabet.ALA], 0)
self.hmm2.convert_scores(units=ScoreUnits.Probability)
self.assertEqual(self.hmm2.score_units, ScoreUnits.Probability)
self.assertEqual(self.hmm2.layers[1][States.Match].emission[ProteinAlphabet.ALA], 1)
def testSegment(self):
segment = self.hmm.segment(1, 2)
self.assertEqual(segment.layers.length, 2)
self.assertEqual(segment.layers[2][States.Match].transitions[States.End].probability, 1)
self.assertRaises(IndexError, self.hmm.segment, 1, 3)
def testSubregion(self):
segment = self.hmm.subregion(1, 2)
self.assertEqual(segment.layers.length, 2)
self.assertEqual(segment.layers[1], self.hmm.layers[1])
self.assertRaises(IndexError, self.hmm.subregion, 1, 3)
def testStructure(self):
s = self.hmm.structure('$', 'abcd')
self.assertEqual(s.chains.length, 1)
self.assertEqual(s.chains['$'].entry_id, 'abcd$')
self.assertEqual(s.chains['$'].sequence, 'AC')
def testChain(self):
c = self.hmm.chain('$')
self.assertEqual(c.id, '$')
self.assertEqual(c.sequence, 'AC')
def testEmissionSimilarity(self):
score = self.hmm.emission_similarity(self.hmm)
self.assertAlmostEqual(score, 9.6405, places=3)
def testToHMM(self):
self.hmm2.convert_scores(units=ScoreUnits.LogScales)
self.assertEqual(self.string, self.hmm2.to_hmm().strip())
@test.functional
class TestPseudocountBuilder(test.Case):
def setUp(self):
super(TestPseudocountBuilder, self).setUp()
self.hmm = HHProfileParser(self.config.getTestFile('d1nz0a_.hhm')).parse()
def runTest(self):
self.hmm.add_emission_pseudocounts()
self.hmm.convert_scores(ScoreUnits.LogScales)
self.hmm.add_transition_pseudocounts()
# TODO: some checks here...
@test.unit
class TestProfileHMMSegment(test.Case):
def setUp(self):
super(TestProfileHMMSegment, self).setUp()
self.hmm = build_hmm()
self.segment = ProfileHMMSegment(self.hmm, 1, 2)
self.string = self.config.getContent('test2.hhm')
def testConstructor(self):
self.segment.convert_scores(ScoreUnits.Probability)
self.assertEqual(self.hmm.segment(1, 1).layers.length, 1)
self.assertEqual(self.segment.layers.length, 2)
self.assertEqual(self.segment.start.transitions[States.Match].probability, 1)
self.assertEqual(self.segment.layers[1][States.Match].emission[ProteinAlphabet.CYS], 0.5)
self.assertRaises(IndexError, self.hmm.segment, 1, 3)
self.hmm.convert_scores(ScoreUnits.LogScales)
segment = ProfileHMMSegment(self.hmm, 1, 2)
self.assertEqual(segment.source_start, 1)
def testToHMM(self):
self.segment.convert_scores(ScoreUnits.LogScales)
self.assertEqual(self.string, self.segment.to_hmm().strip())
@test.unit
class TestHMMLayer(test.Case):
def setUp(self):
super(TestHMMLayer, self).setUp()
self.hmm = build_hmm()
self.layer = self.hmm.layers[1]
self.layer.effective_matches = 5
self.layer.effective_insertions = 4
self.layer.effective_deletions = 3
def testRank(self):
self.assertEqual(self.hmm.layers[1].rank, 1)
self.assertEqual(self.hmm.layers[2].rank, 2)
def testNeff(self):
self.assertEqual(self.layer.effective_matches, 5)
self.assertEqual(self.layer.effective_insertions, 4)
self.assertEqual(self.layer.effective_deletions, 3)
def testResidue(self):
def test(type):
self.layer.residue = ProteinResidue(1, type=type)
self.assertEqual(self.layer.residue.type, ProteinAlphabet.ALA)
self.assertRaises(ValueError, test, ProteinAlphabet.GAP)
test(ProteinAlphabet.ALA)
self.assertEqual(self.layer.residue.type, ProteinAlphabet.ALA)
def testAppend(self):
s = State(States.End)
self.layer.append(s)
self.assertRaises(StateExistsError, self.layer.append, s)
self.assertEqual(self.layer[States.End], s)
def testIndexer(self):
self.assertEqual(self.layer[States.Match].type, States.Match)
@test.unit
class TestState(test.Case):
def setUp(self):
super(TestState, self).setUp()
self.hmm = build_hmm()
self.layer = self.hmm.layers[1]
self.m = self.hmm.layers[1][States.Match]
self.d = self.hmm.layers[1][States.Deletion]
self.i = self.hmm.layers[1][States.Insertion]
self.s = self.hmm.start
def testType(self):
self.assertEqual(self.m.type, States.Match)
def testTransitions(self):
# also covers TransitionTable and Transition
self.assertEqual(self.m.transitions.length, 3)
self.assertEqual(self.m.transitions[States.Match].predecessor, self.m)
self.assertEqual(self.m.transitions[States.Match].successor, self.hmm.layers[2][States.Match])
