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from collections import Counter
import numpy as np
import os
import pytest
import shutil
import tempfile
from numpy.testing import (assert_array_almost_equal as ASIM,
assert_array_equal as AEQ)
from pbcore import data
from pbcore.io import BamReader, IndexedBamReader
from pbcore.io.align._BamSupport import UnavailableFeature
from pbcore.sequence import reverseComplement as RC
from pbcore.chemistry import ChemistryLookupError
from pbcore.io.align.BamIO import AlignmentFile
class _BasicAlnFileReaderTests:
"""
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 files in
pbcore.data.
"""
READER_CONSTRUCTOR = None
CONSTRUCTOR_ARGS = None
@classmethod
def setup_class(cls):
cls.f = cls.READER_CONSTRUCTOR(*cls.CONSTRUCTOR_ARGS)
cls.alns = list(cls.f)
cls.fwdAln = cls.alns[1]
cls.revAln = cls.alns[105]
def testBasicOperations(self):
assert False == self.f.isEmpty
assert True == self.f.isSorted
assert 112 == len(self.f)
def testStrandOrientation(self):
assert True == self.fwdAln.isForwardStrand
assert False == self.fwdAln.isReverseStrand
assert False == self.revAln.isForwardStrand
assert True == self.revAln.isReverseStrand
def testReadName(self):
assert "m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/32328/1_344" == self.fwdAln.readName
assert "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"
assert expectedFwdNative == self.fwdAln.read(aligned=True)
assert expectedFwdNative == self.fwdAln.read()
assert expectedFwdNative == self.fwdAln.read(orientation="genomic")
expectedRevNative = "TAGCCACCGGATATCACCACAGGTGAGGCCGTGTAAGTTG-AGGTTTTTCTACGTCAGATTCTTTTGGGATTGGGCTTGGGTTTATTTCCTGGTGCGTTTCGTT-GAAGGTATTTGCAGTTTTCGCAGATTATGCCTCCGGTGATACTTCGTCGCTGTCTCGCCACACGTCCTCCTTTTCCTGCGGTAGTGGTAACACCCC"
assert expectedRevNative == self.revAln.read(aligned=True)
assert expectedRevNative == self.revAln.read()
assert RC(expectedRevNative) == self.revAln.read(orientation="genomic")
def testUnalignedRead(self):
expectedFwdNative = 'GCCGCGATGATGAAAACTGATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTACAGGCTGCGGCATTTTGTCCGCGCCGGCTTCGCTCACTGTTCAGGCCGGAGCACAGACCGCCGTTGAAATGGGCGGATGCTAATTACTATCTCCCGAAAGAATCGCTACCAGGAAGGGCGATGGGAAACACTGCCCTTTCAGCGGGCATCATGAATGCGATGGGCAGCGACTACATCCGTGAGGTAATGTGGTGAAGTCTGCCGTGTCGGTTATTCCAAAATGCTGCTGGGTGTTATGCCTCGTTTATAGAGCATAAGCAGCGCAACACCTTATCTGGTTGCC'
assert expectedFwdNative == self.fwdAln.read(aligned=False)
assert expectedFwdNative == self.fwdAln.read(
aligned=False, orientation="genomic")
expectedRevNative = "TAGCCACCGGATATCACCACAGGTGAGGCCGTGTAAGTTGAGGTTTTTCTACGTCAGATTCTTTTGGGATTGGGCTTGGGTTTATTTCCTGGTGCGTTTCGTTGAAGGTATTTGCAGTTTTCGCAGATTATGCCTCCGGTGATACTTCGTCGCTGTCTCGCCACACGTCCTCCTTTTCCTGCGGTAGTGGTAACACCCC"
assert expectedRevNative == self.revAln.read(aligned=False)
assert RC(expectedRevNative) == self.revAln.read(
aligned=False, orientation="genomic")
def testAlignedReference(self):
expectedFwdNative = 'GCCGCGCTGGATG--AACTGATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAACAGGCTGCGGCATTTTGTCCGCGCCGGGCTTCGCTCACTGTTCAGGCCGGAGCCACAGACCGCCGTTG-AATGGGCGGATGCTAATTACTATCTCCCGAAAGAATCCGCATACCAGGAAGGGCGCTGGGAAACACTGCCCTTTCAGCGGGCCATCATGAATGCGATGGGCAGCGACTACATCCGTGAGGTGAATGTGGTGAAGTCTGCCCGTGTCGGTTATTCCAAAATGCTGCTGGGTGTTTATGCCTAC-TTTATAGAGCATAAGCAGCGCAACACCCTTATCTGGTTGCC'
assert expectedFwdNative == self.fwdAln.reference(aligned=True)
assert expectedFwdNative == self.fwdAln.reference()
