def test_GembaseHMMReport_extract(self):
system = System(self.cfg, "T2SS", 10)
gene_name = "gspD"
gene = Gene(self.cfg, gene_name, system, self.profile_registry)
shutil.copy(
os.path.join(self._data_dir, "hmm",
gene_name + self.cfg.res_search_suffix),
self.cfg.working_dir)
report_path = os.path.join(self.cfg.working_dir,
gene_name + self.cfg.res_search_suffix)
report = GembaseHMMReport(gene, report_path, self.cfg)
report.extract()
self.assertEqual(len(report.hits), 6)
# gene, system, hit_id, hit_seq_length replicon_name, pos_hit, i_eval, score, profile_coverage, sequence_coverage, begin_match, end_match
hits = [
Hit(gene, system, "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),
Hit(gene, system, "PSAE001c01_006940", 803, "PSAE001c01", 68,
float(1.2e-234), float(779.2), float(1.000000),
(741.0 - 104.0 + 1) / 803, 104, 741),
Hit(gene, system, "PSAE001c01_013980", 759, "PSAE001c01", 69,
float(3.7e-76), float(255.8), float(1.000000),
(736.0 - 105.0 + 1) / 759, 105, 736),
Hit(gene, system, "PSAE001c01_017350", 600, "PSAE001c01", 70,
float(3.2e-27), float(94.2), float(0.500000),
(506.0 - 226.0 + 1) / 600, 226, 506),
Hit(gene, system, "PSAE001c01_018920", 776, "PSAE001c01", 71,
float(6.1e-183), float(608.4), float(1.000000),
(606.0 - 48.0 + 1) / 776, 48, 606),
Hit(gene, system, "PSAE001c01_031420", 658, "PSAE001c01", 73,
float(1.8e-210), float(699.3), float(1.000000),
(614.0 - 55.0 + 1) / 658, 55, 614)
]
self.assertListEqual(hits, report.hits)
def test_GembaseHMMReport_extract_concurent(self):
system = System(self.cfg, "T2SS", 10)
gene_name = "gspD"
gene = Gene(self.cfg, gene_name, system, self.profile_registry)
shutil.copy(
os.path.join(self._data_dir, "hmm",
gene_name + self.cfg.res_search_suffix),
self.cfg.working_dir)
report_path = os.path.join(self.cfg.working_dir,
gene_name + self.cfg.res_search_suffix)
reports = []
for i in range(5):
report = GembaseHMMReport(gene, report_path, self.cfg)
reports.append(report)
import threading
def worker(report):
report.extract()
for report in reports:
t = threading.Thread(target=worker, args=(report, ))
t.start()
main_thread = threading.currentThread()
for t in threading.enumerate():
if t is main_thread:
continue
t.join()
#gene, system, hit_id, hit_seq_length replicon_name, pos_hit, i_eval, score, profile_coverage, sequence_coverage, begin_match, end_match
hits = [
Hit(gene, system, "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),
Hit(gene, system, "PSAE001c01_006940", 803, "PSAE001c01", 68,
float(1.2e-234), float(779.2), float(1.000000),
(741.0 - 104.0 + 1) / 803, 104, 741),
Hit(gene, system, "PSAE001c01_013980", 759, "PSAE001c01", 69,
float(3.7e-76), float(255.8), float(1.000000),
(736.0 - 105.0 + 1) / 759, 105, 736),
Hit(gene, system, "PSAE001c01_017350", 600, "PSAE001c01", 70,
float(3.2e-27), float(94.2), float(0.500000),
(506.0 - 226.0 + 1) / 600, 226, 506),
Hit(gene, system, "PSAE001c01_018920", 776, "PSAE001c01", 71,
float(6.1e-183), float(608.4), float(1.000000),
(606.0 - 48.0 + 1) / 776, 48, 606),
Hit(gene, system, "PSAE001c01_031420", 658, "PSAE001c01", 73,
float(1.8e-210), float(699.3), float(1.000000),
(614.0 - 55.0 + 1) / 658, 55, 614)
]
for report in reports:
report.save_extract()
self.assertEqual(len(report.hits), len(hits))
self.assertListEqual(report.hits, hits)
def test_hit_start(self):
gene_name = "gspD"
