def test_round_trip_gtf(self):
testFile = self.resourceFile("Homo_sapiens.GRCh37.75.trun20.gtf")
ac = ADAMContext(self.sc)
features = ac.loadFeatures(testFile)
tmpPath = self.tmpFile() + ".gtf"
features.save(tmpPath, asSingleFile=True)
savedFeatures = ac.loadFeatures(testFile)
self.assertEquals(features._jvmRdd.jrdd().count(),
savedFeatures._jvmRdd.jrdd().count())
def test_round_trip_bed(self):
testFile = self.resourceFile("gencode.v7.annotation.trunc10.bed")
ac = ADAMContext(self.sc)
features = ac.loadFeatures(testFile)
tmpPath = self.tmpFile() + ".bed"
features.save(tmpPath, asSingleFile=True)
savedFeatures = ac.loadFeatures(testFile)
self.assertEquals(features._jvmRdd.jrdd().count(),
savedFeatures._jvmRdd.jrdd().count())
def test_round_trip_interval_list(self):
testFile = self.resourceFile("SeqCap_EZ_Exome_v3.hg19.interval_list")
ac = ADAMContext(self.sc)
features = ac.loadFeatures(testFile)
tmpPath = self.tmpFile() + ".interval_list"
features.save(tmpPath, asSingleFile=True)
savedFeatures = ac.loadFeatures(testFile)
self.assertEquals(features._jvmRdd.jrdd().count(),
savedFeatures._jvmRdd.jrdd().count())
def test_round_trip_bed(self):
testFile = self.resourceFile("gencode.v7.annotation.trunc10.bed")
ac = ADAMContext(self.ss)
features = ac.loadFeatures(testFile)
tmpPath = self.tmpFile() + ".bed"
features.save(tmpPath,
asSingleFile=True)
savedFeatures = ac.loadFeatures(testFile)
self.assertEqual(features._jvmRdd.jrdd().count(),
savedFeatures._jvmRdd.jrdd().count())
def test_round_trip_gtf(self):
testFile = self.resourceFile("Homo_sapiens.GRCh37.75.trun20.gtf")
ac = ADAMContext(self.ss)
features = ac.loadFeatures(testFile)
tmpPath = self.tmpFile() + ".gtf"
features.save(tmpPath,
asSingleFile=True)
savedFeatures = ac.loadFeatures(testFile)
self.assertEqual(features._jvmRdd.jrdd().count(),
savedFeatures._jvmRdd.jrdd().count())
def test_round_trip_interval_list(self):
testFile = self.resourceFile("SeqCap_EZ_Exome_v3.hg19.interval_list")
ac = ADAMContext(self.ss)
features = ac.loadFeatures(testFile)
tmpPath = self.tmpFile() + ".interval_list"
features.save(tmpPath,
asSingleFile=True)
savedFeatures = ac.loadFeatures(testFile)
self.assertEqual(features._jvmRdd.jrdd().count(),
savedFeatures._jvmRdd.jrdd().count())
def test_round_trip_narrowPeak(self):
testFile = self.resourceFile(
"wgEncodeOpenChromDnaseGm19238Pk.trunc10.narrowPeak")
ac = ADAMContext(self.sc)
features = ac.loadFeatures(testFile)
tmpPath = self.tmpFile() + ".narrowPeak"
features.save(tmpPath, asSingleFile=True)
savedFeatures = ac.loadFeatures(testFile)
self.assertEquals(features._jvmRdd.jrdd().count(),
savedFeatures._jvmRdd.jrdd().count())
def test_round_trip_narrowPeak(self):
testFile = self.resourceFile("wgEncodeOpenChromDnaseGm19238Pk.trunc10.narrowPeak")
ac = ADAMContext(self.ss)
features = ac.loadFeatures(testFile)
tmpPath = self.tmpFile() + ".narrowPeak"
features.save(tmpPath,
asSingleFile=True)
savedFeatures = ac.loadFeatures(testFile)
self.assertEqual(features._jvmRdd.jrdd().count(),
savedFeatures._jvmRdd.jrdd().count())
def test_load_interval_list(self):
testFile = self.resourceFile("SeqCap_EZ_Exome_v3.hg19.interval_list")
ac = ADAMContext(self.ss)
reads = ac.loadFeatures(testFile)
self.assertEqual(reads.toDF().count(), 369)
self.assertEqual(reads._jvmRdd.jrdd().count(), 369)
def test_load_gtf(self):
testFile = self.resourceFile("Homo_sapiens.GRCh37.75.trun20.gtf")
ac = ADAMContext(self.ss)
reads = ac.loadFeatures(testFile)
self.assertEqual(reads.toDF().count(), 15)
self.assertEqual(reads._jvmRdd.jrdd().count(), 15)
def test_load_gtf(self):
testFile = self.resourceFile("Homo_sapiens.GRCh37.75.trun20.gtf")
