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_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(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_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_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_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_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)
