class _BasicAlnFileReaderTests(object):
"""
Abstract base class for tests of the basic reader
functionality---functionality not requiring the bam.pbi index.
The tests are pretty tailored to the BAM/cmp.h5 files in
pbcore.data.
"""
READER_CONSTRUCTOR = None
CONSTRUCTOR_ARGS = None
BAX_FILE = data.getBaxForBam()
def __init__(self):
self.f = self.READER_CONSTRUCTOR(*self.CONSTRUCTOR_ARGS)
self.alns = list(self.f)
self.fwdAln = self.alns[1]
self.revAln = self.alns[105]
def testBasicOperations(self):
EQ(False, self.f.isEmpty)
EQ(True, self.f.isSorted)
EQ(112, len(self.f))
def testStrandOrientation(self):
EQ(True, self.fwdAln.isForwardStrand)
EQ(False, self.fwdAln.isReverseStrand)
EQ(False, self.revAln.isForwardStrand)
EQ(True, self.revAln.isReverseStrand)
def testReadName(self):
EQ("m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/32328/1_344",
self.fwdAln.readName)
EQ("m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/51534/1_200",
self.revAln.readName)
def testAlignedRead(self):
expectedFwdNative = "GCCGCGAT-GATGAAAACTGATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTT-ACAGGCTGCGGCATTTTGTCCGCGCC-GGCTTCGCTCACTGTTCAGGCCGGAG-CACAGACCGCCGTTGAAATGGGCGGATGCTAATTACTATCTCCCGAAAGAAT-CGC-TACCAGGAAGGGCGATGGGAAACACTGCCCTTTCAGCGGG-CATCATGAATGCGATGGGCAGCGACTACATCCGTGAGGT-AATGTGGTGAAGTCTG-CCGTGTCGGTTATTCCAAAATGCTGCTGGGTG-TTATGCCT-CGTTTATAGAGCATAAGCAGCGCAACA-CCTTATCTGGTTGCC"
EQ(expectedFwdNative, self.fwdAln.read(aligned=True))
EQ(expectedFwdNative, self.fwdAln.read())
EQ(expectedFwdNative, self.fwdAln.read(orientation="genomic"))
expectedRevNative = "TAGCCACCGGATATCACCACAGGTGAGGCCGTGTAAGTTG-AGGTTTTTCTACGTCAGATTCTTTTGGGATTGGGCTTGGGTTTATTTCCTGGTGCGTTTCGTT-GAAGGTATTTGCAGTTTTCGCAGATTATGCCTCCGGTGATACTTCGTCGCTGTCTCGCCACACGTCCTCCTTTTCCTGCGGTAGTGGTAACACCCC"
EQ(expectedRevNative, self.revAln.read(aligned=True))
EQ(expectedRevNative, self.revAln.read())
EQ(RC(expectedRevNative), self.revAln.read(orientation="genomic"))
def testUnalignedRead(self):
expectedFwdNative = 'GCCGCGATGATGAAAACTGATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTACAGGCTGCGGCATTTTGTCCGCGCCGGCTTCGCTCACTGTTCAGGCCGGAGCACAGACCGCCGTTGAAATGGGCGGATGCTAATTACTATCTCCCGAAAGAATCGCTACCAGGAAGGGCGATGGGAAACACTGCCCTTTCAGCGGGCATCATGAATGCGATGGGCAGCGACTACATCCGTGAGGTAATGTGGTGAAGTCTGCCGTGTCGGTTATTCCAAAATGCTGCTGGGTGTTATGCCTCGTTTATAGAGCATAAGCAGCGCAACACCTTATCTGGTTGCC'
EQ(expectedFwdNative, self.fwdAln.read(aligned=False))
EQ(expectedFwdNative, self.fwdAln.read(aligned=False, orientation="genomic"))
expectedRevNative = "TAGCCACCGGATATCACCACAGGTGAGGCCGTGTAAGTTGAGGTTTTTCTACGTCAGATTCTTTTGGGATTGGGCTTGGGTTTATTTCCTGGTGCGTTTCGTTGAAGGTATTTGCAGTTTTCGCAGATTATGCCTCCGGTGATACTTCGTCGCTGTCTCGCCACACGTCCTCCTTTTCCTGCGGTAGTGGTAACACCCC"
EQ(expectedRevNative, self.revAln.read(aligned=False))
EQ(RC(expectedRevNative), self.revAln.read(aligned=False, orientation="genomic"))
def testAlignedReference(self):
expectedFwdNative = 'GCCGCGCTGGATG--AACTGATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAACAGGCTGCGGCATTTTGTCCGCGCCGGGCTTCGCTCACTGTTCAGGCCGGAGCCACAGACCGCCGTTG-AATGGGCGGATGCTAATTACTATCTCCCGAAAGAATCCGCATACCAGGAAGGGCGCTGGGAAACACTGCCCTTTCAGCGGGCCATCATGAATGCGATGGGCAGCGACTACATCCGTGAGGTGAATGTGGTGAAGTCTGCCCGTGTCGGTTATTCCAAAATGCTGCTGGGTGTTTATGCCTAC-TTTATAGAGCATAAGCAGCGCAACACCCTTATCTGGTTGCC'
EQ(expectedFwdNative, self.fwdAln.reference(aligned=True))
EQ(expectedFwdNative, self.fwdAln.reference())
EQ(expectedFwdNative, self.fwdAln.reference(orientation="genomic"))
expectedRevNative = 'TAGCCACCGGATATC-CCACAGGTGA-GCCGTGT-AGTTGAAGG-TTTT-TACGTCAGATTCTTTTGGGATT-GGCTTGGGTTTATTT-CTGGTGCGTTTCGTTGGAAGGTATTTGCAGTTTTCGCAGATTATG--T-CGGTGATACTTCGTCGCTGTCTCGCCACACGTCCTCCTTTTCCTGCGGTAGTGGTAACACCCC'
EQ(expectedRevNative, self.revAln.reference(aligned=True))
