def test_compile_pairs0(self):
"""
Test the results of pairing with no tumor or normal samples; should give empty output
"""
samples = []
pairs = compile_pairs(samples)
expected_pairs = {'tumor': [], 'normal': []}
self.assertTrue(pairs == expected_pairs)
def test_compile_pairs3(self):
"""
Test pairing with only a single Normal sample
"""
samples = [{
"bait_set": "IMPACT468_BAITS",
"patient_id": "C-DRKHP7",
"run_id": ["JAX_0397"],
"preservation_type": ["Frozen"],
"tumor_type": "Normal"
}]
pairs = compile_pairs(samples)
expected_pairs = {'tumor': [], 'normal': []}
self.assertTrue(pairs == expected_pairs)
def test_compile_pairs1(self):
"""
Test pairing with a single pair of samples
"""
samples = [{
"patient_id": "C-W86LMR",
"bait_set": "IMPACT468_BAITS",
"run_id": ["JAX_0397"],
"preservation_type": ["Frozen"],
"tumor_type": "Normal",
"sample_id": "my_sample_id2",
"SM": "my_sample_id2"
}, {
"patient_id": "C-W86LMR",
"bait_set": "IMPACT468_BAITS",
"run_id": ["JAX_0397"],
"preservation_type": ["Frozen"],
"tumor_type": "Tumor",
"SM": "my_sample_id1",
"sample_id": "my_sample_id1"
}]
pairs = compile_pairs(samples)
expected_pairs = {
'tumor': [{
'patient_id': 'C-W86LMR',
'bait_set': 'IMPACT468_BAITS',
'tumor_type': 'Tumor',
"run_id": ["JAX_0397"],
"preservation_type": ["Frozen"],
"sample_id": "my_sample_id1",
"SM": "my_sample_id1"
}],
'normal': [{
'patient_id': 'C-W86LMR',
'bait_set': 'IMPACT468_BAITS',
'tumor_type': 'Normal',
"run_id": ["JAX_0397"],
"preservation_type": ["Frozen"],
"sample_id": "my_sample_id2",
"SM": "my_sample_id2"
}]
}
self.assertTrue(pairs == expected_pairs)
def test_compile_pairs_pooled_normal_and_dmp_bam(self):
"""
Test that a DMP bam can be found for a tumor sample without any normal in the current request or other requests
Start with no Normals and add them in reverse order of the Pairing priority (as per docstring header in this document)
and make sure each added Normal results in the correct pairing
"""
lims_filegroup_instance = FileGroup.objects.get(name="LIMS")
poolednormal_filegroup_instance = FileGroup.objects.get(
name="Pooled Normal")
fastq_filetype_instance = FileType.objects.get(name="fastq")
dmp_bam_filegroup_instance = FileGroup.objects.get(name="DMP BAMs")
bam_filetype_instance = FileType.objects.get(name="bam")
# generate tumor samples
# Sample 1 C-8VK0V7
tumor1_R1_file_instance = File.objects.create(
file_type=fastq_filetype_instance,
file_group=lims_filegroup_instance,
file_name="C-8VK0V7.R1.fastq",
path="/C-8VK0V7.R1.fastq")
tumor1_R1_filemetadata_instance = FileMetadata.objects.create(
file=tumor1_R1_file_instance,
metadata={
"R": "R1",
"sex": "F",
"runId": "PITT_0439",
"recipe": "IMPACT468",
"baitSet": "IMPACT468_BAITS",
"species": "Human",
"sampleId": "10075_D_3_5",
"libraryId": None,
"flowCellId": "HFTCNBBXY",
"barcodeId": "DUAL_IDT_LIB_267",
"barcodeIndex": "GTATTGGC-TTGTCGGT",
"runDate": "2019-12-17",
"patientId": "C-8VK0V7",
"requestId": "10075_D_3",
"sequencingCenter": "MSKCC",
"platform": "Illumina",
"sampleName": "C-8VK0V7-R001-d",
"igocomplete": True,
"oncoTreeCode": "MEL",
"preservation": "Frozen",
"sampleOrigin": "Tissue",
"specimenType": "Resection",
"tumorOrNormal": "Tumor",
"cmoSampleClass": "Local Recurrence",
"externalSampleId": "SK_MEL_1091A_T",
"investigatorSampleId": "SK_MEL_1091A_T",
"labHeadEmail": "",
"labHeadName": ""
})
tumor1_R2_file_instance = File.objects.create(
file_type=fastq_filetype_instance,
file_group=lims_filegroup_instance,
file_name="C-8VK0V7.R2.fastq",
path="/C-8VK0V7.R2.fastq")
tumor1_R2_filemetadata_instance = FileMetadata.objects.create(
file=tumor1_R2_file_instance,
metadata={
"R": "R2",
"sex": "F",
"runId": "PITT_0439",
"recipe": "IMPACT468",
"baitSet": "IMPACT468_BAITS",
"species": "Human",
"sampleId": "10075_D_3_5",
"libraryId": None,
"flowCellId": "HFTCNBBXY",
"barcodeId": "DUAL_IDT_LIB_267",
"barcodeIndex": "GTATTGGC-TTGTCGGT",
"runDate": "2019-12-17",
"patientId": "C-8VK0V7",
