def getStats(self):
"""
Returns the GA4GH protocol representation of this read group set's
ReadStats.
"""
stats = protocol.ReadStats()
stats.aligned_read_count = self._numAlignedReads
stats.unaligned_read_count = self._numUnalignedReads
return stats
def getStats(self):
"""
Returns the GA4GH protocol representation of this read group's
ReadStats.
"""
stats = protocol.ReadStats()
stats.aligned_read_count = self.getNumAlignedReads()
stats.unaligned_read_count = self.getNumUnalignedReads()
# TODO base_count requires iterating through all reads
return stats
def toProtocolElement(self):
"""
Returns the GA4GH protocol representation of this ReadGroup.
"""
# TODO this is very incomplete, but we don't have the
# implementation to fill out the rest of the fields currently
readGroup = protocol.ReadGroup()
readGroup.id = self.getId()
readGroup.created = self._creationTime
readGroup.updated = self._updateTime
dataset = self.getParentContainer().getParentContainer()
readGroup.datasetId = dataset.getId()
readGroup.description = None
readGroup.info = {}
readGroup.name = self.getLocalId()
readGroup.predictedInsertSize = self.getPredictedInsertSize()
readGroup.programs = []
referenceSet = self._parentContainer.getReferenceSet()
readGroup.referenceSetId = None
readGroup.sampleId = self.getSampleId()
if referenceSet is not None:
readGroup.referenceSetId = referenceSet.getId()
stats = protocol.ReadStats()
stats.alignedReadCount = self.getNumAlignedReads()
stats.unalignedReadCount = self.getNumUnalignedReads()
stats.baseCount = None # TODO requires iterating through all reads
readGroup.stats = stats
readGroup.programs = self.getPrograms()
readGroup.description = self.getDescription()
experiment = protocol.Experiment()
experiment.id = self.getExperimentId()
experiment.instrumentModel = self.getInstrumentModel()
experiment.sequencingCenter = self.getSequencingCenter()
experiment.description = self.getExperimentDescription()
experiment.info = {}
experiment.instrumentDataFile = None
experiment.library = self.getLibrary()
experiment.libraryLayout = None
experiment.molecule = None
experiment.name = None
experiment.platformUnit = self.getPlatformUnit()
experiment.recordCreateTime = self._iso8601
experiment.recordUpdateTime = self._iso8601
experiment.runTime = self.getRunTime()
experiment.selection = None
experiment.strategy = None
readGroup.experiment = experiment
return readGroup
def toProtocolElement(self):
"""
Returns the GA4GH protocol representation of this ReadGroupSet.
"""
readGroupSet = protocol.ReadGroupSet()
readGroupSet.id = self.getId()
readGroupSet.readGroups = [
readGroup.toProtocolElement()
for readGroup in self.getReadGroups()]
readGroupSet.name = self.getLocalId()
readGroupSet.datasetId = self.getParentContainer().getId()
stats = protocol.ReadStats()
stats.alignedReadCount = self.getNumAlignedReads()
stats.unalignedReadCount = self.getNumUnalignedReads()
readGroupSet.stats = stats
return readGroupSet