EQ(expectedRevNative, self.revAln.reference())
EQ(RC(expectedRevNative), self.revAln.reference(orientation="genomic"))
def testUnalignedReference(self):
expectedFwdNative = "GCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAACAGGCTGCGGCATTTTGTCCGCGCCGGGCTTCGCTCACTGTTCAGGCCGGAGCCACAGACCGCCGTTGAATGGGCGGATGCTAATTACTATCTCCCGAAAGAATCCGCATACCAGGAAGGGCGCTGGGAAACACTGCCCTTTCAGCGGGCCATCATGAATGCGATGGGCAGCGACTACATCCGTGAGGTGAATGTGGTGAAGTCTGCCCGTGTCGGTTATTCCAAAATGCTGCTGGGTGTTTATGCCTACTTTATAGAGCATAAGCAGCGCAACACCCTTATCTGGTTGCC"
EQ(expectedFwdNative, self.fwdAln.reference(aligned=False))
EQ(expectedFwdNative, self.fwdAln.reference(aligned=False, orientation="genomic"))
expectedRevNative = "TAGCCACCGGATATCCCACAGGTGAGCCGTGTAGTTGAAGGTTTTTACGTCAGATTCTTTTGGGATTGGCTTGGGTTTATTTCTGGTGCGTTTCGTTGGAAGGTATTTGCAGTTTTCGCAGATTATGTCGGTGATACTTCGTCGCTGTCTCGCCACACGTCCTCCTTTTCCTGCGGTAGTGGTAACACCCC"
EQ(expectedRevNative, self.revAln.reference(aligned=False))
EQ(RC(expectedRevNative), self.revAln.reference(aligned=False, orientation="genomic"))
def testDeletionQV(self):
expectedFwdNative = (
[ 17, 17, 17, 17, 17, 17, 17, 17,255, 4, 17, 17, 17, 8, 17, 17, 17, 17,
17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,
17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 10, 8, 17,
17, 17, 17, 17, 17, 17,255, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,
17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,255, 17, 17,
17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,
17, 17, 17, 17, 17, 17,255, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,
17, 17, 17, 17, 17, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,
17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 11, 17, 17, 17, 17,
17, 17, 17, 17, 17,255, 17, 17, 17,255, 17, 17, 17, 17, 17, 17, 17, 17,
17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,
17, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,255, 17, 17, 17,
17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,
17, 17, 17, 17, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,
255, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,255,
17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,
17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,255, 17, 17, 17,
17, 17, 17, 17, 17,255, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,
17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,255, 17, 17,
17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] )
AEQ(expectedFwdNative, self.fwdAln.DeletionQV(aligned=True))
AEQ(expectedFwdNative, self.fwdAln.DeletionQV())
AEQ(expectedFwdNative, self.fwdAln.DeletionQV(orientation="genomic"))
expectedRevNative = (
[ 17, 17, 17, 17, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17,
17, 17, 17, 17, 17, 6, 17, 17, 17, 17, 17, 17, 6, 17, 17,
17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 255, 10, 17,
17, 17, 17, 17, 8, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17,
17, 17, 17, 17, 17, 10, 17, 17, 17, 17, 17, 17, 17, 17,
17, 17, 17, 17, 17, 17, 17, 17, 8, 17, 17, 17, 17, 17, 17,
17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,
17, 7, 17, 255, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,
17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,
17, 17, 9, 17, 17, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17,
17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,
17, 17, 17, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,
17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,
17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17 ] )
print self.revAln.DeletionQV(aligned=True)
AEQ(expectedRevNative, self.revAln.DeletionQV(aligned=True))
AEQ(expectedRevNative, self.revAln.DeletionQV())
AEQ(expectedRevNative[::-1], self.revAln.DeletionQV(orientation="genomic"))
