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)
})