c_gene = CoreGene(self.model_location, gene_name, self.profile_factory)
shutil.copy(
self.find_data("hmm", gene_name + self.cfg.res_search_suffix()),
self.cfg.working_dir())
report_path = os.path.join(self.cfg.working_dir(),
gene_name + self.cfg.res_search_suffix())
report = GembaseHMMReport(c_gene, report_path, self.cfg)
self.assertFalse(report._hit_start("NOT starting hit"))
self.assertTrue(report._hit_start(">> starting hit"))
def test_parse_hmm_header(self):
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)
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 = report._parse_hmm_header(hmm_hit)
self.assertEqual(hit_id, 'NC_xxxxx_xx_056141')
def test_GembaseHMMReport_extract(self):
system = System(self.cfg, "T2SS", 10)
gene_name = "gspD"
gene = Gene(self.cfg, gene_name, system, self.profile_registry)
shutil.copy(os.path.join(self._data_dir, "hmm", gene_name + self.cfg.res_search_suffix), self.cfg.working_dir)
report_path = os.path.join(self.cfg.working_dir, gene_name + self.cfg.res_search_suffix)
report = GembaseHMMReport(gene, report_path, self.cfg)
report.extract()
self.assertEqual(len(report.hits), 5)
#gene, system, hit_id, hit_seq_length replicon_name, pos_hit, i_eval, score, profile_coverage, sequence_coverage, begin_match, end_match
hits=[ Hit(gene, system, "PSAE001c01_006940", 803,"PSAE001c01", 68, float(1.2e-234), float(779.2), float(1.000000), (741.0 - 104.0 + 1)/ 803, 104, 741),
Hit(gene, system, "PSAE001c01_013980", 759,"PSAE001c01", 69, float(3.7e-76), float(255.8), float(1.000000), (736.0 - 105.0 + 1)/ 759, 105, 736),
Hit(gene, system, "PSAE001c01_017350", 600,"PSAE001c01", 70, float(3.2e-27), float(94.2), float(0.500000), (506.0 - 226.0 + 1)/ 600, 226, 506),
Hit(gene, system, "PSAE001c01_018920", 776,"PSAE001c01", 71, float(6.1e-183), float(608.4), float(1.000000), (606.0 - 48.0 + 1)/ 776, 48, 606),
Hit(gene, system, "PSAE001c01_031420", 658,"PSAE001c01", 73, float(1.8e-210), float(699.3), float(1.000000), (614.0 - 55.0 + 1)/ 658, 55, 614)
]
self.assertListEqual(hits, report.hits)
def test_str(self):
system = System(self.cfg, "T2SS", 10)
gene_name = "gspD"
gene = Gene(self.cfg, gene_name, system, self.profile_registry)
shutil.copy(
os.path.join(self._data_dir, "hmm",
gene_name + self.cfg.res_search_suffix),
self.cfg.working_dir)
report_path = os.path.join(self.cfg.working_dir,
gene_name + self.cfg.res_search_suffix)
report = GembaseHMMReport(gene, report_path, self.cfg)
report.extract()
hits = [
Hit(gene, system, "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),
Hit(gene, system, "PSAE001c01_006940", 803, "PSAE001c01", 68,
float(1.2e-234), float(779.2), float(1.000000),
(741.0 - 104.0 + 1) / 803, 104, 741),
Hit(gene, system, "PSAE001c01_013980", 759, "PSAE001c01", 69,
float(3.7e-76), float(255.8), float(1.000000),
(736.0 - 105.0 + 1) / 759, 105, 736),
Hit(gene, system, "PSAE001c01_017350", 600, "PSAE001c01", 70,
float(3.2e-27), float(94.2), float(0.500000),
(506.0 - 226.0 + 1) / 600, 226, 506),
Hit(gene, system, "PSAE001c01_018920", 776, "PSAE001c01", 71,
float(6.1e-183), float(608.4), float(1.000000),
(606.0 - 48.0 + 1) / 776, 48, 606),
Hit(gene, system, "PSAE001c01_031420", 658, "PSAE001c01", 73,
float(1.8e-210), float(699.3), float(1.000000),
(614.0 - 55.0 + 1) / 658, 55, 614)
]
s = ""
s = "# gene: {0} extract from {1} hmm output\n".format(
gene.name, report_path)
s += "# profile length= {0:d}\n".format(len(gene.profile))
