def test_productionSubreadsToOriginal(self):
# stitch virtual polymerase record
subreadsBam = self.data.directory + "/polymerase/production.subreads.bam"
scrapsBam = self.data.directory + "/polymerase/production.scraps.bam"
vpr = PacBioBam.VirtualPolymeraseReader(subreadsBam, scrapsBam)
self.assertTrue(vpr.HasNext())
virtualRecord = vpr.Next()
# fetch original polymerase record
polyBam = PacBioBam.DataSet(self.data.directory + "/polymerase/production.polymerase.bam")
polyQuery = PacBioBam.EntireFileQuery(polyBam)
polyIter = polyQuery.begin()
polyEnd = polyQuery.end()
self.assertTrue(polyIter != polyEnd)
polyRecord = polyIter.value()
# compare
self.assertEqual(polyRecord.FullName(), virtualRecord.FullName());
self.assertEqual(polyRecord.HoleNumber(), virtualRecord.HoleNumber());
self.assertEqual(polyRecord.NumPasses(), virtualRecord.NumPasses());
self.assertEqual(polyRecord.Sequence(), virtualRecord.Sequence());
self.assertEqual(polyRecord.DeletionTag(), virtualRecord.DeletionTag());
self.assertEqual(polyRecord.SubstitutionTag(), virtualRecord.SubstitutionTag());
self.assertEqual(polyRecord.IPD(), virtualRecord.IPDV1Frames());
self.assertEqual(polyRecord.ReadGroup(), virtualRecord.ReadGroup());
self.assertAlmostEqual(float(polyRecord.ReadAccuracy()), float(virtualRecord.ReadAccuracy()));
self.assertEqual(polyRecord.Qualities().Fastq(), virtualRecord.Qualities().Fastq());
self.assertEqual(polyRecord.DeletionQV().Fastq(), virtualRecord.DeletionQV().Fastq());
self.assertEqual(polyRecord.InsertionQV().Fastq(), virtualRecord.InsertionQV().Fastq());
self.assertEqual(polyRecord.MergeQV().Fastq(), virtualRecord.MergeQV().Fastq());
self.assertEqual(polyRecord.SubstitutionQV().Fastq(), virtualRecord.SubstitutionQV().Fastq());
def generatedNames(self):
try:
# open dataset on generated BAM file, read in names
dataset = PacBioBam.DataSet(self.generatedBamFn)
entireFile = PacBioBam.EntireFileQuery(dataset)
names_out = []
for record in PacBioBam.Iterate(entireFile):
names_out.append(record.FullName())
return names_out
except RuntimeError:
self.assertTrue(False) # should not throw
def originalNames(self):
# loop over original file, store names, write to generated file
try:
file = PacBioBam.BamFile(self.ex2BamFn)
writer = PacBioBam.BamWriter(self.generatedBamFn, file.Header())
dataset = PacBioBam.DataSet(self.ex2BamFn)
entireFile = PacBioBam.EntireFileQuery(dataset)
names_in = []
for record in PacBioBam.Iterate(entireFile):
names_in.append(record.FullName())
writer.Write(record)
return names_in
except RuntimeError:
self.assertTrue(False) # should not throw
def test_internalHqToOriginal(self):
# stitch virtual polymerase record
hqRegionsBam = self.data.directory + "/polymerase/internal.hqregions.bam"
lqRegionsBam = self.data.directory + "/polymerase/internal.lqregions.bam"
vpr = PacBioBam.VirtualPolymeraseReader(hqRegionsBam, lqRegionsBam)
self.assertTrue(vpr.HasNext())
virtualRecord = vpr.Next()
# fetch original polymerase record
polyBam = PacBioBam.DataSet(self.data.directory + "/polymerase/internal.polymerase.bam")
polyQuery = PacBioBam.EntireFileQuery(polyBam)
polyIter = polyQuery.begin()
polyEnd = polyQuery.end()
self.assertTrue(polyIter != polyEnd)
polyRecord = polyIter.value()
# # compare
self.compare(polyRecord, virtualRecord)
def test_productionHqToOriginal(self):