"requestId": "10075_D_3",
"sequencingCenter": "MSKCC",
"platform": "Illumina",
"sampleName": "C-8VK0V7-R001-d",
"igocomplete": True,
"oncoTreeCode": "MEL",
"preservation": "Frozen",
"sampleOrigin": "Tissue",
"specimenType": "Resection",
"tumorOrNormal": "Tumor",
"cmoSampleClass": "Local Recurrence",
"externalSampleId": "SK_MEL_1091A_T",
"investigatorSampleId": "SK_MEL_1091A_T",
"labHeadEmail": "",
"labHeadName": ""
})
# Sample 2 C-ABCDEF ; dummy sample
tumor2_R1_file_instance = File.objects.create(
file_type=fastq_filetype_instance,
file_group=lims_filegroup_instance,
file_name="C-ABCDEF.R1.fastq",
path="/C-ABCDEF.R1.fastq")
tumor2_R1_filemetadata_instance = FileMetadata.objects.create(
file=tumor2_R1_file_instance,
metadata={
"R": "R1",
"sex": "F",
"runId": "PITT_0439",
"recipe": "IMPACT468",
"baitSet": "IMPACT468_BAITS",
"species": "Human",
"sampleId": "Sample12345",
"libraryId": None,
"flowCellId": "HFTCNBBXY",
"barcodeId": "DUAL_IDT_LIB_267",
"barcodeIndex": "GTATTGGC-TTGTCGGT",
"runDate": "2019-12-17",
"patientId": "C-ABCDEF",
"requestId": "10075_D_3",
"sequencingCenter": "MSKCC",
"platform": "Illumina",
"sampleName": "C-ABCDEF-R001-d",
"igocomplete": True,
"oncoTreeCode": "MEL",
"preservation": "Frozen",
"sampleOrigin": "Tissue",
"specimenType": "Resection",
"tumorOrNormal": "Tumor",
"cmoSampleClass": "Local Recurrence",
"externalSampleId": "SK_MEL_1234_T",
"investigatorSampleId": "SK_MEL_1234_T",
"labHeadEmail": "",
"labHeadName": ""
})
tumor2_R2_file_instance = File.objects.create(
file_type=fastq_filetype_instance,
file_group=lims_filegroup_instance,
file_name="C-ABCDEF.R2.fastq",
path="/C-ABCDEF.R2.fastq")
tumor2_R2_filemetadata_instance = FileMetadata.objects.create(
file=tumor2_R2_file_instance,
metadata={
"R": "R2",
"sex": "F",
"runId": "PITT_0439",
"recipe": "IMPACT468",
"baitSet": "IMPACT468_BAITS",
"species": "Human",
"sampleId": "Sample12345",
"libraryId": None,
"flowCellId": "HFTCNBBXY",
"barcodeId": "DUAL_IDT_LIB_267",
"barcodeIndex": "GTATTGGC-TTGTCGGT",
"runDate": "2019-12-17",
"patientId": "C-ABCDEF",
"requestId": "10075_D_3",
"sequencingCenter": "MSKCC",
"platform": "Illumina",
"sampleName": "C-ABCDEF-R001-d",
"igocomplete": True,
"oncoTreeCode": "MEL",
"preservation": "Frozen",
"sampleOrigin": "Tissue",
"specimenType": "Resection",
"tumorOrNormal": "Tumor",
"cmoSampleClass": "Local Recurrence",
"externalSampleId": "SK_MEL_1234_T",
"investigatorSampleId": "SK_MEL_1234_T",
"labHeadEmail": "",
"labHeadName": ""
})
samples = [{
"bait_set": "IMPACT468_BAITS",
"patient_id": "C-8VK0V7",
"tumor_type": "Tumor",
"sample_id": "10075_D_3_5",
"SM": "10075_D_3_5",
"request_id": "10075_D_3",
'run_id': ['PITT_0439'],
"preservation_type": ["Frozen"]
}]
# test that no pairs are found since there are no Normals loaded yet
pairs = compile_pairs(samples)
self.assertDictEqual(pairs, {'tumor': [], 'normal': []})
# add Pooled Normal from another run
poolednormal_R1_file_instance = File.objects.create(
file_type=fastq_filetype_instance,
file_group=poolednormal_filegroup_instance,
file_name="FROZENPOOLEDNORMAL.R1.fastq",
path="/FROZENPOOLEDNORMAL.R1.fastq")
poolednormal_R1_filemetadata_instance = FileMetadata.objects.create(
file=poolednormal_R1_file_instance,
metadata={
"runId": "PITT_0439",
"recipe": "IMPACT468",
'bait_set': 'IMPACT468_BAITS',
"sequencingCenter": "MSKCC",
"platform": "Illumina",
"preservation": "Frozen"
})
poolednormal_R2_file_instance = File.objects.create(
file_type=fastq_filetype_instance,
file_group=poolednormal_filegroup_instance,
file_name="FROZENPOOLEDNORMAL.R2.fastq",
path="/FROZENPOOLEDNORMAL.R2.fastq")
poolednormal_R2_filemetadata_instance = FileMetadata.objects.create(
file=poolednormal_R2_file_instance,
metadata={
"runId": "PITT_0439",
"recipe": "IMPACT468",
'bait_set': 'IMPACT468_BAITS',
"sequencingCenter": "MSKCC",
"platform": "Illumina",
"preservation": "Frozen"
})
pairs = compile_pairs(samples)
