def test_domains_of_interest(self):
analysis = ActiveSiteAnalysis("not-p450", (self.domain, ),
"PKSI-KR.hmm2", [5, 6], ["C", "S"])
assert analysis.domains_of_interest == []
analysis = ActiveSiteAnalysis("p450", (self.domain, ), "PKSI-KR.hmm2",
[5, 6], ["C", "S"])
assert analysis.domains_of_interest == [self.domain]
def test_bad_args(self):
with self.assertRaisesRegex(ValueError,
"No database file located for"):
ActiveSiteAnalysis("test", tuple(), "bad_db", [5, 6], ["C", "S"])
with self.assertRaisesRegex(
ValueError,
"Number of expected values must match number of positions"):
ActiveSiteAnalysis("test", tuple(), "PKSI-KR.hmm2", [5, 6], ["C"])
with self.assertRaisesRegex(
ValueError,
"Number of expected values must match number of positions"):
ActiveSiteAnalysis("test", tuple(), "PKSI-KR.hmm2", [5],
["C", "S"])
with self.assertRaisesRegex(
ValueError,
"Number of emissions must match number of positions"):
ActiveSiteAnalysis("test",
tuple(),
"PKSI-KR.hmm2", [5, 6], ["C", "S"],
emissions=[1.0, .2, .3])
with self.assertRaisesRegex(
ValueError,
"Number of emissions must match number of positions"):
ActiveSiteAnalysis("test",
tuple(),
"PKSI-KR.hmm2", [5, 6], ["C", "S"],
emissions=[1.0])
def test_domains_of_interest(self):
domain = DummyPFAMDomain(domain="p450")
analysis = ActiveSiteAnalysis("not-p450", (domain, ), "PKSI-KR.hmm2",
[5, 6], ["C", "S"])
assert analysis.domains_of_interest == []
analysis = ActiveSiteAnalysis("p450", (domain, ), "PKSI-KR.hmm2",
[5, 6], ["C", "S"])
assert analysis.domains_of_interest == [domain]
def test_no_candidates_doesnt_break(self):
analysis = ActiveSiteAnalysis("test", tuple(), "PKSI-KR.hmm2", [5, 6],
["C", "S"])
with patch.object(subprocessing,
"run_hmmpfam2",
side_effect=RuntimeError()) as mocked_run:
assert analysis.get_alignments() == []
mocked_run.assert_not_called()
def test_alignment_generation_no_hits(self):
no_hits = list(
SearchIO.parse(
open(path.get_full_path(__file__, 'data', 'no_hits.output')),
"hmmer2-text"))
mock("subprocessing.run_hmmpfam2", returns=no_hits)
for result in no_hits:
assert not result.hsps, "hits shouldn't exist"
domains = self.generate_domains()
analysis = ActiveSiteAnalysis("PKS_KS", domains, "PKSI-KS_N.hmm2",
[176, 186, 187, 188],
['G', 'S', 'S', 'S'])
assert analysis.get_alignments() == []
def test_alignment_generation(self):
pregenerated = list(
SearchIO.parse(
open(path.get_full_path(__file__, 'data', 'KS_N.output')),
"hmmer2-text"))
mock("subprocessing.run_hmmpfam2", returns=pregenerated)
domains = self.generate_domains()
analysis = ActiveSiteAnalysis("PKS_KS", domains, "PKSI-KS_N.hmm2",
[176, 186, 187, 188],
['G', 'S', 'S', 'S'])
assert {"PKS_KS"} == {
domain.domain
for domain in analysis.domains_of_interest
}
alignments = analysis.get_alignments()
assert len(alignments) == 4
assert [align.domain for align in alignments[:4]] == domains[:4]
def create_analysis(self, positions, expected):
return ActiveSiteAnalysis("test", tuple(), "PKSI-KR.hmm2", positions,
expected)
def test_bad_candidates(self):
with self.assertRaisesRegex(TypeError,
"Candidates must be Domains, not"):
ActiveSiteAnalysis("not-p450", ("not a Domain", ), "PKSI-KR.hmm2",
[5, 6], ["C", "S"])
def test_no_candidates_doesnt_break(self):
mock("subprocessing.run_hmmpfam2", returns=RuntimeError)
analysis = ActiveSiteAnalysis("test", tuple(), "PKSI-KR.hmm2", [5, 6],
["C", "S"])
assert analysis.get_alignments() == []