def test_sheet_donors(sheet_cancer):
"""Tests for the sheet's ``donors`` attribute"""
cancer_cases = shortcuts.CancerCaseSheet(sheet_cancer)
assert len(cancer_cases.donors) == 2
assert str(cancer_cases.donors[0].bio_entity.pk) == '1'
assert str(cancer_cases.donors[0].bio_entity.secondary_id) == 'EX_001'
assert str(cancer_cases.donors[1].bio_entity.pk) == '8'
assert str(cancer_cases.donors[1].bio_entity.secondary_id) == 'EX_002'
def test_cancer_bio_sample(sheet_cancer):
"""Test for ``CancerBioSample``"""
cancer_cases = shortcuts.CancerCaseSheet(sheet_cancer)
tumor_sample = cancer_cases.donors[0].primary_pair.tumor_sample
assert tumor_sample.name == 'EX_001-T1-000005'
assert tumor_sample.is_tumor
normal_sample = cancer_cases.donors[0].primary_pair.normal_sample
assert normal_sample.name == 'EX_001-N1-000002'
assert not normal_sample.is_tumor
def test_cancer_donor(sheet_cancer):
"""Test for ``CancerDonor``"""
cancer_cases = shortcuts.CancerCaseSheet(sheet_cancer)
donor = cancer_cases.donors[0]
assert str(donor).startswith('CancerDonor(')
assert donor.primary_pair
assert donor.primary_pair.tumor_sample.name == 'EX_001-T1-000005'
assert donor.primary_pair.normal_sample.name == 'EX_001-N1-000002'
assert len(donor.all_pairs) == 1
def test_sample_pairs_primary(sheet_cancer):
"""Test for the sheet's ``primary_sample_pairs`` attribute"""
cancer_cases = shortcuts.CancerCaseSheet(sheet_cancer)
assert len(cancer_cases.primary_sample_pairs) == 2
assert cancer_cases.primary_sample_pairs[0].donor.name == 'EX_001-000001'
assert cancer_cases.primary_sample_pairs[
0].tumor_sample.name == 'EX_001-T1-000005'
assert cancer_cases.primary_sample_pairs[
0].normal_sample.name == 'EX_001-N1-000002'
assert cancer_cases.primary_sample_pairs[
1].tumor_sample.name == 'EX_002-T1-000012'
assert cancer_cases.primary_sample_pairs[
1].normal_sample.name == 'EX_002-N1-000009'
def test_sample_pair_shortcuts(sheet_cancer):
"""Test shortcuts of the ``CancerMatchedSamplePair`` objects
Also tests the shortcuts of ``CancerSample``
"""
cancer_cases = shortcuts.CancerCaseSheet(sheet_cancer)
pair = cancer_cases.donors[0].primary_pair
assert str(pair).startswith('CancerMatchedSamplePair(')
assert pair.donor.name == 'EX_001-000001'
# Tumor sample: test samples
assert pair.tumor_sample.name == 'EX_001-T1-000005'
assert pair.tumor_sample.dna_test_sample.name == 'EX_001-T1-DNA1-000006'
assert pair.tumor_sample.dna_test_sample.assay_sample.name == 'EX_001-T1-DNA1-WES1-000007'
assert pair.tumor_sample.rna_test_sample is None
# Normal sample: test samples
assert pair.normal_sample.name == 'EX_001-N1-000002'
assert pair.normal_sample.dna_test_sample.name == 'EX_001-N1-DNA1-000003'
assert pair.normal_sample.dna_test_sample.assay_sample.name == 'EX_001-N1-DNA1-WES1-000004'
assert pair.normal_sample.rna_test_sample is None
def test_donor_shortcuts(sheet_cancer):
"""Tests for shortcuts of the Donor objects"""
cancer_cases = shortcuts.CancerCaseSheet(sheet_cancer)
# First donor
assert str(cancer_cases.donors[0].pk) == '1'
assert str(cancer_cases.donors[0].secondary_id) == 'EX_001'
assert str(cancer_cases.donors[0].name) == 'EX_001-000001'
assert cancer_cases.donors[0].primary_pair
assert len(cancer_cases.donors[0].all_pairs) == 1
assert cancer_cases.donors[0].enabled
assert not cancer_cases.donors[0].disabled
# Second donor
assert str(cancer_cases.donors[1].pk) == '8'
assert str(cancer_cases.donors[1].secondary_id) == 'EX_002'
assert str(cancer_cases.donors[1].name) == 'EX_002-000008'
assert cancer_cases.donors[1].primary_pair
assert len(cancer_cases.donors[1].all_pairs) == 1
assert cancer_cases.donors[1].enabled
assert not cancer_cases.donors[1].disabled
def main():
"""Main program entry point"""
cancer_cases = shortcuts.CancerCaseSheet(load_sheet())
print('Donors\n')
for donor in cancer_cases.donors:
print(' {}'.format(donor.name))
print('\nLibraries of all tumor/normal pairs\n')
for pair in cancer_cases.all_sample_pairs:
print(' {}'.format(pair.donor.name))
print(' normal DNA: {}'.format(
pair.normal_sample.dna_ngs_library.name))
if pair.normal_sample.rna_ngs_library:
print(' normal RNA: {}'.format(
pair.normal_sample.rna_ngs_library.name))
print(' tumor DNA: {}'.format(
pair.tumor_sample.dna_ngs_library.name))
if pair.tumor_sample.rna_ngs_library:
print(' tumor RNA: {}'.format(
pair.tumor_sample.rna_ngs_library.name))