# remove the R1_bid and R2_bid for testing because they are non-deterministic
# TODO: mock this ^^
pairs['normal'][0]['R1_bid'].pop()
pairs['normal'][0]['R2_bid'].pop()
expected_pairs = {
'tumor': [{
'bait_set': 'IMPACT468_BAITS',
'patient_id': 'C-8VK0V7',
'tumor_type': 'Tumor',
'sample_id': '10075_D_3_5',
'SM': '10075_D_3_5',
'request_id': '10075_D_3',
'run_id': ['PITT_0439'],
'preservation_type': ['Frozen']
}],
'normal': [{
'CN':
'MSKCC',
'PL':
'Illumina',
'PU': ['PN_FCID_FROZENPOOLEDNORMAL'],
'LB':
'FROZENPOOLEDNORMAL_PITT_0439_1',
'tumor_type':
'Normal',
'ID':
['FROZENPOOLEDNORMAL_PITT_0439_PN_FCID_FROZENPOOLEDNORMAL'],
'SM':
'FROZENPOOLEDNORMAL_PITT_0439',
'species':
'',
'patient_id':
'PN_PATIENT_ID',
'bait_set':
'IMPACT468',
'sample_id':
'FROZENPOOLEDNORMAL_PITT_0439',
'run_date': [''],
'specimen_type':
'',
'R1': ['/FROZENPOOLEDNORMAL.R1.fastq'],
'R2': ['/FROZENPOOLEDNORMAL.R2.fastq'],
'R1_bid': [], # UUID('cf065d86-3096-47b3-9b6f-cf711a1d6e0f')
'R2_bid': [], # UUID('51232bdd-6b31-4a4d-80c4-3aef13965fcd')
'bam': [],
'bam_bid': [],
'specimen_type':
'Pooled Normal',
'request_id':
'FROZENPOOLEDNORMAL_PITT_0439',
'pi':
'',
'pi_email':
'',
'run_id': [''],
'preservation_type': [['Frozen']]
}]
}
print(
"Running test_compile_pairs_pooled_normal_and_dmp_bam (pn part): pairs ---\n",
json.dumps(pairs, cls=UUIDEncoder))
print(
"Running test_compile_pairs_pooled_normal_and_dmp_bam (pn part): expected ---\n",
json.dumps(expected_pairs, cls=UUIDEncoder))
self.assertDictEqual(pairs, expected_pairs)
# Add a DMP Bam for the tumor sample to the database
dmp_bam_file_instance = File.objects.create(
file_type=bam_filetype_instance,
file_group=dmp_bam_filegroup_instance,
file_name="C-8VK0V7.bam",
path="/C-8VK0V7.bam")
dmp_bam_filemetadata_instance = FileMetadata.objects.create(
file=dmp_bam_file_instance,
version=1,
metadata={
"bai": "/C-8VK0V7.bai",
"bam": "/C-8VK0V7.bam",
"type": "N",
"assay": "IM6",
"sample": "P-1234567-N01-IM6",
"anon_id": "ABCDEF-N",
"patient": {
"cmo": "8VK0V7",
"dmp": "P-1234567",
"updated": "2020-03-19T23:57:51.941963Z",
"imported": "2020-03-19T23:57:51.941945Z"
},
"updated": "2020-03-25T19:45:16.421154Z",
"sequencingCenter": "MSKCC",
"platform": "Illumina",
"version": 1,
"coverage": 648,
"imported": "2020-03-25T19:45:16.421137Z",
"cmo_assay": "IMPACT468",
"tumor_type": "MBC",
"external_id": "C-8VK0V7-N901-dZ-IM6",
"sample_type": "0",
"tissue_type": "Breast",
"primary_site": "Breast",
"project_name": "UK12344567890VB",
"patient_group": "Group_12344567890",
"part_c_consent": 1,
"metastasis_site": "Not Applicable",
"somatic_calling_status": "Matched",
"major_allele_contamination": 0.452,
"minor_allele_contamination": 0.00069
})
# test that the DMP bam gets chosen as the sample's matched normal now instead of the pooled normal
pairs = compile_pairs(samples)
expected_pairs = {
'tumor': [{
'bait_set': 'IMPACT468_BAITS',
'patient_id': 'C-8VK0V7',
'tumor_type': 'Tumor',
'sample_id': '10075_D_3_5',
'SM': '10075_D_3_5',
'request_id': '10075_D_3',
'run_id': ['PITT_0439'],
'preservation_type': ['Frozen']
}],
'normal': [{
'CN': 'MSKCC',
'PL': 'Illumina',
'PU': ['DMP_FCID_DMP_BARCODEIDX'],
'LB': 'C-8VK0V7-N901-dZ-IM6_1',
'tumor_type': 'Normal',
'ID': ['s_C_8VK0V7_N901_dZ_IM6_DMP_FCID_DMP_BARCODEIDX'],
'SM': 's_C_8VK0V7_N901_dZ_IM6',
'species': '',
'patient_id': 'C-8VK0V7',
'bait_set': 'IMPACT468_BAITS',
'sample_id': 'C-8VK0V7-N901-dZ-IM6',
'run_date': [''],
'specimen_type': 'DMP Normal',
'R1': [],
'R2': [],
'R1_bid': [],
'R2_bid': [],
'bam': ['/C-8VK0V7.bam'],
'bam_bid': [], # UUID('77b9a78f-1bed-475c-9799-c18a6f57b347')
'request_id': 'C-8VK0V7-N901-dZ-IM6',
'pi': '',
'pi_email': '',
'run_id': [''],
'preservation_type': ['']
}]
}
# remove the bam_bid for testing because it is non-deterministic
# TODO: mock this ^^
pairs['normal'][0]['bam_bid'].pop()
print(
"Running test_compile_pairs_pooled_normal_and_dmp_bam (dmp part): pairs ---\n",
json.dumps(pairs, cls=UUIDEncoder))
print(
