def testInstantiation(self):
for localId in self.localIds:
path = self.getFullPath(localId)
variantSet = variants.HtslibVariantSet(self.dataset, localId)
variantSet.populateFromDirectory(path)
with self.assertRaises(exceptions.InconsistentCallSetIdException):
variantSet.checkConsistency()
def getDataModelInstance(self, localId, dataPath):
variantSet = variants.HtslibVariantSet(self._dataset, localId)
variantSet.populateFromDirectory(dataPath)
referenceSet = references.AbstractReferenceSet("test")
variantSet.setReferenceSet(referenceSet)
variantSet.setPatientId("patient1")
variantSet.setSampleId("sample1")
return variantSet
def _createVariantAnnotationSet(self, vcfDir):
"""
Creates a VariantAnnotationSet from the specified directory of
VCF files.
"""
self._variantSetName = "testVariantSet"
self._repo = datarepo.SqlDataRepository(paths.testDataRepo)
self._repo.open(datarepo.MODE_READ)
self._dataset = datasets.Dataset("testDs")
self._variantSet = variants.HtslibVariantSet(self._dataset,
self._variantSetName)
self._variantSet.populateFromDirectory(vcfDir)
self._variantAnnotationSet = variants.HtslibVariantAnnotationSet(
self._variantSet, "testVAs")
self._variantAnnotationSet.setOntology(
self._repo.getOntologyByName(paths.ontologyName))
def getDataModelInstance(self, localId, dataPath):
dataset = datasets.Dataset("ds")
variantSet = variants.HtslibVariantSet(dataset, localId)
variantSet.populateFromDirectory(dataPath)
referenceSet = references.AbstractReferenceSet("rs")
variantSet.setReferenceSet(referenceSet)
variantSet.setPatientId("patient1")
variantSet.setSampleId("sample1")
if variantSet.isAnnotated():
sequenceOntology = ontologies.Ontology(paths.ontologyName)
sequenceOntology.populateFromFile(paths.ontologyPath)
annotationSet = variantSet.getVariantAnnotationSets()[0]
annotationSet.setOntology(sequenceOntology)
return annotationSet
else:
return variantSet
def createRepo(self):
"""
Creates the repository for all the data we've just downloaded.
"""
repo = datarepo.SqlDataRepository(self.repoPath)
repo.open("w")
repo.initialise()
referenceSet = references.HtslibReferenceSet("GRCh37-subset")
referenceSet.populateFromFile(self.fastaFilePath)
referenceSet.setDescription("Subset of GRCh37 used for demonstration")
referenceSet.setSpeciesFromJson(
'{"id": "9606",'
+ '"term": "H**o sapiens", "source_name": "NCBI"}')
for reference in referenceSet.getReferences():
reference.setSpeciesFromJson(
'{"id": "9606",'
+ '"term": "H**o sapiens", "source_name": "NCBI"}')
reference.setSourceAccessions(
self.accessions[reference.getName()] + ".subset")
repo.insertReferenceSet(referenceSet)
dataset = datasets.Dataset("1kg-p3-subset")
dataset.setDescription("Sample data from 1000 Genomes phase 3")
repo.insertDataset(dataset)
variantSet = variants.HtslibVariantSet(dataset, "mvncall")
variantSet.setReferenceSet(referenceSet)
dataUrls = [vcfFile for vcfFile, _ in self.vcfFilePaths]
indexFiles = [indexFile for _, indexFile in self.vcfFilePaths]
variantSet.populateFromFile(dataUrls, indexFiles)
variantSet.checkConsistency()
repo.insertVariantSet(variantSet)
for sample, (bamFile, indexFile) in zip(
self.samples, self.bamFilePaths):
readGroupSet = reads.HtslibReadGroupSet(dataset, sample)
readGroupSet.populateFromFile(bamFile, indexFile)
readGroupSet.setReferenceSet(referenceSet)
repo.insertReadGroupSet(readGroupSet)
repo.commit()
repo.close()
self.log("Finished creating the repository; summary:\n")
repo.open("r")
repo.printSummary()
def addVariantSet(self, variantFileName, dataset, referenceSet, ontology,
biosamples):
inputVcf = os.path.join(self.inputDirectory, variantFileName)
outputVcf = os.path.join(self.outputDirectory, variantFileName)
shutil.copy(inputVcf, outputVcf)
pysam.tabix_index(outputVcf, preset="vcf")
variantSet = variants.HtslibVariantSet(dataset,
variantFileName.split('_')[1])
variantSet.setReferenceSet(referenceSet)
variantSet.populateFromFile([os.path.abspath(outputVcf + ".gz")],
[os.path.abspath(outputVcf + ".gz.tbi")])
variantSet.checkConsistency()
for callSet in variantSet.getCallSets():
for biosample in biosamples:
if biosample.getLocalId() == callSet.getLocalId():
callSet.setBiosampleId(biosample.getId())
self.repo.insertVariantSet(variantSet)
for annotationSet in variantSet.getVariantAnnotationSets():
annotationSet.setOntology(ontology)
self.repo.insertVariantAnnotationSet(annotationSet)
def testInstantiation(self):
for localId in self.localIds:
path = self.getFullPath(localId)
variantSet = variants.HtslibVariantSet(self.dataset, localId)
with self.assertRaises(exceptions.OverlappingVcfException):
variantSet.populateFromDirectory(path)
