def run(options):
panel = mykrobe.Panel(options.panel_dir)
species = panel.metadata['species']
if panel.metadata['is_built_in']:
custom_probe_and_json = None
panel_name = panel.metadata['name']
else:
custom_probe_and_json = (panel.probes_fasta, panel.var_to_res_json)
panel_name = None
# This is for when we run the test in nextflow_mykrobe_predict_test.py.
# Depending on sample, we want it to be resistant, susceptible,
# or the run to fail
if options.testing and options.sample_name.endswith('1_2'):
sys.exit(1)
mykrobe.run_predict(
options.reads_files,
options.output_dir,
options.sample_name,
species,
panel=panel_name,
custom_probe_and_json=custom_probe_and_json,
unittest=options.testing,
)
def test_run_predict_and_check_susceptibility(self):
'''test run_predict and susceptibility_dict_from_json_file'''
reads_file = os.path.join(data_dir, 'run_predict.reads.fq.gz')
tmp_out = 'tmp.mykrobe_run_predict'
mykrobe.run_predict([reads_file], tmp_out, 'sample_name', 'tb')
json_file = os.path.join(tmp_out, 'out.json')
suscept_data = mykrobe.susceptibility_dict_from_json_file(json_file)
for drug in suscept_data:
if drug == 'Isoniazid':
self.assertEqual('R', suscept_data[drug]['predict'])
else:
self.assertEqual('S', suscept_data[drug]['predict'])
shutil.rmtree(tmp_out)
def test_run_predict_and_check_susceptibility_fake_run_susceptible(self):
'''test run_predict and susceptibility_dict_from_json_file in unittest mode with no resistant calls'''
reads_file = os.path.join(data_dir, 'run_predict.reads.fq.gz')
tmp_out = 'tmp.mykrobe_run_predict'
mykrobe.run_predict([reads_file],
tmp_out,
'sample_name',
'tb',
unittest=True,
unittest_resistant=False)
json_file = os.path.join(tmp_out, 'out.json')
suscept_data = mykrobe.susceptibility_dict_from_json_file(json_file)
for drug in suscept_data:
self.assertEqual('S', suscept_data[drug]['predict'])
shutil.rmtree(tmp_out)
def test_run_predict_and_check_susceptibility_custom_panel(self):
'''test run_predict and susceptibility_dict_from_json_file with custom panel'''
# rerun the prvious test, but with custom probe and js on file. These just have the
# embB_D328Y muatation. Should be susceptible
reads_file = os.path.join(data_dir, 'run_predict.reads.fq.gz')
tmp_out = 'tmp.mykrobe_run_predict'
custom_probe = os.path.join(data_dir, 'run_predict.probes.fa')
custom_json = os.path.join(data_dir, 'run_predict.json')
mykrobe.run_predict([reads_file, reads_file],
tmp_out,
'sample_name',
'tb',
custom_probe_and_json=(custom_probe, custom_json))
json_file = os.path.join(tmp_out, 'out.json')
suscept_data = mykrobe.susceptibility_dict_from_json_file(json_file)
for drug in suscept_data:
if drug == 'Ethambutol':
self.assertEqual('S', suscept_data[drug]['predict'])
else:
self.assertEqual('N', suscept_data[drug]['predict'])
shutil.rmtree(tmp_out)