"Running test_compile_pairs_pooled_normal_and_dmp_bam (dmp part): expected ---\n",
json.dumps(expected_pairs, cls=UUIDEncoder))
self.assertDictEqual(pairs, expected_pairs)
# Now add a matched normal to the original request for the sample
# Sample 1 C-8VK0V7
normal1_R1_file_instance = File.objects.create(
file_type=fastq_filetype_instance,
file_group=lims_filegroup_instance,
file_name="C-8VK0V7-N.R1.fastq",
path="/C-8VK0V7-N.R1.fastq")
normal1_R1_filemetadata_instance = FileMetadata.objects.create(
file=normal1_R1_file_instance,
metadata={
"R": "R1",
"sex": "F",
"runId": "PITT_0439",
"recipe": "IMPACT468",
"baitSet": "IMPACT468_BAITS",
"species": "Human",
"sampleId": "10075_D_2_3",
"libraryId": None,
"flowCellId": "HFTCNBBXY",
"barcodeId": "DUAL_IDT_LIB_267",
"barcodeIndex": "GTATTGGC-TTGTCGGT",
"runDate": "2019-12-17",
"patientId": "C-8VK0V7",
"requestId": "10075_D_3",
"sequencingCenter": "MSKCC",
"platform": "Illumina",
"sampleName": "C-8VK0V7-N001-d",
"igocomplete": True,
"oncoTreeCode": "MEL",
"preservation": "Frozen",
"sampleOrigin": "Tissue",
"specimenType": "Resection",
"tumorOrNormal": "Normal",
"cmoSampleClass": "Normal",
"externalSampleId": "SK_MEL_1091A_N",
"investigatorSampleId": "SK_MEL_1091A_N",
"labHeadEmail": "",
"labHeadName": ""
})
normal1_R2_file_instance = File.objects.create(
file_type=fastq_filetype_instance,
file_group=lims_filegroup_instance,
file_name="C-8VK0V7-N.R2.fastq",
path="/C-8VK0V7-N.R2.fastq")
normal1_R2_filemetadata_instance = FileMetadata.objects.create(
file=normal1_R2_file_instance,
metadata={
"R": "R2",
"sex": "F",
"runId": "PITT_0439",
"recipe": "IMPACT468",
"baitSet": "IMPACT468_BAITS",
"species": "Human",
"sampleId": "10075_D_2_3",
"libraryId": None,
"flowCellId": "HFTCNBBXY",
"barcodeId": "DUAL_IDT_LIB_267",
"barcodeIndex": "GTATTGGC-TTGTCGGT",
"runDate": "2019-12-17",
"patientId": "C-8VK0V7",
"requestId": "10075_D_3",
"sequencingCenter": "MSKCC",
"platform": "Illumina",
"sampleName": "C-8VK0V7-N001-d",
"igocomplete": True,
"oncoTreeCode": "MEL",
"preservation": "Frozen",
"sampleOrigin": "Tissue",
"specimenType": "Resection",
"tumorOrNormal": "Normal",
"cmoSampleClass": "Normal",
"externalSampleId": "SK_MEL_1091A_N",
"investigatorSampleId": "SK_MEL_1091A_N",
"labHeadEmail": "",
"labHeadName": ""
})
# test that the paired normal from the same request gets chosen instead for the pairing
pairs = compile_pairs(samples)
# remove the R1_bid and R2_bid for testing because they are non-deterministic
# TODO: mock this ^^
pairs['normal'][0]['R1_bid'].pop()
pairs['normal'][0]['R2_bid'].pop()
expected_pairs = {
'tumor': [{
'bait_set': 'IMPACT468_BAITS',
'patient_id': 'C-8VK0V7',
'tumor_type': 'Tumor',
'sample_id': '10075_D_3_5',
'SM': '10075_D_3_5',
'request_id': '10075_D_3',
'run_id': ['PITT_0439'],
'preservation_type': ['Frozen']
}],
'normal': [{
'CN': 'MSKCC',
'PL': 'Illumina',
'PU': ['HFTCNBBXY_GTATTGGC-TTGTCGGT'],
'LB': 's_C_8VK0V7_N001_d_1',
'tumor_type': 'Normal',
'ID': ['s_C_8VK0V7_N001_d_HFTCNBBXY_GTATTGGC-TTGTCGGT'],
'SM': 's_C_8VK0V7_N001_d',
'species': 'Human',
'patient_id': 'C-8VK0V7',
'bait_set': 'IMPACT468_BAITS',
'sample_id': '10075_D_2_3',
'run_date': ['2019-12-17'],
'specimen_type': 'Resection',
'R1': ['/C-8VK0V7-N.R1.fastq'],
'R2': ['/C-8VK0V7-N.R2.fastq'],
'R1_bid': [], # UUID('bfb94fe6-bf46-431a-8f72-6ee47ee72fc9')
'R2_bid': [], # UUID('1e8b68f8-c333-499c-b22d-50fbef2d2ea7')
'bam': [],
'bam_bid': [],
'request_id': '10075_D_3',
'pi': '',
'pi_email': '',
'run_id': ['PITT_0439'],
'preservation_type': ['Frozen']
}]
}
print(
"Running test_compile_pairs_pooled_normal_and_dmp_bam (third variation): pairs ---\n",
json.dumps(pairs, cls=UUIDEncoder))
print(
"Running test_compile_pairs_pooled_normal_and_dmp_bam (third variation): expected ---\n",
json.dumps(expected_pairs, cls=UUIDEncoder))
self.assertDictEqual(pairs, expected_pairs)
def test_get_most_recent_normal1(self):
"""
Test that when retreiving a normal from other requests, the most recent Normal is returned
