/usr/lib/python2.7/dist-packages/csb/test/cases/bio/io/hhpred/__init__.py is in python-csb 1.2.3+dfsg-1.
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from csb.bio.hmm import ScoreUnits, States
from csb.bio.io.hhpred import HHProfileParser, HHOutputParser
from csb.bio.sequence import SequenceAlphabets
from csb.bio.structure import SecStructures
@test.regression
class TestHHOutputRegressions(test.Case):
def setUp(self):
super(TestHHOutputRegressions, self).setUp()
filename = self.config.getTestFile('d1ea0a1.hhr')
self.hitlist = HHOutputParser().parse_file(filename)
def testLargeHitlist(self):
"""
@see: [CSB 0000056]
"""
hit = self.hitlist[-1]
self.assertEqual(hit.rank, 10000)
self.assertEqual(hit.id, 'd1v8qa_')
@test.regression
class TestHHProfileRegressions(test.Case):
def testParseRedundantA3M(self):
"""
@see: [CSB 0000068], [CSB 0000128]
"""
def strip(s):
return s.replace('\t', '').replace(' ', '')
filename = self.config.getTestFile('d1b24a2.hhm')
content = self.config.getContent('d1b24a2.hhm')
hmm = HHProfileParser(filename).parse()
with self.config.getTempStream() as tmp:
hmm.to_hmm(tmp.name)
tmp.flush()
generated = open(tmp.name).read()
self.assertEqual(strip(content), strip(generated))
# should not raise DuplicateSequenceError, see [CSB 0000128]
hmm.segment(1, 2)
@test.unit
class TestHHProfileParser(test.Case):
def setUp(self):
super(TestHHProfileParser, self).setUp()
self.hhm = self.config.getTestFile('d1nz0a_.hhm')
self.pdb = self.config.getTestFile('d1nz0a_.pdb')
#self.profile = HHProfileParser(self.hhm, self.pdb).parse()
def testParseLogScales(self):
hmm = HHProfileParser(self.hhm, self.pdb).parse()
self.assertEqual(hmm.score_units, ScoreUnits.LogScales)
self.assertEqual(hmm.name, 'd1nz0a_ d.14.1.2 (A:) RNase P protein {Thermotoga maritima [TaxId: 2336]}')
self.assertEqual(hmm.id, 'd1nz0a_')
self.assertEqual(hmm.family, 'd.14.1.2')
self.assertEqual(hmm.length.matches, 109)
self.assertEqual(hmm.length.layers, 109)
self.assertEqual(hmm.alignment.size, 9)
self.assertEqual(hmm.consensus.sequence, 'eRLkxxxdFxxvxxxgxxxxxxxxxlxxxxxxxxxxRxGxxvsKKvgxAVxRNriKRxlRexxrxxxxxlxxxxdivvixrxxxxxxxxxxxxxxlxxxlxxlxkkixg')
self.assertEqual(hmm.alignment.rows[1][0].id, 'd1nz0a_')
self.assertEqual(hmm.alignment.rows[1].strip().sequence, 'ERLRLRRDFLLIFKEGKSLQNEYFVVLFRKNGMDYSRLGIVVKRKFGKATRRNKLKRWVREIFRRNKGVIPKGFDIVVIPRKKLSEEFERVDFWTVREKLLNLLKRIEG')
self.assertEqual(hmm.dssp[1].type, SecStructures.Coil)
self.assertEqual(hmm.psipred[1].type, SecStructures.Coil)
self.assertEqual(hmm.dssp.to_string(), 'CCCCHHHHHHHHHHHSEEEECSSEEEEEEECSSSSCEEEECCCGGGCSHHHHHHHHHHHHHHHHHHTTTSCSSEEEEEEECHHHHHHGGGSCHHHHHHHHHHHHTTCCC')
self.assertEqual(hmm.psipred.to_string(), 'CCCCCHHHHHHHHHCCCEEECCCEEEEEECCCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHCC')
self.assertEqual(hmm.effective_matches, 7.4)
self.assertEqual(hmm.pseudocounts, False)
self.assertEqual(hmm.start.silent, True)
self.assertEqual(hmm.start.type, States.Start)
self.assertEqual(set(hmm.start.transitions), set([States.Match]))
self.assertEqual(hmm.end.silent, True)
self.assertEqual(hmm.end.type, States.End)