assert expectedFwdNative == self.fwdAln.reference(
orientation="genomic")
expectedRevNative = 'TAGCCACCGGATATC-CCACAGGTGA-GCCGTGT-AGTTGAAGG-TTTT-TACGTCAGATTCTTTTGGGATT-GGCTTGGGTTTATTT-CTGGTGCGTTTCGTTGGAAGGTATTTGCAGTTTTCGCAGATTATG--T-CGGTGATACTTCGTCGCTGTCTCGCCACACGTCCTCCTTTTCCTGCGGTAGTGGTAACACCCC'
assert expectedRevNative == self.revAln.reference(aligned=True)
assert expectedRevNative == self.revAln.reference()
assert RC(expectedRevNative) == self.revAln.reference(
orientation="genomic")
def testUnalignedReference(self):
expectedFwdNative = "GCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAACAGGCTGCGGCATTTTGTCCGCGCCGGGCTTCGCTCACTGTTCAGGCCGGAGCCACAGACCGCCGTTGAATGGGCGGATGCTAATTACTATCTCCCGAAAGAATCCGCATACCAGGAAGGGCGCTGGGAAACACTGCCCTTTCAGCGGGCCATCATGAATGCGATGGGCAGCGACTACATCCGTGAGGTGAATGTGGTGAAGTCTGCCCGTGTCGGTTATTCCAAAATGCTGCTGGGTGTTTATGCCTACTTTATAGAGCATAAGCAGCGCAACACCCTTATCTGGTTGCC"
assert expectedFwdNative == self.fwdAln.reference(aligned=False)
assert expectedFwdNative == self.fwdAln.reference(
aligned=False, orientation="genomic")
expectedRevNative = "TAGCCACCGGATATCCCACAGGTGAGCCGTGTAGTTGAAGGTTTTTACGTCAGATTCTTTTGGGATTGGCTTGGGTTTATTTCTGGTGCGTTTCGTTGGAAGGTATTTGCAGTTTTCGCAGATTATGTCGGTGATACTTCGTCGCTGTCTCGCCACACGTCCTCCTTTTCCTGCGGTAGTGGTAACACCCC"
assert expectedRevNative == self.revAln.reference(aligned=False)
assert 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 testTranscript(self):
assert ('MMMMMMRMDMMMMIIMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM'
'MMDMMMMMMMMMMMMMMMMMMMMMMMMMMDMMMMMMMMMMMMMMMMMMMMMMMMMMDM'
'MMMMMMMMMMMMMMIMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMDMMMDMM'
'MMMMMMMMMMMMRMMMMMMMMMMMMMMMMMMMMMMMMMDMMMMMMMMMMMMMMMMMMM'
'MMMMMMMMMMMMMMMMMMMMDMMMMMMMMMMMMMMMMDMMMMMMMMMMMMMMMMMMMM'
'MMMMMMMMMMMMDMMMMMMMMDMIMMMMMMMMMMMMMMMMMMMMMMMMMDMMMMMMMM'
'MMMMMMM') == self.fwdAln.transcript()
assert ("MMMMMMMMMMMMMMMIMMMMMMMMMMIMMMMMMMIMMMMMDMMMIMMMMIMMMMMMMM"
"MMMMMMMMMMMMMMIMMMMMMMMMMMMMMMIMMMMMMMMMMMMMMMDMMMMMMMMMMM"
"MMMMMMMMMMMMMMMMMMIIMIMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM"
"MMMMMMMMMMMMMMMMMMMMMMMMMMM") == self.revAln.transcript()
def testClippedAlignments(self):
# Get a more interesting (more gappy) fwd strand aln
a = self.fwdAln
assert [(980, 'C', 'C'),
(981, 'C', 'C'),
(982, 'T', 'T'),
(983, 'A', '-'),
(984, 'C', 'C'),
(985, '-', 'G'),
(985, 'T', 'T'),
(986, 'T', 'T')] == list(zip(
a.referencePositions(),
a.reference(),
a.read()))[308:316]
ac1 = a.clippedTo(983, 985)
assert 983 == ac1.referenceStart
assert 985 == ac1.referenceEnd
assert [
(983, 'A', '-'),
(984, 'C', 'C')] == list(zip(
ac1.referencePositions(),
ac1.reference(),
ac1.read()))
ac2 = a.clippedTo(982, 986)
assert 982 == ac2.referenceStart
assert 986 == ac2.referenceEnd
assert [
(982, 'T', 'T'),
(983, 'A', '-'),
(984, 'C', 'C'),
(985, '-', 'G'),
(985, 'T', 'T')] == list(zip(
ac2.referencePositions(),
ac2.reference(),
ac2.read()))
ac3 = a.clippedTo(984, 985)
assert 984 == ac3.referenceStart
assert 985 == ac3.referenceEnd
assert [
(984, 'C', 'C')] == list(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 testReadsInRange(self):
wLen = 1000
for wStart in range(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))])
assert expectedNames == set(
[a.readName for a in self.f.readsInRange("lambda_NEB3011", wStart, wEnd)])
def testReadGroupTable(self):
rgFwd = self.fwdAln.readGroupInfo
assert [
('ID', '<i4'),
('MovieName', 'O'),
('ReadType', 'O'),
('SequencingChemistry', 'O'),
