def test_sort_result_xenopi(self):
input_file = 'data/xenopi.tab'
input_data = read_file(input_file)
pct_threshold = 1
num_threshold = 10000
result = parse_kraken2.read_kraken2(input_data, pct_threshold,
num_threshold)
sorted_result = parse_kraken2.sort_result(result, pct_threshold,
num_threshold)
self.assertTrue(
sorted_result['Family'][0]['name'] == "Mycobacteriaceae")
self.assertTrue(
sorted_result['Family'][1]['name'] == "Streptococcaceae")
self.assertTrue(sorted_result['Family'][2]['name'] == "Nocardiaceae")
self.assertTrue(sorted_result['Genus'][0]['name'] == "Mycobacterium")
self.assertTrue(sorted_result['Genus'][1]['name'] == "Streptococcus")
self.assertTrue(
sorted_result['Genus'][2]['name'] == "Mycolicibacterium")
self.assertTrue(sorted_result['Species complex'][0]['name'] ==
'Mycobacterium avium complex (MAC)')
self.assertTrue(sorted_result['Species complex'][1]['name'] ==
'Mycobacterium simiae complex')
self.assertTrue(
sorted_result['Species'][0]['name'] == "Streptococcus gordonii")
self.assertTrue(
sorted_result['Species'][1]['name'] == "Mycobacterium avium")
self.assertTrue(sorted_result['Species'][2]['name'] == "H**o sapiens")
self.assertTrue(sorted_result['Warnings']['mykrobe'] == False)
def test_read_kraken2(self):
input_file = 'data/tb.tab'
input_data = read_file(input_file)
pct_threshold = 1
num_threshold = 10000
result = parse_kraken2.read_kraken2(input_data, pct_threshold,
num_threshold)
self.assertTrue('Family' in result.keys())
self.assertTrue('Genus' in result.keys())
self.assertTrue('Species complex' in result.keys())
self.assertTrue('Species' in result.keys())
self.assertTrue('Warnings' in result.keys())
def test_sort_result_unclassified(self):
input_file = 'data/unclassified.tab'
input_data = read_file(input_file)
pct_threshold = 1
num_threshold = 10000
result = parse_kraken2.read_kraken2(input_data, pct_threshold,
num_threshold)
sorted_result = parse_kraken2.sort_result(result, pct_threshold,
num_threshold)
self.assertTrue('notes' in sorted_result['Family'].keys())
self.assertTrue('notes' in sorted_result['Genus'].keys())
self.assertTrue('notes' in sorted_result['Species complex'].keys())
self.assertTrue('notes' in sorted_result['Species'].keys())
self.assertTrue(sorted_result['Warnings']['mykrobe'] == False)
def test_sort_result_abscessus(self):
input_file = 'data/abscessus.tab'
input_data = read_file(input_file)
pct_threshold = 1
num_threshold = 10000
result = parse_kraken2.read_kraken2(input_data, pct_threshold,
num_threshold)
sorted_result = parse_kraken2.sort_result(result, pct_threshold,
num_threshold)
self.assertTrue(
sorted_result['Family'][0]['name'] == "Mycobacteriaceae")
self.assertTrue(sorted_result['Genus'][0]['name'] == "Mycobacteroides")
self.assertTrue('notes' in sorted_result['Species complex'].keys())
self.assertTrue(
sorted_result['Species'][0]['name'] == "Mycobacteroides abscessus")
self.assertTrue(sorted_result['Species'][1]['name'] == "H**o sapiens")
self.assertTrue(sorted_result['Warnings']['mykrobe'] == True)
def test_sort_result_tb(self):
input_file = 'data/tb.tab'
input_data = read_file(input_file)
pct_threshold = 1
num_threshold = 10000
result = parse_kraken2.read_kraken2(input_data, pct_threshold,
num_threshold)
sorted_result = parse_kraken2.sort_result(result, pct_threshold,
num_threshold)
self.assertTrue(
sorted_result['Family'][0]['name'] == "Mycobacteriaceae")
self.assertTrue(sorted_result['Genus'][0]['name'] == "Mycobacterium")
self.assertTrue(sorted_result['Species complex'][0]['name'] ==
"Mycobacterium tuberculosis complex")
self.assertTrue(sorted_result['Species'][0]['name'] ==
"Mycobacterium tuberculosis")
self.assertTrue(sorted_result['Species'][1]['name'] == "H**o sapiens")
self.assertTrue(sorted_result['Warnings']['mykrobe'] == True)
def test_sort_result_kansasii(self):
input_file = 'data/kansasii.tab'
input_data = read_file(input_file)
pct_threshold = 1
num_threshold = 10000
result = parse_kraken2.read_kraken2(input_data, pct_threshold,
num_threshold)
sorted_result = parse_kraken2.sort_result(result, pct_threshold,
num_threshold)
self.assertTrue(sorted_result['Family'][0]['name'] == "Bacillaceae")
self.assertTrue(
sorted_result['Family'][1]['name'] == "Mycobacteriaceae")
self.assertTrue(sorted_result['Genus'][0]['name'] == "Bacillus")
self.assertTrue(sorted_result['Genus'][1]['name'] == "Mycobacterium")
self.assertTrue('notes' in sorted_result['Species complex'].keys())
self.assertTrue(sorted_result['Species'][0]['name'] ==
"Bacillus paralicheniformis")
self.assertTrue(
sorted_result['Species'][1]['name'] == "Mycobacterium kansasii")
self.assertTrue(sorted_result['Species'][2]['name'] == "H**o sapiens")
self.assertTrue(sorted_result['Warnings']['mykrobe'] == False)