in the event that a patient has several normals
Return the Normal with the most recent run_date
"""
call_command('loaddata',
os.path.join(settings.TEST_FIXTURE_DIR,
"10075_D_2.file.json"),
verbosity=0)
call_command('loaddata',
os.path.join(settings.TEST_FIXTURE_DIR,
"10075_D_2.filemetadata.json"),
verbosity=0)
call_command('loaddata',
os.path.join(settings.TEST_FIXTURE_DIR,
"10075_D_4.file.json"),
verbosity=0)
call_command('loaddata',
os.path.join(settings.TEST_FIXTURE_DIR,
"10075_D_4.filemetadata.json"),
verbosity=0)
# check the total number of db entries now
self.assertTrue(len(File.objects.all()) == 4)
self.assertTrue(len(FileMetadata.objects.all()) == 4)
samples = [{
"bait_set": "IMPACT468_BAITS",
"patient_id": "C-8VK0V7",
"tumor_type": "Tumor",
"sample_id": "10075_D_3_5",
"SM": "10075_D_3_5",
"request_id": "10075_D_3",
'run_id': ['JAX_0397'],
"preservation_type": ["EDTA-Streck"]
}]
pairs = compile_pairs(samples)
expected_pairs = {
'tumor': [{
'bait_set': 'IMPACT468_BAITS',
'patient_id': 'C-8VK0V7',
'tumor_type': 'Tumor',
'sample_id': '10075_D_3_5',
"SM": "10075_D_3_5",
'request_id': '10075_D_3',
'run_id': ['JAX_0397'],
"preservation_type": ["EDTA-Streck"]
}],
'normal': [{
'CN':
'MSKCC',
'PL':
'Illumina',
'PU': ['HCYYWBBXY'],
'LB':
'10075_D_4_3',
'tumor_type':
'Normal',
'ID': ['s_C_8VK0V7_N001_d_HCYYWBBXY'],
'SM':
's_C_8VK0V7_N001_d',
'species':
'Human',
'patient_id':
'C-8VK0V7',
'bait_set':
'IMPACT468_BAITS',
'sample_id':
'10075_D_4_3',
'run_date': ['2019-12-13'],
'specimen_type':
'Blood',
'R1': [
'/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D_4/Sample_JW_MEL_007_NORM_IGO_10075_D_4_3/JW_MEL_007_NORM_IGO_10075_D_4_3_S15_R1_001.fastq.gz'
],
'R2': [
'/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D_4/Sample_JW_MEL_007_NORM_IGO_10075_D_4_3/JW_MEL_007_NORM_IGO_10075_D_4_3_S15_R2_001.fastq.gz'
],
'R1_bid': [UUID('08072445-84ff-4b43-855d-d8d2dc87e2d5')],
'R2_bid': [UUID('f0d9a1e1-9414-42df-a749-08776732ee04')],
'bam': [],
'bam_bid': [],
'request_id':
'10075_D_4',
'run_id': ['JAX_0397'],
"preservation_type": ["EDTA-Streck"],
'pi':
'John Smith',
'pi_email':
'*****@*****.**'
}]
}
print("Running get_most_recent_normal1 ---")
print(json.dumps(pairs, cls=UUIDEncoder))
print(json.dumps(expected_pairs, cls=UUIDEncoder))
self.assertTrue(pairs == expected_pairs)
def test_get_pair_from_other_request(self):
"""
Test that you can get the correct Normal sample for a patient when the
Normal sample is part of another request
"""
# Load fixtures
# only normals
call_command('loaddata',
os.path.join(settings.TEST_FIXTURE_DIR,
"10075_D_2.file.json"),
verbosity=0)
call_command('loaddata',
os.path.join(settings.TEST_FIXTURE_DIR,
"10075_D_2.filemetadata.json"),
verbosity=0)
# only tumors
call_command('loaddata',
os.path.join(settings.TEST_FIXTURE_DIR,
"10075_D_3.file.json"),
verbosity=0)
call_command('loaddata',
os.path.join(settings.TEST_FIXTURE_DIR,
"10075_D_3.filemetadata.json"),
verbosity=0)
# check the total number of db entries now
self.assertTrue(len(File.objects.all()) == 4)
self.assertTrue(len(FileMetadata.objects.all()) == 4)
samples = [{
"bait_set": "IMPACT468_BAITS",
"patient_id": "C-8VK0V7",
"tumor_type": "Tumor",
'run_id': ['JAX_0397'],
"preservation_type": ["EDTA-Streck"],
"sample_id": "10075_D_3_5",
"SM": "10075_D_3_5",
"request_id": "10075_D_3"
}]
pairs = compile_pairs(samples)
expected_pairs = {
'tumor': [{
'bait_set': 'IMPACT468_BAITS',
'patient_id': 'C-8VK0V7',
'run_id': ['JAX_0397'],
"preservation_type": ["EDTA-Streck"],
'tumor_type': 'Tumor',
'sample_id': '10075_D_3_5',
"SM": "10075_D_3_5",
'request_id': '10075_D_3'
}],
'normal': [{
'CN':
'MSKCC',
'PL':
'Illumina',
'PU': ['HCYYWBBXY'],
'LB':
'10075_D_2_3',
'tumor_type':
'Normal',
'ID': ['s_C_8VK0V7_N001_d_HCYYWBBXY'],
'SM':
's_C_8VK0V7_N001_d',
'species':
'Human',
'patient_id':
'C-8VK0V7',
'bait_set':
'IMPACT468_BAITS',
'sample_id':
'10075_D_2_3',