s += "# i_evalue threshold= {0:.3f}\n".format(self.cfg.i_evalue_sel)
s += "# coverage threshold= {0:.3f}\n".format(
self.cfg.coverage_profile)
s += "# hit_id replicon_name position_hit hit_sequence_length gene_name gene_system i_eval score profile_coverage sequence_coverage begin end\n"
for h in hits:
s += str(h)
self.assertEqual(str(report), s)
def test_str(self):
gene_name = 'gspD'
c_gene = CoreGene(self.model_location, gene_name, self.profile_factory)
shutil.copy(
self.find_data("hmm", gene_name + self.cfg.res_search_suffix()),
self.cfg.working_dir())
report_path = os.path.join(self.cfg.working_dir(),
gene_name + self.cfg.res_search_suffix())
report = GembaseHMMReport(c_gene, report_path, self.cfg)
report.extract()
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),
CoreHit(c_gene, "PSAE001c01_006940", 803, "PSAE001c01", 68,
float(1.2e-234), float(779.2), float(1.000000),
(741.0 - 104.0 + 1) / 803, 104, 741),
CoreHit(c_gene, "PSAE001c01_013980", 759, "PSAE001c01", 69,
float(3.7e-76), float(255.8), float(1.000000),
(736.0 - 105.0 + 1) / 759, 105, 736),
CoreHit(c_gene, "PSAE001c01_017350", 600, "PSAE001c01", 70,
float(3.2e-27), float(94.2), float(0.500000),
(506.0 - 226.0 + 1) / 600, 226, 506),
CoreHit(c_gene, "PSAE001c01_018920", 776, "PSAE001c01", 71,
float(6.1e-183), float(608.4), float(1.000000),
(606.0 - 48.0 + 1) / 776, 48, 606),
CoreHit(c_gene, "PSAE001c01_031420", 658, "PSAE001c01", 73,
float(1.8e-210), float(699.3), float(1.000000),
(614.0 - 55.0 + 1) / 658, 55, 614)
]
s = f"# gene: {c_gene.name} extract from {report_path} hmm output\n"
s += f"# profile length= {len(c_gene.profile):d}\n"
s += f"# i_evalue threshold= {self.cfg.i_evalue_sel():.3f}\n"
s += f"# coverage threshold= {self.cfg.coverage_profile():.3f}\n"
s += "# hit_id replicon_name position_hit hit_sequence_length gene_name gene_system i_eval score " \
"profile_coverage sequence_coverage begin end\n"
for h in hits:
s += str(h)
self.assertMultiLineEqual(str(report), s)
def test_build_my_db(self):
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)
gspD_hmmer_path = self.find_data(
os.path.join('hmm', 'gspD.search_hmm.out'))
db = report._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_fill_my_db(self):
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)
idx = Indexes(self.cfg)
gspD_hmmer_path = self.find_data(
os.path.join('hmm', 'gspD.search_hmm.out'))
db = report._build_my_db(gspD_hmmer_path)
report._fill_my_db(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_str(self):
system = System(self.cfg, "T2SS", 10)
gene_name = "gspD"
gene = Gene(self.cfg, gene_name, system, self.profile_registry)
shutil.copy(os.path.join(self._data_dir, "hmm", gene_name + self.cfg.res_search_suffix), self.cfg.working_dir)
report_path = os.path.join(self.cfg.working_dir, gene_name + self.cfg.res_search_suffix)
report = GembaseHMMReport(gene, report_path, self.cfg)
report.extract()
hits=[ Hit(gene, system, "PSAE001c01_006940", 803,"PSAE001c01", 68, float(1.2e-234), float(779.2), float(1.000000), (741.0 - 104.0 + 1)/ 803, 104, 741),
Hit(gene, system, "PSAE001c01_013980", 759,"PSAE001c01", 69, float(3.7e-76), float(255.8), float(1.000000), (736.0 - 105.0 + 1)/ 759, 105, 736),
Hit(gene, system, "PSAE001c01_017350", 600,"PSAE001c01", 70, float(3.2e-27), float(94.2), float(0.500000), (506.0 - 226.0 + 1)/ 600, 226, 506),
