def test_find_unmapped_samples(tmp_path):
runs_root = tmp_path
run1_path = runs_root / '200101_M11111_0001_0000000-J1HRQ'
run1_path.mkdir()
samples_csv = StringIO("""\
sample,run,pid
E0001-NFLHIVDNA_S1,200101_M11111,P1
E0002-NFLHIVDNA_S2,200101_M11111,P2
""")
outcome_summary_csv = StringIO("""\
sample,run,passed,error
E0001-NFLHIVDNA_S1,200101_M11111,True,
E0002-NFLHIVDNA_S2,200101_M11111,False,primer error
E0003-NFLHIVDNA_S3,200101_M11111,False,multiple contigs
""")
expected_participant_counts = {
'P1': dict(samples=1, passed=1),
'P2': dict(samples=1, errors=1, no_primer=1),
'E0003': dict(samples=1, errors=1, multiple_contigs=1)
}
expected_unmapped_samples = [('200101_M11111', 'E0003-NFLHIVDNA_S3')]
summary = StudySummary()
summary.load_samples(samples_csv, runs_root)
summary.load_outcome(outcome_summary_csv)
assert summary.participant_counts == expected_participant_counts
assert summary.unmapped_samples == expected_unmapped_samples
def test_load_samples(tmp_path):
runs_root = tmp_path
run1_path = runs_root / '200101_M11111_0001_0000000-J1HRQ'
run1_path.mkdir()
run2_path = runs_root / '200115_M22222_0003_0000000-Y8E4T'
run2_path.mkdir()
samples_csv = StringIO("""\
sample,run,pid
E0001_S1,200101_M11111,P1
E0002_S2,200101_M11111,P2
E0003_S1,200115_M22222,P2
""")
summary = StudySummary()
summary.load_samples(samples_csv, runs_root)
assert summary.run_paths == (run1_path, run2_path)
def test_load_runs_not_in_samples(tmp_path):
runs_root = tmp_path
run1_path = runs_root / '200101_M11111_0001_0000000-J1HRQ'
run1_path.mkdir()
run2_path = runs_root / '200115_M22222_0003_0000000-Y8E4T'
run2_path.mkdir()
samples_csv = StringIO("""\
sample,run,pid
E0001-NFLHIVDNA_S1,200101_M11111,P1
E0002-NFLHIVDNA_S2,200101_M11111,P2
""")
requested_runs = [str(run1_path), str(run2_path)]
summary = StudySummary()
summary.load_runs(requested_runs)
summary.load_samples(samples_csv, runs_root)
assert summary.run_paths == (run1_path, run2_path)