def test_vcf_round_trip(self):
testFile = self.resourceFile("small.vcf")
ac = ADAMContext(self.ss)
variants = ac.loadVariants(testFile)
tmpPath = self.tmpFile() + ".vcf"
variants.toVariantContexts().saveAsVcf(tmpPath)
savedVariants = ac.loadVariants(testFile)
self.assertEqual(variants._jvmRdd.jrdd().count(),
savedVariants._jvmRdd.jrdd().count())
def test_vcf_round_trip(self):
testFile = self.resourceFile("small.vcf")
ac = ADAMContext(self.sc)
variants = ac.loadVariants(testFile)
tmpPath = self.tmpFile() + ".vcf"
variants.toVariantContexts().saveAsVcf(tmpPath)
savedVariants = ac.loadVariants(testFile)
self.assertEquals(variants._jvmRdd.jrdd().count(),
savedVariants._jvmRdd.jrdd().count())
def test_load_variants(self):
testFile = self.resourceFile("small.vcf")
ac = ADAMContext(self.sc)
reads = ac.loadVariants(testFile)
self.assertEqual(reads.toDF().count(), 6)
self.assertEqual(reads._jvmRdd.jrdd().count(), 6)
def test_transform(self):
variantPath = self.resourceFile("small.vcf")
ac = ADAMContext(self.ss)
variants = ac.loadVariants(variantPath)
transformedVariants = variants.transform(lambda x: x.filter(x.start < 19190))
self.assertEquals(transformedVariants.toDF().count(), 3)
def test_transform(self):
variantPath = self.resourceFile("small.vcf")
ac = ADAMContext(self.ss)
variants = ac.loadVariants(variantPath)
transformedVariants = variants.transform(lambda x: x.filter(x.start < 19190))
self.assertEqual(transformedVariants.toDF().count(), 3)
def test_load_variants(self):
testFile = self.resourceFile("small.vcf")
ac = ADAMContext(self.ss)
reads = ac.loadVariants(testFile)
self.assertEqual(reads.toDF().count(), 6)
self.assertEqual(reads._jvmRdd.jrdd().count(), 6)
def test_realignIndels_known_indels(self):
readsPath = self.resourceFile("small.1.sam")
variantsPath = self.resourceFile("small.vcf")
ac = ADAMContext(self.ss)
reads = ac.loadAlignments(readsPath)
knownIndels = ac.loadVariants(variantsPath)
realigned = reads.realignIndelsFromKnownIndels(knownIndels)
self.assertEqual(realigned.toDF().count(), 20)
def test_visualize_variants(self):
# load file
ac = ADAMContext(self.ss)
testFile = self.resourceFile("bqsr1.vcf")
variants = ac.loadVariants(testFile)
variantViz = VariantSummary(ac, variants)
contig = "chrM"
start = 1
end = 2000
x = variantViz.viewPileup(contig, start, end)
assert (x != None)
def test_visualize_variants(self):
genomicRDD = GenomicVizRDD(self.ss)
# load file
ac = ADAMContext(self.ss)
testFile = self.resourceFile("bqsr1.vcf")
# read alignments
variants = ac.loadVariants(testFile)
contig = "chrM"
start = 1
end = 2000
genomicRDD.ViewVariants(variants, contig, start, end)
assert (True)