self.assertEqual(set(hmm.end.transitions), set([]))
self.assertEqual(hmm.has_structure, True)
self.assertEqual(hmm.chain().sequence, 'ERLRLRRDFLLIFKEGKSLQNEYFVVLFRKNGMDYSRLGIVVKRKFGKATRRNKLKRWVREIFRRNKGVIPKGFDIVVIPRKKLSEEFERVDFWTVREKLLNLLKRIEG')
layer = hmm.layers[2]
self.assertEqual(layer.rank, 2)
self.assertAlmostEqual(layer.effective_matches, 6.9939, places=3)
self.assertAlmostEqual(layer.effective_insertions, 0)
self.assertAlmostEqual(layer.effective_deletions, 0)
self.assertEqual(set(layer), set([States.Match, States.Insertion]))
self.assertEqual(layer.residue.type, SequenceAlphabets.Protein.ARG)
self.assertEqual(layer.residue.has_structure, True)
self.assertEqual(layer.residue.atoms['CA'].vector.tolist(), [3.996, -10.515, 45.483])
self.assertEqual(layer.residue.torsion.psi, 72.153702504057748)
self.assertEqual(layer.residue.secondary_structure.type, SecStructures.Coil)
self.assertEqual(layer.residue.secondary_structure.end, 4)
match = layer[States.Match]
self.assertEqual(match.type, States.Match)
self.assertEqual(match.rank, 2)
self.assertEqual(match.background[SequenceAlphabets.Protein.ALA], 3706.0)
self.assertEqual(match.emission[SequenceAlphabets.Protein.LYS], 3316.0)
self.assertEqual(set(match.transitions), set([States.Match]))
self.assertEqual(match.transitions[States.Match].predecessor, match)
self.assertEqual(match.transitions[States.Match].successor.rank, 3)
self.assertEqual(match.transitions[States.Match].successor.type, States.Match)
self.assertEqual(repr(match.transitions[States.Match].type), 'M->M')
self.assertEqual(match.transitions[States.Match].probability, 0.0)
def testParseProbability(self):
hmm = HHProfileParser(self.hhm, self.pdb).parse(ScoreUnits.Probability)
self.assertEqual(hmm.score_units, ScoreUnits.Probability)
layer = hmm.layers[2]
self.assertAlmostEqual(layer.effective_matches, 6.9939, places=3)
self.assertAlmostEqual(layer.effective_insertions, 0.0)
self.assertAlmostEqual(layer.effective_deletions, 0.0)
match = layer[States.Match]
self.assertAlmostEqual(match.background[SequenceAlphabets.Protein.ALA], 0.07662, places=4)
self.assertAlmostEqual(match.emission[SequenceAlphabets.Protein.LYS], 0.10041, places=4)
self.assertAlmostEqual(match.transitions[States.Match].probability, 1.0)
def testFormatStructure(self):
with self.config.getTempStream() as tmp:
p = HHProfileParser(self.hhm)
p.format_structure(self.pdb, 'A', tmp.name)
tmp.flush()
hmm = HHProfileParser(self.hhm, tmp.name).parse()
for layer in hmm.layers:
residue = layer.residue
self.assertEqual(residue.rank, layer.rank)
self.assertEqual(residue.sequence_number, layer.rank)
@test.unit
class TestHHOutputParser(test.Case):
def setUp(self):
super(TestHHOutputParser, self).setUp()
filename = self.config.getTestFile('d1ea0a1.hhr')
content = open(filename).read()
tmp = HHOutputParser(True)
self.hitlist = tmp.parse_file(filename)
self.hitlist2 = tmp.parse_string(content)
def testParseFile(self):
# header
self.assertEqual(self.hitlist.command, './hhsearch -i /ebio/abt1/kopec/projects/hhpred_on_cluster/split_fastas/d1ea0a1.hhm -d /ebio/abt1/kopec/projects/hhpred_on_cluster/astral_scop70_all_beta_only_v1.75_hhpred_database.hhm')
