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monikaBrandtmonikaBrandt
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Merge pull request #24 from MatildaAslin/reads_per_sample_handler
Reads per sample handler
2 parents 7839c13 + 4f604fd commit 813b484

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‎checkQC/default_config/config.yaml

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@@ -30,6 +30,9 @@ hiseq2500_rapidhighoutput_v4:
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- name: ErrorRateHandler
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warning: 1.5
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error: unknown
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- name: ReadsPerSampleHandler
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warning: 90 # 50 % of threshold for clusters pass filter
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error: unknown
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100-110:
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handlers:
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- name: ClusterPFHandler
@@ -41,6 +44,9 @@ hiseq2500_rapidhighoutput_v4:
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- name: ErrorRateHandler
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warning: 2
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error: unknown
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- name: ReadsPerSampleHandler
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warning: 90 # 50 % of threshold for clusters pass filter
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error: unknown
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120-130:
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handlers:
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- name: ClusterPFHandler
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- name: ErrorRateHandler
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warning: 2
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error: unknown
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- name: ReadsPerSampleHandler
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warning: 90 # 50 % of threshold for clusters pass filter
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error: unknown
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hiseq2500_rapidrun_v2:
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50-70:
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- name: ErrorRateHandler
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warning: 1.5
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error: unknown
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- name: ReadsPerSampleHandler
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warning: 55 # 50 % of threshold for clusters pass filter
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error: unknown
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100-125:
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handlers:
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- name: ClusterPFHandler
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- name: ErrorRateHandler
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warning: 2
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error: unknown
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- name: ReadsPerSampleHandler
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warning: 55 # 50 % of threshold for clusters pass filter
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error: unknown
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handlers:
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- name: ClusterPFHandler
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- name: ErrorRateHandler
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warning: unknown
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error: 3
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- name: ReadsPerSampleHandler
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warning: 55 # 50 % of threshold for clusters pass filter
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error: unknown
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250-265:
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handlers:
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- name: ClusterPFHandler
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- name: ErrorRateHandler
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warning: 5
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error: unknown
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- name: ReadsPerSampleHandler
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warning: 55 # 50 % of threshold for clusters pass filter
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error: unknown
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hiseqx_v2:
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- name: ErrorRateHandler
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warning: 5
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error: unknown
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- name: ReadsPerSampleHandler
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warning: 200 # 50 % of threshold for clusters pass filter
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error: unknown
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# TODO These are not the real novaseq qc criteria, but they need to be determined
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# once we know what they are. /JD 2017-10-05
@@ -139,6 +163,9 @@ miseq_v2:
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- name: ErrorRateHandler
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warning: 1
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error: unknown
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- name: ReadsPerSampleHandler
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warning: 5 # 50 % of threshold for clusters pass filter
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error: unknown
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handlers:
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- name: ClusterPFHandler
@@ -150,6 +177,9 @@ miseq_v2:
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- name: ErrorRateHandler
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warning: 2
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error: uknown
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- name: ReadsPerSampleHandler
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warning: 5 # 50 % of threshold for clusters pass filter
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error: unknown
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handlers:
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- name: ClusterPFHandler
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- name: ErrorRateHandler
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warning: 5
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error: unknown
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- name: ReadsPerSampleHandler
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warning: 5 # 50 % of threshold for clusters pass filter
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error: unknown
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miseq_v3:
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@@ -174,6 +207,9 @@ miseq_v3:
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- name: ErrorRateHandler
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warning: 1.5
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error: unknown
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- name: ReadsPerSampleHandler
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warning: 9 # 50 % of threshold for clusters pass filter
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error: unknown
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handlers:
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- name: ClusterPFHandler
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- name: ErrorRateHandler
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warning: 5
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error: unknown
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- name: ReadsPerSampleHandler
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warning: 9 # 50 % of threshold for clusters pass filter
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error: unknown