'run_date': ['2019-12-12'],
'specimen_type':
'Blood',
'R1': [
'/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D_2/Sample_JW_MEL_007_NORM_IGO_10075_D_2_3/JW_MEL_007_NORM_IGO_10075_D_2_3_S15_R1_001.fastq.gz'
],
'R2': [
'/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D_2/Sample_JW_MEL_007_NORM_IGO_10075_D_2_3/JW_MEL_007_NORM_IGO_10075_D_2_3_S15_R2_001.fastq.gz'
],
'R1_bid': [UUID('a46c5e6b-0793-4cd2-b5dd-92b3d71cf1ac')],
'R2_bid': [UUID('c71c259a-ebc0-4490-9af1-bc99387a70d7')],
'bam': [],
'bam_bid': [],
'request_id':
'10075_D_2',
'run_id': ['JAX_0397'],
"preservation_type": ["EDTA-Streck"],
'pi':
'John Smith',
'pi_email':
'*****@*****.**'
}]
}
print("Running get_pair_from_other_request ---")
print(json.dumps(pairs, cls=UUIDEncoder))
print(json.dumps(expected_pairs, cls=UUIDEncoder))
self.assertTrue(pairs == expected_pairs)
def test_compile_pairs5(self):
"""
Test pairing with a single unpaired tumor sample
Test that the correct Normal sample is found from within the same request
This time also load File entries from another request to make sure they do not confound the pairing
"""
# Load fixtures
call_command('loaddata',
os.path.join(settings.TEST_FIXTURE_DIR,
"10075_D.file.json"),
verbosity=0)
call_command('loaddata',
os.path.join(settings.TEST_FIXTURE_DIR,
"10075_D.filemetadata.json"),
verbosity=0)
call_command('loaddata',
os.path.join(settings.TEST_FIXTURE_DIR,
"05257_CB.file.json"),
verbosity=0)
call_command('loaddata',
os.path.join(settings.TEST_FIXTURE_DIR,
"05257_CB.filemetadata.json"),
verbosity=0)
# check the total number of db entries now
self.assertTrue(len(File.objects.all()) == 14)
self.assertTrue(len(FileMetadata.objects.all()) == 18)
samples = [{
"bait_set": "IMPACT468_BAITS",
"patient_id": "C-DRKHP7",
"tumor_type": "Tumor",
'run_id': ['JAX_0397'],
"preservation_type": ["Frozen"],
"SM": "10075_D_1",
"sample_id": "10075_D_1"
}]
pairs = compile_pairs(samples)
expected_pairs = {
'normal': [{
'CN':
'MSKCC',
'ID': ['s_C_DRKHP7_N001_d_HCYYWBBXY'],
'LB':
'10075_D_2',
'PL':
'Illumina',
'PU': ['HCYYWBBXY'],
'R1': [
'/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D/Sample_31-N_IGO_10075_D_2/31-N_IGO_10075_D_2_S14_R1_001.fastq.gz'
],
'R1_bid': [UUID('40a07e9a-2198-40b7-9f7f-7696c9d6429e')],
'R2': [
'/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D/Sample_31-N_IGO_10075_D_2/31-N_IGO_10075_D_2_S14_R2_001.fastq.gz'
],
'R2_bid': [UUID('bb7ff922-b741-4df7-ba2a-4f3b8549e8b5')],
'bam': [],
'bam_bid': [],
'SM':
's_C_DRKHP7_N001_d',
'bait_set':
'IMPACT468_BAITS',
'sample_id':
'10075_D_2',
'patient_id':
'C-DRKHP7',
'request_id':
'10075_D',
'run_id': ['JAX_0397'],
"preservation_type": ["Frozen"],
'run_date': ['2019-12-12'],
'species':
'Human',
'specimen_type':
'Blood',
'tumor_type':
'Normal',
'pi':
'John Smith',
'pi_email':
'*****@*****.**'
}],
'tumor': [{
'bait_set': 'IMPACT468_BAITS',
'sample_id': '10075_D_1',
'SM': '10075_D_1',
'patient_id': 'C-DRKHP7',
'run_id': ['JAX_0397'],
"preservation_type": ["Frozen"],
'tumor_type': 'Tumor'
}]
}
print("Running test_compile_pairs5 ----")
print(json.dumps(pairs, cls=UUIDEncoder))
print(json.dumps(expected_pairs, cls=UUIDEncoder))
self.assertTrue(pairs == expected_pairs)
def test_compile_pairs4(self):
"""
Test pairing with only a single unpaired Tumor sample
Test that the appropriate Normal sample is found from the other samples in the same request
missing normal for sample 10075_D_1; querying patient C-DRKHP7
"""
# Load fixtures:
test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR,
"10075_D.file.json")
call_command('loaddata', test_files_fixture, verbosity=0)
test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR,
"10075_D.filemetadata.json")
call_command('loaddata', test_files_fixture, verbosity=0)
samples = [{
"bait_set": "IMPACT468_BAITS",
"patient_id": "C-DRKHP7",
"run_id": ["JAX_0397"],
"preservation_type": ["Frozen"],
"tumor_type": "Tumor",
"SM": "10075_D_1",
"sample_id": "10075_D_1"
}]