Hit(gene, system, "PSAE001c01_018920", 776,"PSAE001c01", 71, float(6.1e-183), float(608.4), float(1.000000), (606.0 - 48.0 + 1)/ 776, 48, 606),
Hit(gene, system, "PSAE001c01_031420", 658,"PSAE001c01", 73, float(1.8e-210), float(699.3), float(1.000000), (614.0 - 55.0 + 1)/ 658, 55, 614)
]
s = ""
s = "# gene: %s extract from %s hmm output\n" % (gene.name, report_path)
s += "# profile length= %d\n" % len(gene.profile)
s += "# i_evalue threshold= %f\n" % self.cfg.i_evalue_sel
s += "# coverage threshold= %f\n" % self.cfg.coverage_profile
s += "# hit_id replicon_name position_hit hit_sequence_length gene_name gene_system i_eval score profile_coverage sequence_coverage begin end\n"
for h in hits:
s += str(h)
self.assertEqual(str(report), s)
def test_save_extract(self):
gene_name = "gspD"
gene = CoreGene(self.model_location, gene_name, self.profile_factory)
shutil.copy(
self.find_data("hmm", gene_name + self.cfg.res_search_suffix()),
self.cfg.working_dir())
report_path = os.path.join(self.cfg.working_dir(),
gene_name + self.cfg.res_search_suffix())
report = GembaseHMMReport(gene, report_path, self.cfg)
report.extract()
report.save_extract()
extract_filename = gene_name + self.cfg.res_extract_suffix()
extract_path = os.path.join(self.cfg.working_dir(),
self.cfg.hmmer_dir(), extract_filename)
self.assertTrue(os.path.exists(extract_path))
self.assertTrue(os.path.isfile(extract_path))
hits = [
CoreHit(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),
CoreHit(gene, "PSAE001c01_006940", 803, "PSAE001c01", 68,
float(1.2e-234), float(779.2), float(1.000000),
(741.0 - 104.0 + 1) / 803, 104, 741),
CoreHit(gene, "PSAE001c01_013980", 759, "PSAE001c01", 69,
float(3.7e-76), float(255.8), float(1.000000),
(736.0 - 105.0 + 1) / 759, 105, 736),
CoreHit(gene, "PSAE001c01_017350", 600, "PSAE001c01", 70,
float(3.2e-27), float(94.2), float(0.500000),
(506.0 - 226.0 + 1) / 600, 226, 506),
CoreHit(gene, "PSAE001c01_018920", 776, "PSAE001c01", 71,
float(6.1e-183), float(608.4), float(1.000000),
(606.0 - 48.0 + 1) / 776, 48, 606),
CoreHit(gene, "PSAE001c01_031420", 658, "PSAE001c01", 73,
float(1.8e-210), float(699.3), float(1.000000),
(614.0 - 55.0 + 1) / 658, 55, 614)
]
expected_extract_path = os.path.join(self.cfg.working_dir(),
'expected_extract')
with open(expected_extract_path, 'w') as expected_extract:
extract = """# gene: {name} extract from {path} hmm output
# profile length= {len_profile:d}
# i_evalue threshold= {i_evalue:.3f}
# coverage threshold= {cov:.3f}
# hit_id replicon_name position_hit hit_sequence_length gene_name gene_system i_eval score profile_coverage sequence_coverage begin end
""".format(name=gene.name,
path=report_path,
len_profile=len(gene.profile),
i_evalue=self.cfg.i_evalue_sel(),
cov=self.cfg.coverage_profile())
expected_extract.write(extract)
for h in hits:
expected_extract.write(str(h))
self.assertFileEqual(extract_path, expected_extract_path)
def test_GembaseHMMReport_extract_concurent(self):
system = System(self.cfg, "T2SS", 10)
gene_name = "gspD"
gene = Gene(self.cfg, gene_name, system, self.profile_registry)
shutil.copy(os.path.join(self._data_dir, "hmm", gene_name + self.cfg.res_search_suffix), self.cfg.working_dir)
report_path = os.path.join(self.cfg.working_dir, gene_name + self.cfg.res_search_suffix)
reports = []
for i in range(5):
report = GembaseHMMReport(gene, report_path, self.cfg)
reports.append(report)
