def test_parse_output(self): """Test functionality of parse_output """ output_exp = ["0.99", "0.01"] output = parse_output(hgt_results_fp=self.consel_output_hgt_fp, method="consel") self.assertEqual(output_exp, output) output_exp = "1" output = parse_output(hgt_results_fp=self.riatahgt_output_hgt_fp, method="riata-hgt") self.assertEqual(output_exp, output) output_exp = ("WP_011672248.1\t372461\tBuchnera aphidicola\tProteobac" "teria;Gammaproteobacteria;Enterobacteriales;Enterobact" "eriaceae;Buchnera;Buchnera aphidicola\t37.5\t99.14\nWP" "_045117937.1\t580331\tThermoanaerobacter italicus\tFir" "micutes;Clostridia;Thermoanaerobacterales;Thermoanaero" "bacteraceae;Thermoanaerobacter;Thermoanaerobacter ital" "icus\t42.6\t93.84") output = parse_output(hgt_results_fp=self.hgtector_output_hgt_fp, method="hgtector") self.assertEqual(output_exp, output) output_exp = None output = parse_output(hgt_results_fp=self.empty_output_hgt_fp, method="darkhorse") self.assertEqual(output_exp, output)
def test_parse_output(self): """Test functionality of parse_output """ output_exp = ["0.99", "0.01"] output = parse_output(hgt_results_fp=self.consel_output_hgt_fp, method="consel") self.assertEqual(output_exp, output) output_exp = "1" output = parse_output(hgt_results_fp=self.riatahgt_output_hgt_fp, method="riata-hgt") self.assertEqual(output_exp, output)
def test_parse_output_empty(self): """Test functionality of parse_output with empty file """ output_exp = 'NaN' output = parse_output(hgt_results_fp=self.empty_output_hgt_fp, method="riata-hgt") self.assertEqual(output_exp, output)
def test_parse_output(self): """Test functionality of parse_output """ output_exp = ["0.99", "0.01"] output = parse_output(hgt_results_fp=self.consel_output_hgt_fp, method="consel") self.assertEqual(output_exp, output) output_exp = "1" output = parse_output(hgt_results_fp=self.riatahgt_output_hgt_fp, method="riata-hgt") self.assertEqual(output_exp, output) output_exp = ("WP_011672248.1\t372461\tBuchnera aphidicola\tProteobac" "teria;Gammaproteobacteria;Enterobacteriales;Enterobact" "eriaceae;Buchnera;Buchnera aphidicola\t37.5\t99.14\nWP" "_045117937.1\t580331\tThermoanaerobacter italicus\tFir" "micutes;Clostridia;Thermoanaerobacterales;Thermoanaero" "bacteraceae;Thermoanaerobacter;Thermoanaerobacter ital" "icus\t42.6\t93.84") output = parse_output(hgt_results_fp=self.hgtector_output_hgt_fp, method="hgtector") self.assertEqual(output_exp, output) output_exp = ("G2311_SE001,\tgi|557307555|ref|YP_008766893.1|\t140749" "3\tShigella phage SfIV\tViruses;Caudovirales;Myovirida" "e\t67.4\t100\t0.002\nG1250_SE001,\tgi|9630468|ref|NP_0" "46899.1|\t40631\tEnterobacteria phage N15\tViruses;Cau" "dovirales;Siphoviridae;N15likevirus\t79.4\t100\t0.002\n" "G1252_SE001,\tgi|428782382|ref|YP_007112139.1|\t114714" "4\tEnterobacteria phage HK225\tViruses;Caudovirales;Si" "phoviridae;Lambdalikevirus\t88.2\t100\t0.002\nG1251_SE" "001,\tgi|428782381|ref|YP_007112138.1|\t1147144\tEnter" "obacteria phage HK225\tViruses;Caudovirales;Siphovirid" "ae;Lambdalikevirus\t94.9\t100\t0.002") output = parse_output(hgt_results_fp=self.darkhorse_output_hgt_fp, method="darkhorse") self.assertEqual(output_exp, output) output_exp = "AAA98667.1" output = parse_output(hgt_results_fp=self.egid_output_hgt_fp, genbank_fp=self.genbank_input_fp, method="egid") self.assertEqual(output_exp, output) output_exp = "AAA98667.1" output = parse_output(hgt_results_fp=self.genemark_output_hgt_fp, genbank_fp=self.genbank_input_fp, method="genemark") self.assertEqual(output_exp, output)