self.assertEqual(self.hitlist.query_name, 'd1ea0a1 b.80.4.1 (A:1203-1472) Alpha subunit of glutamate synthase, C-terminal domain {Azospirillum brasilense [TaxId: 192]}')
self.assertEqual(self.hitlist.neff, float('5.2'))
self.assertEqual(self.hitlist.searched_hmms, 2936)
# alignments
segments = list(self.hitlist[9].alignment.segments)
self.assertEqual(len(segments), 3)
for s, l in zip(segments, [(9, 21), (22, 35), (37, 52)]):
self.assertEqual(s.start, l[0])
self.assertEqual(s.end, l[1])
self.assertEqual(s.end - s.start, l[1] - l[0])
# hits
self.assertEqual(len(self.hitlist), 11)
self.assertRaises(IndexError, self.hitlist.__getitem__, 20)
self.assertEqual(self.hitlist[0].rank, 1)
hit = self.hitlist[4]
self.assertEqual(hit.rank, 5)
self.assertEqual(hit.id, 'd1g3pa1')
self.assertEqual(hit.start, 34)
self.assertEqual(hit.end, 49)
self.assertEqual(hit.qstart, 161)
self.assertEqual(hit.qend, 176)
self.assertEqual(hit.qlength, 270)
self.assertEqual(hit.probability * 100, 35.1)
self.assertEqual(hit.length, 16)
self.assertEqual(hit.slength, 65)
self.assertEqual(hit.evalue, 1.2)
self.assertEqual(hit.pvalue, 0.00041)
self.assertEqual(hit.score, 27.0)
self.assertEqual(hit.identity, 31.0)
self.assertEqual(hit.similarity, 0.659)
self.assertEqual(hit.prob_sum, 13.1)
def testParseString(self):
# header
self.assertEqual(self.hitlist.command, './hhsearch -i /ebio/abt1/kopec/projects/hhpred_on_cluster/split_fastas/d1ea0a1.hhm -d /ebio/abt1/kopec/projects/hhpred_on_cluster/astral_scop70_all_beta_only_v1.75_hhpred_database.hhm')
self.assertEqual(self.hitlist.query_name, 'd1ea0a1 b.80.4.1 (A:1203-1472) Alpha subunit of glutamate synthase, C-terminal domain {Azospirillum brasilense [TaxId: 192]}')
self.assertEqual(self.hitlist.neff, float('5.2'))
self.assertEqual(self.hitlist.searched_hmms, 2936)
# alignments
segments = list(self.hitlist[9].alignment.segments)
self.assertEqual(len(segments), 3)
for s, l in zip(segments, [(9, 21), (22, 35), (37, 52)]):
self.assertEqual(s.start, l[0])
self.assertEqual(s.end, l[1])
self.assertEqual(s.end - s.start, l[1] - l[0])
self.assertEqual(self.hitlist[9].score, s.score)
self.assertEqual(self.hitlist[9].ss_score, s.ss_score)
self.assertEqual(self.hitlist[9].probability, s.probability)
# hits
self.assertEqual(len(self.hitlist), 11)
self.assertRaises(IndexError, self.hitlist.__getitem__, 20)
self.assertEqual(self.hitlist[0].rank, 1)
hit = self.hitlist[4]
self.assertEqual(hit.rank, 5)
self.assertEqual(hit.id, 'd1g3pa1')
self.assertEqual(hit.start, 34)
self.assertEqual(hit.end, 49)
self.assertEqual(hit.qstart, 161)
self.assertEqual(hit.qend, 176)
self.assertEqual(hit.qlength, 270)
self.assertEqual(hit.probability * 100, 35.1)
self.assertEqual(hit.length, 16)
self.assertEqual(hit.slength, 65)
self.assertEqual(hit.evalue, 1.2)
self.assertEqual(hit.pvalue, 0.00041)
self.assertEqual(hit.score, 27.0)
self.assertEqual(hit.identity, 31.0)
self.assertEqual(hit.similarity, 0.659)
self.assertEqual(hit.prob_sum, 13.1)
if __name__ == '__main__':
test.Console()
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