import threading
def worker(report):
report.extract()
for report in reports:
t = threading.Thread(target = worker, args = (report,))
t.start()
main_thread = threading.currentThread()
for t in threading.enumerate():
if t is main_thread:
continue
t.join()
#gene, system, hit_id, hit_seq_length replicon_name, pos_hit, i_eval, score, profile_coverage, sequence_coverage, begin_match, end_match
hits=[ Hit(gene, system, "PSAE001c01_006940", 803,"PSAE001c01", 68, float(1.2e-234), float(779.2), float(1.000000), (741.0 - 104.0 + 1)/ 803, 104, 741),
Hit(gene, system, "PSAE001c01_013980", 759,"PSAE001c01", 69, float(3.7e-76), float(255.8), float(1.000000), (736.0 - 105.0 + 1)/ 759, 105, 736),
Hit(gene, system, "PSAE001c01_017350", 600,"PSAE001c01", 70, float(3.2e-27), float(94.2), float(0.500000), (506.0 - 226.0 + 1)/ 600, 226, 506),
Hit(gene, system, "PSAE001c01_018920", 776,"PSAE001c01", 71, float(6.1e-183), float(608.4), float(1.000000), (606.0 - 48.0 + 1)/ 776, 48, 606),
Hit(gene, system, "PSAE001c01_031420", 658,"PSAE001c01", 73, float(1.8e-210), float(699.3), float(1.000000), (614.0 - 55.0 + 1)/ 658, 55, 614)
]
for report in reports:
report.save_extract()
self.assertEqual(len(report.hits), len(hits))
self.assertListEqual(hits, report.hits)
def test_extract(self):
gene_name = "gspD"
c_gene = CoreGene(self.model_location, gene_name, self.profile_factory)
shutil.copy(
self.find_data("hmm", gene_name + self.cfg.res_search_suffix()),
self.cfg.working_dir())
report_path = os.path.join(self.cfg.working_dir(),
gene_name + self.cfg.res_search_suffix())
report = GembaseHMMReport(c_gene, report_path, self.cfg)
report.extract()
self.assertEqual(len(report.hits), 6)
# gene, model, hit_id, hit_seq_ length replicon_name, pos_hit, i_eval,
# score, profile_coverage, sequence_coverage, begin_match, end_match
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),
CoreHit(c_gene, "PSAE001c01_006940", 803, "PSAE001c01", 68,
float(1.2e-234), float(779.2), float(1.000000),
(741.0 - 104.0 + 1) / 803, 104, 741),
CoreHit(c_gene, "PSAE001c01_013980", 759, "PSAE001c01", 69,
float(3.7e-76), float(255.8), float(1.000000),
(736.0 - 105.0 + 1) / 759, 105, 736),
CoreHit(c_gene, "PSAE001c01_017350", 600, "PSAE001c01", 70,
float(3.2e-27), float(94.2), float(0.500000),
(506.0 - 226.0 + 1) / 600, 226, 506),
CoreHit(c_gene, "PSAE001c01_018920", 776, "PSAE001c01", 71,
float(6.1e-183), float(608.4), float(1.000000),
(606.0 - 48.0 + 1) / 776, 48, 606),
CoreHit(c_gene, "PSAE001c01_031420", 658, "PSAE001c01", 73,
float(1.8e-210), float(699.3), float(1.000000),
(614.0 - 55.0 + 1) / 658, 55, 614)
]
self.assertListEqual(hits, report.hits)
report = GembaseHMMReport(c_gene, report_path, self.cfg)
report.hits = hits
self.assertIsNone(report.extract())
def test_best_hit(self):
gene_name = 'gspD'
c_gene = CoreGene(self.model_location, gene_name, self.profile_factory)
shutil.copy(
self.find_data("hmm", gene_name + self.cfg.res_search_suffix()),
self.cfg.working_dir())
report_path = os.path.join(self.cfg.working_dir(),
gene_name + self.cfg.res_search_suffix())
report = GembaseHMMReport(c_gene, report_path, self.cfg)
self.assertIsNone(report.best_hit())
report.extract()
best_hit = report.best_hit()
hit_expected = 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.assertEqual(hit_expected, best_hit)
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'""")
