def test_fill_my_db(self):
gene_name = "gspD"
args = argparse.Namespace()
args.db_type = 'gembase'
args.models_dir = self.find_data('models')
args.log_level = 30
args.sequence_db = self.find_data("base", "test_base.fa")
args.index_dir = self.tmpdir
cfg = Config(MacsyDefaults(), args)
gspD_hmmer_path = self.find_data('hmm', 'gspD.search_hmm.out')
idx = Indexes(cfg)
macsyfinder_idx = idx.build()
hmm_prof = macsyprofile.HmmProfile(gene_name, 596, gspD_hmmer_path,
cfg)
db = hmm_prof._build_my_db(gspD_hmmer_path)
hmm_prof._fill_my_db(macsyfinder_idx, db)
self.assertDictEqual(
db, {
'PSAE001c01_031420': (658, 73),
'PSAE001c01_051090': (714, 75),
'PSAE001c01_018920': (776, 71),
'PSAE001c01_043580': (416, 74),
'PSAE001c01_017350': (600, 70),
'PSAE001c01_013980': (759, 69),
'PSAE001c01_026600': (273, 72),
'NC_xxxxx_xx_056141': (803, 141),
'PSAE001c01_006940': (803, 68)
})
def test_build_my_db(self):
gene_name = "gspD"
args = argparse.Namespace()
args.db_type = 'gembase'
args.models_dir = self.find_data('models')
args.log_level = 30
self.cfg = Config(MacsyDefaults(), args)
gspD_hmmer_path = self.find_data(
os.path.join('hmm', 'gspD.search_hmm.out'))
hmm_prof = macsyprofile.HmmProfile(gene_name, 596, gspD_hmmer_path,
self.cfg)
db = hmm_prof._build_my_db(gspD_hmmer_path)
self.assertDictEqual(
db, {
'PSAE001c01_031420': None,
'PSAE001c01_051090': None,
'PSAE001c01_018920': None,
'PSAE001c01_043580': None,
'PSAE001c01_017350': None,
'PSAE001c01_013980': None,
'PSAE001c01_026600': None,
'NC_xxxxx_xx_056141': None,
'PSAE001c01_006940': None
})
def test_hit_start(self):
gene_name = "gspD"
args = argparse.Namespace()
args.db_type = 'gembase'
args.models_dir = self.find_data('models')
args.log_level = 30
self.cfg = Config(MacsyDefaults(), args)
gspD_hmmer_path = self.find_data(
os.path.join('hmm', 'gspD.search_hmm.out'))
hmm_prof = macsyprofile.HmmProfile(gene_name, 596, gspD_hmmer_path,
self.cfg)
self.assertFalse(hmm_prof._hit_start("NOT starting hit"))
self.assertTrue(hmm_prof._hit_start(">> starting hit"))
def test_parse_hmm_header(self):
gene_name = "gspD"
args = argparse.Namespace()
args.db_type = 'gembase'
args.models_dir = self.find_data('models')
args.log_level = 30
cfg = Config(MacsyDefaults(), args)
gspD_hmmer_path = self.find_data(
os.path.join('hmm', 'gspD.search_hmm.out'))
hmm_prof = macsyprofile.HmmProfile(gene_name, 596, gspD_hmmer_path,
cfg)
hmm_hit = [
">> NC_xxxxx_xx_056141 C ATG TAA 6260390 6261757 Valid PA5567 1368 _NP_254254.1_ PA5567 1 "
"6260390 6261757 | tRNA modific"
]
hit_id = hmm_prof._parse_hmm_header(hmm_hit)
self.assertEqual(hit_id, 'NC_xxxxx_xx_056141')
def test_parse(self):
gene_name = "gspD"
args = argparse.Namespace()
args.db_type = 'gembase'
args.models_dir = self.find_data('models')
args.log_level = 30
args.sequence_db = self.find_data("base", "test_base.fa")
args.profile_coverage = -1
args.i_evalue_sel = 10e9
args.index_dir = self.tmpdir
cfg = Config(MacsyDefaults(), args)
gspD_hmmer_path = self.find_data('hmm', 'gspD.search_hmm.out')
hmm_prof = macsyprofile.HmmProfile(gene_name, 596, gspD_hmmer_path,
cfg)
expected_hits = [
macsyprofile.LightHit('gspD', 'NC_xxxxx_xx_056141', 803,
'NC_xxxxx_xx', 141, 2.000e-236, 779.200,
1.000, (741.0 - 104.0 + 1) / 803, 104, 741),
macsyprofile.LightHit('gspD', 'PSAE001c01_006940', 803,
'PSAE001c01', 68, 1.2e-234, 779.2, 1.0,
(741.0 - 104.0 + 1) / 803, 104, 741),
macsyprofile.LightHit('gspD', 'PSAE001c01_031420', 658,
'PSAE001c01', 73, 1.8e-210, 699.3, 1.0,
(614.0 - 55.0 + 1) / 658, 55, 614),
macsyprofile.LightHit('gspD', 'PSAE001c01_018920', 776,
'PSAE001c01', 71, 6.1e-183, 608.4, 1.0,
(606.0 - 48.0 + 1) / 776, 48, 606),
macsyprofile.LightHit('gspD', 'PSAE001c01_013980', 759,
'PSAE001c01', 69, 3.7e-76, 255.8, 1.0,
(736.0 - 105.0 + 1) / 759, 105, 736),
macsyprofile.LightHit('gspD', 'PSAE001c01_017350', 600,
'PSAE001c01', 70, 3.2e-27, 94.2, 0.5,
(506.0 - 226.0 + 1) / 600, 226, 506),
]
hits = hmm_prof.parse()
self.assertListEqual(expected_hits, hits)
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"
args = argparse.Namespace()
args.db_type = 'gembase'
args.models_dir = self.find_data('models')
args.log_level = 30
cfg = Config(MacsyDefaults(), args)
gspD_hmmer_path = self.find_data(
os.path.join('hmm', 'gspD.search_hmm.out'))
hmm_prof = macsyprofile.HmmProfile(gene_name, 596, gspD_hmmer_path,
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 = hmm_prof._parse_hmm_body('NC_xxxxx_xx_056141', 596, 803, 0.5,
'NC_xxxxx_xx', 141, 0.5, body)
expected_hits = [
macsyprofile.LightHit(gene_name, "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 = hmm_prof._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 = hmm_prof._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:
hmm_prof._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'""")