pairs = compile_pairs(samples)
expected_pairs = {
'normal': [{
'CN':
'MSKCC',
'ID': ['s_C_DRKHP7_N001_d_HCYYWBBXY'],
'LB':
'10075_D_2',
'PL':
'Illumina',
'PU': ['HCYYWBBXY'],
'R1': [
'/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D/Sample_31-N_IGO_10075_D_2/31-N_IGO_10075_D_2_S14_R1_001.fastq.gz'
],
'R1_bid': [UUID('40a07e9a-2198-40b7-9f7f-7696c9d6429e')],
'R2': [
'/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D/Sample_31-N_IGO_10075_D_2/31-N_IGO_10075_D_2_S14_R2_001.fastq.gz'
],
'R2_bid': [UUID('bb7ff922-b741-4df7-ba2a-4f3b8549e8b5')],
'bam': [],
'bam_bid': [],
'SM':
's_C_DRKHP7_N001_d',
'bait_set':
'IMPACT468_BAITS',
'sample_id':
'10075_D_2',
'patient_id':
'C-DRKHP7',
'request_id':
'10075_D',
'run_id': ['JAX_0397'],
"preservation_type": ["Frozen"],
'run_date': ['2019-12-12'],
'species':
'Human',
'specimen_type':
'Blood',
'tumor_type':
'Normal',
'pi':
'John Smith',
'pi_email':
'*****@*****.**'
}],
'tumor': [{
'bait_set': 'IMPACT468_BAITS',
'sample_id': '10075_D_1',
'SM': '10075_D_1',
'patient_id': 'C-DRKHP7',
"run_id": ["JAX_0397"],
"preservation_type": ["Frozen"],
'tumor_type': 'Tumor'
}]
}
print("Running test_compile_pairs4 ----")
print(json.dumps(pairs, cls=UUIDEncoder))
print(json.dumps(expected_pairs, cls=UUIDEncoder))
self.assertTrue(pairs == expected_pairs)
def test_compile_pairs2(self):
"""
Test pairing with multiple samples in a request
"""
samples = [{
"bait_set": "IMPACT468_BAITS",
"patient_id": "C-DRKHP7",
"run_id": ["JAX_0397"],
"preservation_type": ["Frozen"],
"tumor_type": "Normal",
"SM": "my_sample_id1",
"sample_id": "my_sample_id1"
}, {
"bait_set": "IMPACT468_BAITS",
"patient_id": "C-8VK0V7",
"run_id": ["JAX_0397"],
"preservation_type": ["Frozen"],
"tumor_type": "Normal",
"SM": "my_sample_id2",
"sample_id": "my_sample_id2"
}, {
"bait_set": "IMPACT468_BAITS",
"patient_id": "C-DRKHP7",
"run_id": ["JAX_0397"],
"preservation_type": ["Frozen"],
"tumor_type": "Tumor",
"SM": "my_sample_id3",
"sample_id": "my_sample_id3"
}, {
"bait_set": "IMPACT468_BAITS",
"patient_id": "C-8VK0V7",
"run_id": ["JAX_0397"],
"preservation_type": ["Frozen"],
"tumor_type": "Tumor",
"SM": "my_sample_id4",
"sample_id": "my_sample_id4"
}, {
"bait_set": "IMPACT468_BAITS",
"patient_id": "C-DRKHP7",
"run_id": ["JAX_0397"],
"preservation_type": ["Frozen"],
"tumor_type": "Tumor",
"SM": "my_sample_id5",
"sample_id": "my_sample_id5"
}]
pairs = compile_pairs(samples)
expected_pairs = {
'tumor': [{
'bait_set': 'IMPACT468_BAITS',
'patient_id': 'C-DRKHP7',
'tumor_type': 'Tumor',
"run_id": ["JAX_0397"],
"preservation_type": ["Frozen"],
"sample_id": "my_sample_id3",
"SM": "my_sample_id3"
}, {
'bait_set': 'IMPACT468_BAITS',
'patient_id': 'C-8VK0V7',
'tumor_type': 'Tumor',
"run_id": ["JAX_0397"],
"preservation_type": ["Frozen"],
"sample_id": "my_sample_id4",
"SM": "my_sample_id4"
}, {
'bait_set': 'IMPACT468_BAITS',
'patient_id': 'C-DRKHP7',
'tumor_type': 'Tumor',
"run_id": ["JAX_0397"],
"preservation_type": ["Frozen"],
"sample_id": "my_sample_id5",
"SM": "my_sample_id5"
}],
'normal': [{
'bait_set': 'IMPACT468_BAITS',
'patient_id': 'C-DRKHP7',
'tumor_type': 'Normal',
"run_id": ["JAX_0397"],
"preservation_type": ["Frozen"],
"sample_id": "my_sample_id1",
"SM": "my_sample_id1"
}, {
'bait_set': 'IMPACT468_BAITS',
'patient_id': 'C-8VK0V7',
'tumor_type': 'Normal',
"run_id": ["JAX_0397"],
"preservation_type": ["Frozen"],
"sample_id": "my_sample_id2",
"SM": "my_sample_id2"
}, {
'bait_set': 'IMPACT468_BAITS',
'patient_id': 'C-DRKHP7',
'tumor_type': 'Normal',
"run_id": ["JAX_0397"],
"preservation_type": ["Frozen"],
"sample_id": "my_sample_id1",
"SM": "my_sample_id1"
}]
}
print("Running test_compile_pairs2 ---")
print(json.dumps(pairs, cls=UUIDEncoder))
print(json.dumps(expected_pairs, cls=UUIDEncoder))
self.assertTrue(pairs == expected_pairs)
def test_compile_pairs_custom1(self):
"""
Test the ability to compile pairs with a custom sample set
TODO: what pair attributes is this testing?