‎checkQC/handlers/reads_per_sample_handler.py

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from checkQC.handlers.qc_handler import QCHandler, QCErrorFatal, QCErrorWarning
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from checkQC.parsers.stats_json_parser import StatsJsonParser
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from math import pow
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class ReadsPerSampleHandler(QCHandler):
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def __init__(self, *args, **kwargs):
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super().__init__(*args, **kwargs)
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self.conversion_results = None
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def parser(self):
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return StatsJsonParser
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def collect(self, signal):
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key, value = signal
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if key == "ConversionResults":
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self.conversion_results = value
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def check_qc(self):
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for lane_dict in self.conversion_results:
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lane_nbr = lane_dict["LaneNumber"]
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lane_demux = lane_dict["DemuxResults"]
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for sample_id_info in lane_demux:
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sample_id = sample_id_info["SampleId"]
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sample_total_reads = sample_id_info["NumberReads"] / pow(10,6)
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if self.error() != self.UNKNOWN and sample_total_reads <= (float(self.error()) / float(len(lane_demux))):
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yield QCErrorFatal("Number of reads for sample {} was too low on lane {}, it was: {} M".format(sample_id, lane_nbr, sample_total_reads),
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ordering=int(lane_nbr))
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elif self.warning() != self.UNKNOWN and sample_total_reads <= (float(self.warning()) / float(len(lane_demux))):
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yield QCErrorWarning("Number of reads for sample {} was too low on lane {}, it was: {} M".format(sample_id, lane_nbr, sample_total_reads),
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ordering=int(lane_nbr))
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else:
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continue

‎tests/handlers/test_reads_per_sample_handler.py

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import unittest
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from checkQC.handlers.reads_per_sample_handler import ReadsPerSampleHandler
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from tests.test_utils import get_stats_json
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from tests.handlers.handler_test_base import HandlerTestBase
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class TestReadsPerSampleHandler(HandlerTestBase):
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def setUp(self):
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key = "ConversionResults"
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qc_config = {'name': 'ReadsPerSampleHandler', 'error': 'unknown', 'warning': '90'}
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value = get_stats_json()["ConversionResults"]
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reads_per_sample_handler = ReadsPerSampleHandler(qc_config)
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reads_per_sample_handler.collect((key, value))
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self.reads_per_sample_handler = reads_per_sample_handler
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def set_qc_config(self, qc_config):
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self.reads_per_sample_handler.qc_config = qc_config
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def test_all_is_fine(self):
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qc_config = {'name': 'ReadsPerSampleHandler', 'error': '70', 'warning': '90'}
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self.set_qc_config(qc_config)
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errors_and_warnings = list(self.reads_per_sample_handler.check_qc())
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self.assertEqual(errors_and_warnings, [])
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def test_warning(self):
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qc_config = {'name': 'ReadsPerSampleHandler', 'error': '100', 'warning': '400'}
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self.set_qc_config(qc_config)
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errors_and_warnings = list(self.reads_per_sample_handler.check_qc())
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self.assertEqual(len(errors_and_warnings), 4)
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class_names = self.map_errors_and_warnings_to_class_names(errors_and_warnings)
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self.assertListEqual(class_names, ['QCErrorWarning', 'QCErrorWarning',
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'QCErrorWarning', 'QCErrorWarning'])
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def test_error(self):
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qc_config = {'name': 'ReadsPerSampleHandler', 'error': '400', 'warning': '500'}
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self.set_qc_config(qc_config)
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errors_and_warnings = list(self.reads_per_sample_handler.check_qc())
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self.assertEqual(len(errors_and_warnings), 4)
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class_names = self.map_errors_and_warnings_to_class_names(errors_and_warnings)
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self.assertListEqual(class_names, ['QCErrorFatal', 'QCErrorFatal',
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'QCErrorFatal', 'QCErrorFatal'])
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def test_warning_when_error_unknown(self):
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qc_config = {'name': 'ReadsPerSampleHandler', 'error': 'unknown', 'warning': '400'}
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self.set_qc_config(qc_config)
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errors_and_warnings = list(self.reads_per_sample_handler.check_qc())
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self.assertEqual(len(errors_and_warnings), 4)
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class_names = self.map_errors_and_warnings_to_class_names(errors_and_warnings)
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self.assertListEqual(class_names, ['QCErrorWarning', 'QCErrorWarning',
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'QCErrorWarning', 'QCErrorWarning'])
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if __name__ == '__main__':
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unittest.main()

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