# stitch virtual polymerase record
hqRegionsBam = self.data.directory + "/polymerase/production_hq.hqregion.bam"
lqRegionsBam = self.data.directory + "/polymerase/production_hq.scraps.bam"
vpr = PacBioBam.VirtualPolymeraseReader(hqRegionsBam, lqRegionsBam)
self.assertTrue(vpr.HasNext())
virtualRecord = vpr.Next()
# fetch original polymerase record
polyBam = PacBioBam.DataSet(self.data.directory + "/polymerase/production.polymerase.bam")
polyQuery = PacBioBam.EntireFileQuery(polyBam)
polyIter = polyQuery.begin()
polyEnd = polyQuery.end()
self.assertTrue(polyIter != polyEnd)
polyRecord = polyIter.value()
# compare
self.assertFalse(polyRecord.HasPulseCall());
self.assertFalse(virtualRecord.HasPulseCall());
self.assertEqual(polyRecord.FullName(), virtualRecord.FullName());
self.assertEqual(polyRecord.HoleNumber(), virtualRecord.HoleNumber());
self.assertEqual(polyRecord.NumPasses(), virtualRecord.NumPasses());
self.assertEqual(polyRecord.Sequence(), virtualRecord.Sequence());
self.assertEqual(polyRecord.DeletionTag(), virtualRecord.DeletionTag());
self.assertEqual(polyRecord.SubstitutionTag(), virtualRecord.SubstitutionTag());
self.assertEqual(polyRecord.IPD(), virtualRecord.IPDV1Frames());
self.assertEqual(polyRecord.ReadGroup(), virtualRecord.ReadGroup());
self.assertAlmostEqual(float(polyRecord.ReadAccuracy()), float(virtualRecord.ReadAccuracy()));
self.assertEqual(polyRecord.Qualities().Fastq(), virtualRecord.Qualities().Fastq());
self.assertEqual(polyRecord.DeletionQV().Fastq(), virtualRecord.DeletionQV().Fastq());
self.assertEqual(polyRecord.InsertionQV().Fastq(), virtualRecord.InsertionQV().Fastq());
self.assertEqual(polyRecord.MergeQV().Fastq(), virtualRecord.MergeQV().Fastq());
self.assertEqual(polyRecord.SubstitutionQV().Fastq(), virtualRecord.SubstitutionQV().Fastq());
self.assertTrue(polyRecord.HasDeletionQV());
self.assertTrue(polyRecord.HasDeletionTag());
self.assertTrue(polyRecord.HasInsertionQV());
self.assertTrue(polyRecord.HasMergeQV());
self.assertTrue(polyRecord.HasSubstitutionQV());
self.assertTrue(polyRecord.HasSubstitutionTag());
self.assertTrue(polyRecord.HasIPD());
self.assertFalse(polyRecord.HasLabelQV());
self.assertFalse(polyRecord.HasAltLabelQV());
self.assertFalse(polyRecord.HasAltLabelTag());
self.assertFalse(polyRecord.HasPkmean());
self.assertFalse(polyRecord.HasPkmid());
self.assertFalse(polyRecord.HasPulseCall());
self.assertFalse(polyRecord.HasPulseWidth());
self.assertFalse(polyRecord.HasPrePulseFrames());
self.assertFalse(polyRecord.HasPulseCallWidth());
self.assertTrue(virtualRecord.HasDeletionQV());
self.assertTrue(virtualRecord.HasDeletionTag());
self.assertTrue(virtualRecord.HasInsertionQV());
self.assertTrue(virtualRecord.HasMergeQV());
self.assertTrue(virtualRecord.HasSubstitutionQV());
self.assertTrue(virtualRecord.HasSubstitutionTag());
self.assertTrue(virtualRecord.HasIPD());
self.assertFalse(virtualRecord.HasLabelQV());
self.assertFalse(virtualRecord.HasAltLabelQV());
self.assertFalse(virtualRecord.HasAltLabelTag());
self.assertFalse(virtualRecord.HasPkmean());
self.assertFalse(virtualRecord.HasPkmid());
self.assertFalse(virtualRecord.HasPulseCall());
self.assertFalse(virtualRecord.HasPulseWidth());
self.assertFalse(virtualRecord.HasPrePulseFrames());
self.assertFalse(virtualRecord.HasPulseCallWidth());