"""
samples = [{
'CN':
'MSKCC',
'ID': ['s_juno_argos_demo1_3_HCYYWBBXY'],
'LB':
'juno_argos_demo1_3',
'PL':
'Illumina',
'PU': ['HCYYWBBXY'],
'R1': [
'/juno/work/ci/argos-test/data/fastq/DU874145-N/DU874145-N_IGO_00000_TEST_L001_R1_001.fastq.gz'
],
'R1_bid': [UUID('a46c5e6b-0793-4cd2-b5dd-92b3d71cf1ac')],
'R2': [
'/juno/work/ci/argos-test/data/fastq/DU874145-N/DU874145-N_IGO_00000_TEST_L001_R2_001.fastq.gz'
],
'R2_bid': [UUID('c71c259a-ebc0-4490-9af1-bc99387a70d7')],
'bam': [],
'bam_bid': [],
'SM':
's_juno_argos_demo1_3',
'bait_set':
'IMPACT468_BAITS',
'sample_id':
's_juno_argos_demo1_3',
'patient_id':
'DU874145',
'request_id':
'juno_argos_demo1',
'run_id': ['JAX_0397'],
"preservation_type": ["EDTA-Streck"],
'run_date': ['2019-12-12'],
'species':
'Human',
'specimen_type':
'Blood',
'tumor_type':
'Normal'
}, {
'CN':
'MSKCC',
'ID': ['s_juno_argos_demo1_5_HFTCNBBXY_GTATTGGC-TTGTCGGT'],
'LB':
'juno_argos_demo1_5_1_1_1',
'PL':
'Illumina',
'PU': ['HFTCNBBXY_GTATTGGC-TTGTCGGT'],
'R1': [
'/juno/work/ci/argos-test/data/fastq/DU874145-T/DU874145-T_IGO_00000_TEST_L001_R1_001.fastq.gz'
],
'R1_bid': [UUID('d2d8ed36-d8f4-4e93-b038-d38328fad021')],
'R2': [
'/juno/work/ci/argos-test/data/fastq/DU874145-T/DU874145-T_IGO_00000_TEST_L001_R2_001.fastq.gz'
],
'R2_bid': [UUID('2f77f3ac-ab25-4a02-90bd-86542401ac89')],
'bam': [],
'bam_bid': [],
'SM':
's_juno_argos_demo1_5',
'bait_set':
'IMPACT468_BAITS',
'sample_id':
's_juno_argos_demo1_5',
'patient_id':
'DU874145',
'request_id':
'juno_argos_demo1',
'run_id': ['JAX_0397'],
"preservation_type": ["EDTA-Streck"],
'run_date': ['2019-12-17'],
'species':
'Human',
'specimen_type':
'Resection',
'tumor_type':
'Tumor'
}]
pairs = compile_pairs(samples)
expected_pairs = {
'tumor': [{
'CN':
'MSKCC',
'ID': ['s_juno_argos_demo1_5_HFTCNBBXY_GTATTGGC-TTGTCGGT'],
'LB':
'juno_argos_demo1_5_1_1_1',
'PL':
'Illumina',
'PU': ['HFTCNBBXY_GTATTGGC-TTGTCGGT'],
'R1': [
'/juno/work/ci/argos-test/data/fastq/DU874145-T/DU874145-T_IGO_00000_TEST_L001_R1_001.fastq.gz'
],
'R1_bid': [UUID('d2d8ed36-d8f4-4e93-b038-d38328fad021')],
'R2': [
'/juno/work/ci/argos-test/data/fastq/DU874145-T/DU874145-T_IGO_00000_TEST_L001_R2_001.fastq.gz'
],
'R2_bid': [UUID('2f77f3ac-ab25-4a02-90bd-86542401ac89')],
'SM':
's_juno_argos_demo1_5',
'bait_set':
'IMPACT468_BAITS',
'sample_id':
's_juno_argos_demo1_5',
'patient_id':
'DU874145',
'request_id':
'juno_argos_demo1',
'run_id': ['JAX_0397'],
'run_date': ['2019-12-17'],
'species':
'Human',
'specimen_type':
'Resection',
'tumor_type':
'Tumor',
"preservation_type": ["EDTA-Streck"],
'bam': [],
'bam_bid': []
}],
'normal': [{
'CN':
'MSKCC',
'ID': ['s_juno_argos_demo1_3_HCYYWBBXY'],
'LB':
'juno_argos_demo1_3',
'PL':
'Illumina',
'PU': ['HCYYWBBXY'],
'R1': [
'/juno/work/ci/argos-test/data/fastq/DU874145-N/DU874145-N_IGO_00000_TEST_L001_R1_001.fastq.gz'
],
'R1_bid': [UUID('a46c5e6b-0793-4cd2-b5dd-92b3d71cf1ac')],
'R2': [
'/juno/work/ci/argos-test/data/fastq/DU874145-N/DU874145-N_IGO_00000_TEST_L001_R2_001.fastq.gz'
],
'R2_bid': [UUID('c71c259a-ebc0-4490-9af1-bc99387a70d7')],
'SM':
's_juno_argos_demo1_3',
'bait_set':
'IMPACT468_BAITS',
'sample_id':
's_juno_argos_demo1_3',
'patient_id':
'DU874145',
'request_id':
'juno_argos_demo1',
'run_id': ['JAX_0397'],
'run_date': ['2019-12-12'],
'species':
'Human',
'specimen_type':
'Blood',
'tumor_type':
'Normal',
"preservation_type": ["EDTA-Streck"],
'bam': [],
'bam_bid': []
}]
}
print("Running test_compile_pairs_custom1 ----")
print(json.dumps(pairs, cls=UUIDEncoder))
print(json.dumps(expected_pairs, cls=UUIDEncoder))
self.assertTrue(pairs == expected_pairs)