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)
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_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)
