def setUp(self):
key = "ConversionResults"
qc_config = {'name': 'UndeterminedPercentageHandler', 'error': 10, 'warning': 20}
value = get_stats_json()["ConversionResults"]
undetermined_handler = UndeterminedPercentageHandler(qc_config)
undetermined_handler.collect((key, value))
self.undetermined_handler = undetermined_handler
def test_no_yield(self):
key = "ConversionResults"
value = get_stats_json()["ConversionResults"]
value[0]["Yield"] = 0
self.undetermined_handler.collect((key, value))
errors_and_warnings = list(self.undetermined_handler.check_qc())
class_names = self.map_errors_and_warnings_to_class_names(errors_and_warnings)
self.assertListEqual(class_names, ['QCErrorFatal'])
def setUp(self):
key = "ConversionResults"
qc_config = {
'name': 'TotalClustersPF',
'error': '50',
'warning': '110'
}
value = get_stats_json()["ConversionResults"]
cluster_pf_handler = ClusterPFHandler(qc_config)
cluster_pf_handler.collect((key, value))
self.cluster_pf_handler = cluster_pf_handler
def setUp(self):
key = "ConversionResults"
qc_config = {
'name': 'ReadsPerSampleHandler',
'error': 'unknown',
'warning': '90'
}
value = get_stats_json()["ConversionResults"]
reads_per_sample_handler = ReadsPerSampleHandler(qc_config)
reads_per_sample_handler.collect((key, value))
self.reads_per_sample_handler = reads_per_sample_handler
def setUp(self):
qc_config = {
'name': 'UnidentifiedIndexHandler',
'significance_threshold': 1,
'white_listed_indexes': ['.*N.*', 'G{8,}']
}
self.unidentifiedIndexHandler = UnidentifiedIndexHandler(qc_config)
conversion_results_key = "ConversionResults"
conversion_results = get_stats_json()["ConversionResults"]
samplesheet_key = "samplesheet"
self.samplesheet = SampleSheet()
sample_1 = Sample(
dict(Lane=1,
Sample_ID='1823A',
Sample_Name='1823A-tissue',
index='AAAA'))
sample_2 = Sample(
dict(Lane=2,
Sample_ID='1823B',
Sample_Name='1823B-tissue',
index='TTTT'))
sample_3 = Sample(
dict(Lane=3,
Sample_ID='1823C',
Sample_Name='1823C-tissue',
index='AAAA',
index2='TTTT'))
sample_4 = Sample(
dict(Lane=4,
Sample_ID='1823D',
Sample_Name='1823D-tissue',
index='GGGG',
index2='CCCC'))
sample_5 = Sample(
dict(Lane=6,
Sample_ID='1823E',
Sample_Name='1823D-tissue',
index='ATCG'))
self.samplesheet.add_sample(sample_1)
self.samplesheet.add_sample(sample_2)
self.samplesheet.add_sample(sample_3)
self.samplesheet.add_sample(sample_4)
self.samplesheet.add_sample(sample_5)
self.unidentifiedIndexHandler.collect(
(conversion_results_key, conversion_results))
self.unidentifiedIndexHandler.collect(
(samplesheet_key, self.samplesheet))
self.samplesheet_searcher = _SamplesheetSearcher(self.samplesheet)
def setUp(self):
conversion_key = "ConversionResults"
qc_config = {
'name': 'UndeterminedPercentageHandler',
'error': 10,
'warning': 20
}
conversion_results_value = get_stats_json()["ConversionResults"]
undetermined_handler = UndeterminedPercentageHandler(qc_config)
undetermined_handler.collect(
(conversion_key, conversion_results_value))
percentage_phix_key = "percent_phix"
percentage_phix_value_lane_1_read_1 = {
"lane": 1,
"read": 1,
"percent_phix": 1
}
percentage_phix_value_lane_1_read_2 = {
"lane": 1,
"read": 2,
"percent_phix": 1
}
percentage_phix_value_lane_2_read_1 = {
"lane": 2,
"read": 1,
"percent_phix": 1
}
percentage_phix_value_lane_2_read_2 = {
"lane": 2,
"read": 2,
"percent_phix": 1
}
undetermined_handler.collect(
(percentage_phix_key, percentage_phix_value_lane_1_read_1))
undetermined_handler.collect(
(percentage_phix_key, percentage_phix_value_lane_1_read_2))
undetermined_handler.collect(
(percentage_phix_key, percentage_phix_value_lane_2_read_1))
undetermined_handler.collect(
(percentage_phix_key, percentage_phix_value_lane_2_read_2))
self.undetermined_handler = undetermined_handler
def test_multiple_sampleIDs_per_sampleName(self):
key = "ConversionResults"
qc_config = {
'name': 'ReadsPerSampleHandler',
'error': 'unknown',
'warning': '1000'
}
value = get_stats_json(
"180925_A00001_0001_BABCDEFGXX")["ConversionResults"]
custom_reads_per_sample_handler = ReadsPerSampleHandler(qc_config)
custom_reads_per_sample_handler.collect((key, value))
errors_and_warnings = list(custom_reads_per_sample_handler.check_qc())
self.assertEqual(len(errors_and_warnings), 4)
class_names = self.map_errors_and_warnings_to_class_names(
errors_and_warnings)
self.assertListEqual(class_names, [
'QCErrorWarning', 'QCErrorWarning', 'QCErrorWarning',
'QCErrorWarning'
])