# # def testInsertionQV(self):
# # pass
# # def testSubstitutionQV(self):
# # pass
# # def testIPD(self):
# # pass
# def testDeletionTag(self):
# expectedFwdNative = [78, 78, 84, 78, 78, 67, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78,
# 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 65, 78,
# 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78]
# AEQ(expectedFwdNative, self.fwdAln.DeletionTag(aligned=True))
# AEQ(expectedFwdNative, self.fwdAln.DeletionTag())
# AEQ(expectedFwdNative, self.fwdAln.DeletionTag(orientation="genomic"))
# expectedRevNative = [78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78,
# 78, 78, 78, 78, 45, 67, 78, 78, 78, 78, 78, 45, 84, 78, 78, 78, 78,
# 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 45, 78, 78, 78, 78,
# 78, 78, 78, 78, 78, 78, 78, 78, 78, 78]
# AEQ(expectedRevNative, self.revAln.DeletionTag(aligned=True))
# AEQ(expectedRevNative, self.revAln.DeletionTag())
# # TODO: what is the correct behavior here?
# #AEQ(expectedRevNative[::-1], self.revAln.DeletionTag(orientation="genomic"))
def testTranscript(self):
EQ('MMMMMMRMDMMMMIIMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMDMMMMMMMMMMMMMMMMMMMMMMMMMMDMMMMMMMMMMMMMMMMMMMMMMMMMMDMMMMMMMMMMMMMMMIMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMDMMMDMMMMMMMMMMMMMMRMMMMMMMMMMMMMMMMMMMMMMMMMDMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMDMMMMMMMMMMMMMMMMDMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMDMMMMMMMMDMIMMMMMMMMMMMMMMMMMMMMMMMMMDMMMMMMMMMMMMMMM',
self.fwdAln.transcript())
EQ("MMMMMMMMMMMMMMMIMMMMMMMMMMIMMMMMMMIMMMMMDMMMIMMMMIMMMMMMMMMMMMMMMMMMMMMMIMMMMMMMMMMMMMMMIMMMMMMMMMMMMMMMDMMMMMMMMMMMMMMMMMMMMMMMMMMMMMIIMIMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM",
self.revAln.transcript())
def testClippedAlignments(self):
# Get a more interesting (more gappy) fwd strand aln
a = self.fwdAln
EQ([(980, 'C', 'C'),
(981, 'C', 'C'),
(982, 'T', 'T'),
(983, 'A', '-'),
(984, 'C', 'C'),
(985, '-', 'G'),
(985, 'T', 'T'),
(986, 'T', 'T') ],
zip(a.referencePositions(), a.reference(), a.read())[308:316])
ac1 = a.clippedTo(983, 985)
EQ(983, ac1.referenceStart)
EQ(985, ac1.referenceEnd)
EQ([(983, 'A', '-'),
(984, 'C', 'C')],
zip(ac1.referencePositions(), ac1.reference(), ac1.read()))
ac2 = a.clippedTo(982, 986)
EQ(982, ac2.referenceStart)
EQ(986, ac2.referenceEnd)
EQ([(982, 'T', 'T'),
(983, 'A', '-'),
(984, 'C', 'C'),
(985, '-', 'G'),
(985, 'T', 'T')],
zip(ac2.referencePositions(), ac2.reference(), ac2.read()))
ac3 = a.clippedTo(984, 985)
EQ(984, ac3.referenceStart)
EQ(985, ac3.referenceEnd)
EQ([(984, 'C', 'C')],
zip(ac3.referencePositions(), ac3.reference(), ac3.read()))