self.assertEqual(self.m.transitions[States.Match].probability, 0.8)
self.assertEqual(self.m.transitions[States.Insertion].type.source_state, States.Match)
self.assertEqual(self.m.transitions[States.Insertion].type.target_state, States.Insertion)
def testEmission(self):
# also covers EmissionTable
self.assertEqual(self.m.emission.length, 3)
self.assertEqual(set(self.m.emission), set([ProteinAlphabet.ALA, ProteinAlphabet.CYS, ProteinAlphabet.GLU]))
self.assertEqual(self.m.emission[ProteinAlphabet.CYS], 0.5)
self.assertRaises(lambda: self.m.emission[ProteinAlphabet.GAP])
self.assertRaises(UnobservableStateError, lambda: self.d.emission)
self.m.emission.append(ProteinAlphabet.ILE, 0.5)
self.assertEqual(self.m.emission[ProteinAlphabet.ILE], 0.5)
self.m.emission.append('L', 0)
self.assertRaises(EmissionExistsError, lambda:self.m.emission.append('I', 0))
self.assertRaises(KeyError, lambda:self.m.emission.append('BUG', 0))
def testSilent(self):
self.assertTrue(self.d.silent)
self.assertFalse(self.m.silent)
def testBackground(self):
# also covers EmissionTable
self.assertEqual(self.m.background.length, 3)
self.assertEqual(set(self.m.background), set([ProteinAlphabet.ALA, ProteinAlphabet.CYS, ProteinAlphabet.GLU]))
self.assertEqual(self.m.background[ProteinAlphabet.CYS], 0.00325358)
self.assertRaises(lambda: self.m.background[ProteinAlphabet.GAP])
self.m.background.append(ProteinAlphabet.ILE, 0.5)
self.assertEqual(self.m.background[ProteinAlphabet.ILE], 0.5)
self.m.background.append('L', 0)
self.assertRaises(EmissionExistsError, lambda:self.m.background.append('I', 0))
self.assertRaises(KeyError, lambda:self.m.background.append('BUG', 0))
@test.unit
class TestHit(test.Case):
def setUp(self):
super(TestHit, self).setUp()
self.h1 = HHpredHit(1, 'hit1', 2, 5, 3, 6, 0.5, 10)
self.h2 = HHpredHit(2, 'hit2', 3, 5, 4, 6, 0.2, 10)
def testEquals(self):
hit = HHpredHit(1, 'hit1', 2, 5, 3, 6, 0.5, 10)
self.assertTrue(self.h1.equals(hit))
def testSurpasses(self):
self.assertTrue(self.h1.surpasses(HHpredHit(5, 'hitX', 2, 3, 3, 4, 0.5, 10)))
self.assertTrue(self.h1.surpasses(HHpredHit(5, 'hitX', 2, 5, 3, 6, 0.3, 10)))
def testIncludes(self):
self.assertTrue(self.h1.includes(HHpredHit(5, 'hit1', 2, 3, 3, 4, 0.5, 10)))
self.assertTrue(self.h1.includes(HHpredHit(5, 'hit1', 2, 4, 3, 5, 0.3, 10)))
self.assertTrue(self.h1.includes(HHpredHit(5, 'hit1', 2, 8, 3, 9, 0.3, 10), tolerance=3))
self.assertFalse(self.h1.includes(HHpredHit(5, 'hit1', 2, 8, 3, 9, 0.3, 10), tolerance=2))
self.assertTrue(self.h1.includes(HHpredHit(5, 'hit1', 1, 5, 2, 6, 0.3, 10), tolerance=1))
self.assertFalse(self.h1.includes(HHpredHit(5, 'hit1', 1, 5, 2, 6, 0.3, 10), tolerance=0))
def testLength(self):
self.assertEqual(self.h1.length, 4)
def testAlignment(self):
q, s = 'AB-D', 'A-CD'
self.h1.add_alignment(q, s)
# query, subject
self.assertEqual(self.h1.alignment.query, q)
self.assertEqual(self.h1.alignment.subject, s)
# segments
segments = list(self.h1.alignment.segments)
self.assertEqual(len(segments), 2)
self.assertEqual(segments[0].qstart, 3)
self.assertEqual(segments[0].qend, 3)
self.assertEqual(segments[0].start, 2)
self.assertEqual(segments[0].end, 2)
self.assertEqual(segments[1].qstart, 5)
self.assertEqual(segments[1].qend, 5)
self.assertEqual(segments[1].start, 4)
self.assertEqual(segments[1].end, 4)
# to_a3m
a3m = self.h1.alignment.to_a3m().format(headers=False)
self.assertEqual(a3m.strip(), 'ABD\nA-cD')
@test.unit
class TestHitList(test.Case):
def setUp(self):
super(TestHitList, self).setUp()
self.h1 = HHpredHit(1, 'hit1', 2, 5, 3, 6, 0.5, 10)
self.h2 = HHpredHit(2, 'hit2', 3, 5, 4, 6, 0.2, 10)
self.h1.add_alignment('A-CD', 'A-CD')
self.h2.add_alignment('BCD', 'BCD')
self.hits = HHpredHitList([self.h1, self.h2])
def testLength(self):
self.assertEqual(len(self.hits), 2)
def testSort(self):
hits = HHpredHitList([self.h2, self.h1])
self.assertEqual(hits[0], self.h2)
self.assertEqual(hits[1], self.h1)
hits.sort()
self.assertEqual(hits[0], self.h1)
self.assertEqual(hits[1], self.h2)
def testIterator(self):
self.assertEqual(list(self.hits), [self.h1, self.h2])
if __name__ == '__main__':
test.Console()
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