def _write_mlst_reports(cls,
mlst_profile_file,
ariba_report_tsv,
outprefix,
verbose=False):
if os.path.exists(mlst_profile_file):
if verbose:
print('\nMaking MLST reports', flush=True)
reporter = mlst_reporter.MlstReporter(ariba_report_tsv,
mlst_profile_file, outprefix)
reporter.run()
def test_new_set(self):
'''test when allele combination is new'''
profile_in = os.path.join(data_dir, 'mlst_reporter.profile.in.tsv')
report_in = os.path.join(data_dir, 'mlst_reporter.new_st.report.in.tsv')
expected_out_simple = os.path.join(data_dir, 'mlst_reporter.new_st.report.out.tsv')
expected_out_all = os.path.join(data_dir, 'mlst_reporter.new_st.report.out.details.tsv')
tmp_out = 'tmp.mlst_reporter.test_new_st'
got_simple = tmp_out + '.tsv'
got_details = tmp_out + '.details.tsv'
reporter = mlst_reporter.MlstReporter(report_in, profile_in, tmp_out)
reporter.run()
self.assertTrue(filecmp.cmp(expected_out_simple, got_simple, shallow=False))
self.assertTrue(filecmp.cmp(expected_out_all, got_details, shallow=False))
os.unlink(got_simple)
os.unlink(got_details)
def test_het_snps(self):
'''test when one gene has two het snps'''
profile_in = os.path.join(data_dir, 'mlst_reporter.profile.in.tsv')
report_in = os.path.join(data_dir, 'mlst_reporter.het_snps.in.tsv')
expected_out_simple = os.path.join(data_dir, 'mlst_reporter.het_snps.out.tsv')
expected_out_all = os.path.join(data_dir, 'mlst_reporter.het_snps.out.details.tsv')
tmp_out = 'tmp.mlst_reporter.test_het_snps'
got_simple = tmp_out + '.tsv'
got_details = tmp_out + '.details.tsv'
reporter = mlst_reporter.MlstReporter(report_in, profile_in, tmp_out)
reporter.run()
self.assertTrue(filecmp.cmp(expected_out_simple, got_simple, shallow=False))
self.assertTrue(filecmp.cmp(expected_out_all, got_details, shallow=False))
os.unlink(got_simple)
os.unlink(got_details)
def test_all_present_perfect(self):
'''test when all alleles 100% there no variants'''
profile_in = os.path.join(data_dir, 'mlst_reporter.profile.in.tsv')
report_in = os.path.join(data_dir, 'mlst_reporter.all_present_perfect.report.in.tsv')
expected_out_simple = os.path.join(data_dir, 'mlst_reporter.all_present_perfect.report.out.tsv')
expected_out_all = os.path.join(data_dir, 'mlst_reporter.all_present_perfect.report.out.details.tsv')
tmp_out = 'tmp.mlst_reporter.test_all_present_perfect'
got_simple = tmp_out + '.tsv'
got_details = tmp_out + '.details.tsv'
reporter = mlst_reporter.MlstReporter(report_in, profile_in, tmp_out)
reporter.run()
self.assertTrue(filecmp.cmp(expected_out_simple, got_simple, shallow=False))
self.assertTrue(filecmp.cmp(expected_out_all, got_details, shallow=False))
os.unlink(got_simple)
os.unlink(got_details)