# # Get a more interesting (more gappy) rev strand aln
# b = self.alns[3]
# EQ([(2216, 'G', 'G'),
# (2215, 'G', 'G'),
# (2214, '-', 'C'),
# (2214, 'C', 'C'),
# (2213, 'A', 'A'),
# (2212, 'T', 'T'),
# (2211, 'G', 'G'),
# (2210, 'C', 'C'),
# (2209, 'T', 'T'),
# (2208, 'G', '-'),
# (2207, 'G', 'G'),
# (2206, 'C', 'C')],
# zip(b.referencePositions(), b.reference(), b.read())[188:200])
# bc1 = b.clippedTo(2208, 2214)
# EQ([(2213, 'A', 'A'),
# (2212, 'T', 'T'),
# (2211, 'G', 'G'),
# (2210, 'C', 'C'),
# (2209, 'T', 'T'),
# (2208, 'G', '-')],
# zip(bc1.referencePositions(), bc1.reference(), bc1.read()))
# bc2 = b.clippedTo(2207, 2215)
# EQ([(2214, 'C', 'C'),
# (2213, 'A', 'A'),
# (2212, 'T', 'T'),
# (2211, 'G', 'G'),
# (2210, 'C', 'C'),
# (2209, 'T', 'T'),
# (2208, 'G', '-'),
# (2207, 'G', 'G')],
# zip(bc2.referencePositions(), bc2.reference(), bc2.read()))
# bc3 = b.clippedTo(2209, 2214)
# EQ([(2213, 'A', 'A'),
# (2212, 'T', 'T'),
# (2211, 'G', 'G'),
# (2210, 'C', 'C'),
# (2209, 'T', 'T')],
# zip(bc3.referencePositions(), bc3.reference(), bc3.read()))
# # Test clipping in a large deletion
# d = self.alns[52]
# EQ([(16191, 'C', 'C'),
# (16192, 'A', 'A'),
# (16193, 'G', 'G'),
# (16194, 'C', 'C'),
# (16195, 'A', 'A'),
# (16196, 'G', '-'),
# (16197, 'G', '-'),
# (16198, 'T', '-'),
# (16199, 'G', 'G'),
# (16200, 'A', 'A'),
# (16201, 'G', 'G')],
# zip(d.referencePositions(), d.reference(), d.read())[129:140])
# dc1 = d.clippedTo(16196, 16198)
# # where's the test code?
def testBaxAttaching(self):
# Before attaching, should get sane exceptions
with assert_raises(ValueError):
self.fwdAln.zmw
with assert_raises(ValueError):
self.fwdAln.zmwRead
# Now attach
self.f.attach(self.BAX_FILE)
EQ("m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/32328/1_344",
self.fwdAln.readName)
EQ("m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/32328",
self.fwdAln.zmwName)
EQ("<Zmw: m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/32328>",
repr(self.fwdAln.zmw))
EQ("<ZmwRead: m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/32328/1_344>",
repr(self.fwdAln.zmwRead))
# Check read contents, for every aln.
for aln in self.alns:
EQ(aln.read(aligned=False, orientation="native"), aln.zmwRead.basecalls())
def testClippingsVsBaxData(self):
self.f.attach(self.BAX_FILE)
for aln in [self.fwdAln, self.revAln]:
for cS in xrange(aln.tStart, aln.tEnd + 1):
for cE in xrange(cS + 1, min(aln.tEnd, cS + 10)):
ca = aln.clippedTo(cS, cE)
EQ(ca.zmwRead.basecalls(),
ca.read(aligned=False, orientation="native"))
def testReadsInRange(self):
wLen = 1000
for wStart in xrange(0, 50000, wLen):
wEnd = wStart + wLen
expectedNames = set([ a.readName for a in self.alns
if (a.referenceName == "lambda_NEB3011" and
a.overlapsReferenceRange(wStart, wEnd)) ])
EQ(expectedNames,
set([ a.readName for a in self.f.readsInRange("lambda_NEB3011", wStart, wEnd) ]))
def testReadGroupTable(self):
rgFwd = self.fwdAln.readGroupInfo
EQ([('ID', '<i4'), ('MovieName', 'O'), ('ReadType', 'O'), ('SequencingChemistry', 'O'), ('FrameRate', '<f8')], rgFwd.dtype)
EQ("P6-C4", rgFwd.SequencingChemistry)
EQ("m140905_042212_sidney_c100564852550000001823085912221377_s1_X0", rgFwd.MovieName)
#EQ("bar", rgFwd.ReadType)
def testSequencingChemistry(self):
EQ(["P6-C4"], self.f.sequencingChemistry)
EQ("P6-C4", self.fwdAln.sequencingChemistry)
EQ("P6-C4", self.revAln.sequencingChemistry)
def __init__(self):
self.bam = BamReader (data.getUnalignedBam())
self.bax = BaxH5Reader(data.getBaxForBam())
self.baxRead0 = next(self.bax.subreads())
self.bamRead0 = next(iter(self.bam))
def __init__(self):
self.bam = BamReader(data.getUnalignedBam())
self.bax = BaxH5Reader(data.getBaxForBam())
self.baxRead0 = next(self.bax.subreads())
self.bamRead0 = next(iter(self.bam))
def __init__(self):
self.V = ZmwReadStitcher(getUnalignedBam())
self.B = BasH5Reader(getBaxForBam())
self.VZ = self.V[1650]
self.BZ = self.B[1650]
def __init__(self):
self.V = ZmwReadStitcher(getUnalignedBam())
self.B = BasH5Reader(getBaxForBam())
self.VZ = self.V[1650]
self.BZ = self.B[1650]
def setup_class(self):
self.bam = BamReader (data.getUnalignedBam())
self.bax = BaxH5Reader(data.getBaxForBam())
self.baxRead0 = next(self.bax.subreads())
self.bamRead0 = next(iter(self.bam))