def test_parse_hmm_body(self):
def make_hmm_group(hmm_string):
hmm_file = StringIO(hmm_string)
hmm_hits = (
x[1] for x in groupby(hmm_file, lambda l: l.startswith('>>')))
header = next(hmm_hits)
body = next(hmm_hits)
return body
gene_name = "gspD"
c_gene = CoreGene(self.model_location, gene_name, self.profile_factory)
report_path = os.path.join(self.cfg.working_dir(),
gene_name + self.cfg.res_search_suffix())
report = GembaseHMMReport(c_gene, report_path, self.cfg)
# with one significant hit
hmm = """>> NC_xxxxx_xx_056141 C ATG TAA 6260390 6261757 Valid PA5567 1368 _NP_254254.1_ PA5567 1 6260390 6261757 | tRNA modific
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 779.2 5.5 1.4e-237 2e-236 1 596 [] 104 741 .. 104 741 .. 0.93
Alignments for each domain:
"""
body = make_hmm_group(hmm)
hits = report._parse_hmm_body('NC_xxxxx_xx_056141', 596, 803, 0.5,
'NC_xxxxx_xx', 141, 0.5, body)
expected_hits = [
CoreHit(c_gene, "NC_xxxxx_xx_056141", 803, "NC_xxxxx_xx", 141,
float(2e-236), float(779.2), float(1.000000),
(741.0 - 104.0 + 1) / 803, 104, 741)
]
self.assertListEqual(hits, expected_hits)
# with no significant hit
hmm = """>> PSAE001c01_051090 C ATG TGA 5675714 5677858 Valid pilQ 2145 _PA5040_NP_253727.1_ PA5040 1 5675714 5677858 | type 4 f
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 27.1 0.2 6.3e-10 6.6e-07 1 120 [. 286 402 .. 286 407 .. 0.86
2 ! 186.2 0.1 4.2e-58 4.3e-55 294 590 .. 405 709 .. 397 712 .. 0.84
Alignments for each domain:
"""
body = make_hmm_group(hmm)
hits = report._parse_hmm_body('NC_xxxxx_xx_056141', 596, 803, 0.5,
'NC_xxxxx_xx', 141, 0.5, body)
expected_hits = []
self.assertListEqual(hits, expected_hits)
# with no hit
hmm = """>> PSAE001c01_051090 C ATG TGA 5675714 5677858 Valid pilQ 2145 _PA5040_NP_253727.1_ PA5040 1 5675714 5677858 | type 4 f
bla bla
"""
body = make_hmm_group(hmm)
hits = report._parse_hmm_body('NC_xxxxx_xx_056141', 596, 803, 0.5,
'NC_xxxxx_xx', 141, 0.5, body)
expected_hits = []
self.assertListEqual(hits, expected_hits)
# with invalid hmm
hmm = """>> NC_xxxxx_xx_056141 C ATG TAA 6260390 6261757 Valid PA5567 1368 _NP_254254.1_ PA5567 1 6260390 6261757 | tRNA modific
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 779.2 5.5 1.4e-237 foo 1 596 [] 104 741 .. 104 741 .. 0.93
Alignments for each domain:
"""
body = make_hmm_group(hmm)
with self.assertRaises(ValueError) as ctx:
report._parse_hmm_body('NC_xxxxx_xx_056141', 596, 803, 0.5,
'NC_xxxxx_xx', 141, 0.5, body)
self.assertEqual(
str(ctx.exception),
"""Invalid line to parse : 1 ! 779.2 5.5 1.4e-237 foo 1 596 [] 104 741 .. 104 741 .. 0.93
:could not convert string to float: 'foo'""")
