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 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_virtualRegions(self):
subreadBam = self.data.directory + "/polymerase/internal.subreads.bam"
scrapsBam = self.data.directory + "/polymerase/internal.scraps.bam"
vpr = PacBioBam.VirtualPolymeraseReader(subreadBam, scrapsBam)
virtualRecord = vpr.Next()
# NOTE: this method is disabled
#
# Any attempt to retrive this value resulted in several
# "swig/python detected a memory leak of type 'unknown', no destructor found."
# errors (& an empty dictionary result). The same info is available via the
# VirtualRegionsTable(regionType) method, though a bit clunkier if you just want
# to iterate. But access to region info for specific types are available & correct,
# so I'm just going to leave this one out for now. - DB
#
# regionMap = virtualRecord.VirtualRegionsMap();
# ADAPTER
adapter = virtualRecord.VirtualRegionsTable(PacBioBam.VirtualRegionType_ADAPTER)
self.assertEqual(7, len(adapter))
self.assertEqual(3047, adapter[0].beginPos);
self.assertEqual(3095, adapter[0].endPos);
self.assertEqual(3650, adapter[1].beginPos);
self.assertEqual(3700, adapter[1].endPos);
self.assertEqual(4289, adapter[2].beginPos);
self.assertEqual(4335, adapter[2].endPos);
self.assertEqual(4888, adapter[3].beginPos);
self.assertEqual(4939, adapter[3].endPos);
self.assertEqual(5498, adapter[4].beginPos);
self.assertEqual(5546, adapter[4].endPos);
self.assertEqual(6116, adapter[5].beginPos);
self.assertEqual(6173, adapter[5].endPos);
self.assertEqual(6740, adapter[6].beginPos);
self.assertEqual(6790, adapter[6].endPos);
# BARCODE
barcode = virtualRecord.VirtualRegionsTable(PacBioBam.VirtualRegionType_BARCODE)
self.assertEqual(14, len(barcode))
self.assertEqual(3025, barcode[0].beginPos);
self.assertEqual(3047, barcode[0].endPos);
self.assertEqual(3095, barcode[1].beginPos);
self.assertEqual(3116, barcode[1].endPos);
self.assertEqual(3628, barcode[2].beginPos);
self.assertEqual(3650, barcode[2].endPos);
self.assertEqual(3700, barcode[3].beginPos);
self.assertEqual(3722, barcode[3].endPos);
self.assertEqual(4267, barcode[4].beginPos);
self.assertEqual(4289, barcode[4].endPos);
self.assertEqual(4335, barcode[5].beginPos);
self.assertEqual(4356, barcode[5].endPos);
self.assertEqual(4864, barcode[6].beginPos);
self.assertEqual(4888, barcode[6].endPos);
self.assertEqual(4939, barcode[7].beginPos);
self.assertEqual(4960, barcode[7].endPos);
self.assertEqual(5477, barcode[8].beginPos);
self.assertEqual(5498, barcode[8].endPos);
self.assertEqual(5546, barcode[9].beginPos);
self.assertEqual(5571, barcode[9].endPos);
self.assertEqual(6087, barcode[10].beginPos);
self.assertEqual(6116, barcode[10].endPos);
self.assertEqual(6173, barcode[11].beginPos);
self.assertEqual(6199, barcode[11].endPos);
self.assertEqual(6719, barcode[12].beginPos);
self.assertEqual(6740, barcode[12].endPos);
self.assertEqual(6790, barcode[13].beginPos);
self.assertEqual(6812, barcode[13].endPos);
# HQREGION
hqregion = virtualRecord.VirtualRegionsTable(PacBioBam.VirtualRegionType_HQREGION)
self.assertEqual(1, len(hqregion))
self.assertEqual(2659, hqregion[0].beginPos);
self.assertEqual(7034, hqregion[0].endPos);
# LQREGION
lqregion = virtualRecord.VirtualRegionsTable(PacBioBam.VirtualRegionType_LQREGION)
self.assertEqual(2, len(lqregion))
self.assertEqual(0, lqregion[0].beginPos);
self.assertEqual(2659, lqregion[0].endPos);
self.assertEqual(7034, lqregion[1].beginPos);
self.assertEqual(7035, lqregion[1].endPos);
# SUBREAD
subread = virtualRecord.VirtualRegionsTable(PacBioBam.VirtualRegionType_SUBREAD)
self.assertEqual(8, len(subread))
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());