ac = ADAMContext(self.ss)
reads = ac.loadFeatures(testFile)
self.assertEqual(reads.toDF().count(), 15)
self.assertEqual(reads._jvmRdd.jrdd().count(), 15)
def test_load_interval_list(self):
testFile = self.resourceFile("SeqCap_EZ_Exome_v3.hg19.interval_list")
ac = ADAMContext(self.ss)
reads = ac.loadFeatures(testFile)
self.assertEqual(reads.toDF().count(), 369)
self.assertEqual(reads._jvmRdd.jrdd().count(), 369)
def test_load_bed(self):
testFile = self.resourceFile("gencode.v7.annotation.trunc10.bed")
ac = ADAMContext(self.ss)
reads = ac.loadFeatures(testFile)
self.assertEqual(reads.toDF().count(), 10)
self.assertEqual(reads._jvmRdd.jrdd().count(), 10)
def test_load_bed(self):
testFile = self.resourceFile("gencode.v7.annotation.trunc10.bed")
ac = ADAMContext(self.ss)
reads = ac.loadFeatures(testFile)
self.assertEqual(reads.toDF().count(), 10)
self.assertEqual(reads._jvmRdd.jrdd().count(), 10)
def test_transform(self):
featurePath = self.resourceFile("gencode.v7.annotation.trunc10.bed")
ac = ADAMContext(self.ss)
features = ac.loadFeatures(featurePath)
transformedFeatures = features.transform(lambda x: x.filter(x.start < 12613))
self.assertEqual(transformedFeatures.toDF().count(), 6)
def test_load_narrowPeak(self):
testFile = self.resourceFile("wgEncodeOpenChromDnaseGm19238Pk.trunc10.narrowPeak")
ac = ADAMContext(self.ss)
reads = ac.loadFeatures(testFile)
self.assertEqual(reads.toDF().count(), 10)
self.assertEqual(reads._jvmRdd.jrdd().count(), 10)
def test_transform(self):
featurePath = self.resourceFile("gencode.v7.annotation.trunc10.bed")
ac = ADAMContext(self.ss)
features = ac.loadFeatures(featurePath)
transformedFeatures = features.transform(lambda x: x.filter(x.start < 12613))
self.assertEquals(transformedFeatures.toDF().count(), 6)
def test_load_narrowPeak(self):
testFile = self.resourceFile("wgEncodeOpenChromDnaseGm19238Pk.trunc10.narrowPeak")
ac = ADAMContext(self.ss)
reads = ac.loadFeatures(testFile)
self.assertEqual(reads.toDF().count(), 10)
self.assertEqual(reads._jvmRdd.jrdd().count(), 10)
def test_shuffle_right_outer_join_groupBy_left(self):
readsPath = self.resourceFile("small.1.sam")
targetsPath = self.resourceFile("small.1.bed")
ac = ADAMContext(self.ss)
reads = ac.loadAlignments(readsPath)
targets = ac.loadFeatures(targetsPath)
jRdd = reads.rightOuterShuffleRegionJoinAndGroupByLeft(targets)
self.assertEqual(jRdd.toDF().count(), 21)
def test_shuffle_inner_join(self):
readsPath = self.resourceFile("small.1.sam")
targetsPath = self.resourceFile("small.1.bed")
ac = ADAMContext(self.ss)
reads = ac.loadAlignments(readsPath)
targets = ac.loadFeatures(targetsPath)
jRdd = reads.shuffleRegionJoin(targets)
self.assertEqual(jRdd.toDF().count(), 5)
def test_broadcast_right_outer_join(self):
readsPath = self.resourceFile("small.1.sam")
targetsPath = self.resourceFile("small.1.bed")
ac = ADAMContext(self.ss)
reads = ac.loadAlignments(readsPath)
targets = ac.loadFeatures(targetsPath)
jRdd = reads.rightOuterBroadcastRegionJoin(targets)
self.assertEqual(jRdd.toDF().count(), 6)
def test_visualize_features(self):
genomicRDD = GenomicVizRDD(self.ss)
# load file
ac = ADAMContext(self.ss)
testFile = self.resourceFile("smalltest.bed")
# read alignments
features = ac.loadFeatures(testFile)
contig = "chrM"
start = 1
end = 2000
x = genomicRDD.ViewFeatures(features, contig, start, end)
assert (True)
def test_visualize_features(self):
# load file
ac = ADAMContext(self.ss)
testFile = self.resourceFile("smalltest.bed")
# read features
features = ac.loadFeatures(testFile)
featureViz = FeatureSummary(ac, features)
contig = "chrM"
start = 1
end = 2000
x = featureViz.viewPileup(contig, start, end)
assert(x != None)