('FrameRate', '<f8'),
('SampleName', 'O'),
('LibraryName', 'O'),
('BaseFeatures', 'O')] == rgFwd.dtype
assert isinstance(rgFwd.BaseFeatures, frozenset)
assert 'S/P4-C2/5.0-8M' == rgFwd.SequencingChemistry
assert "m140905_042212_sidney_c100564852550000001823085912221377_s1_X0" == rgFwd.MovieName
def testSequencingChemistry(self):
assert ['S/P4-C2/5.0-8M'] == self.f.sequencingChemistry
assert 'S/P4-C2/5.0-8M' == self.fwdAln.sequencingChemistry
assert 'S/P4-C2/5.0-8M' == self.revAln.sequencingChemistry
class _IndexedAlnFileReaderTests(_BasicAlnFileReaderTests):
"""
Abstract base class for tests of the reader functionality
requiring an alignment index (or bam.pbi index)
"""
def testMapQV(self):
c = Counter(self.f.mapQV)
assert Counter({254: 112}) == c
def testHoleNumbers(self):
c = Counter([a.holeNumber for a in self.f]) # from records
c2 = Counter(self.f.holeNumber) # from index
expected = Counter({37134: 14, 6251: 10, 32861: 8, 14743: 4,
35858: 3, 39571: 3, 13473: 3, 32560: 3, 46835: 3, 47698: 3,
16996: 3, 30983: 2, 38025: 2, 36363: 2, 23454: 2, 49194: 2,
24494: 2, 20211: 2, 50621: 2, 12736: 2, 19915: 2, 6469: 2,
31174: 2, 32328: 2, 42827: 2, 7247: 2, 50257: 2, 2771: 2,
1650: 2, 24962: 1, 32901: 1, 36628: 1, 7957: 1, 26262: 1,
15641: 1, 49050: 1, 19360: 1, 42165: 1, 44356: 1, 51534: 1,
29843: 1, 38754: 1, 52206: 1, 49521: 1, 45203: 1, 7670: 1,
54396: 1, 19837: 1})
assert expected == c
assert expected == c2
def testErrorCounts(self):
for aln in [self.fwdAln, self.revAln]:
counts = Counter(aln.transcript())
assert counts["M"] == aln.nM
assert counts["R"] == aln.nMM
assert counts["I"] == aln.nIns
assert counts["D"] == aln.nDel
def testReadsByName(self):
reads2771_1 = self.f.readsByName(
"m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/2771/*")
reads2771_2 = self.f.readsByName(
"m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/2771")
reads2771_3 = self.f.readsByName(
"m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/2771/")
expectedReadNames = ["m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/2771/8741_8874",
"m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/2771/8942_9480"]
assert expectedReadNames == [r.readName for r in reads2771_1]
assert expectedReadNames == [r.readName for r in reads2771_2]
assert expectedReadNames == [r.readName for r in reads2771_3]
class TestBasicBam(_BasicAlnFileReaderTests):
READER_CONSTRUCTOR = BamReader
CONSTRUCTOR_ARGS = (data.getAlignedBam(), data.getLambdaFasta())
def testSpecVersion(self):
assert "3.0.1" == self.f.version
def testReadScore(self):
assert 0.904 == pytest.approx(self.fwdAln.readScore)
def test_sample_name_default(self):
assert "UnnamedSample" == self.f.readGroupTable[0].SampleName
def test_library_name_default(self):
assert "UnnamedLibrary" == self.f.readGroupTable[0].LibraryName
class TestIndexedBam(_IndexedAlnFileReaderTests):
READER_CONSTRUCTOR = IndexedBamReader
CONSTRUCTOR_ARGS = (data.getAlignedBam(), data.getLambdaFasta())
def test_empty_bam(self):
fn = data.getEmptyBam()
bam = IndexedBamReader(fn)
assert len(bam) == 0
def test_alignment_identity(self):
"""
Check that the values of the 'identity' property are consistent
between IndexedBamReader (numpy array) and BamAlignment (float)
"""
fn = data.getAlignedBam()
with IndexedBamReader(fn) as bam_in:
i1 = bam_in.identity
i2 = np.array([rec.identity for rec in bam_in])
assert (i2 == i1).all()
def test_alignment_identity_unindexed(self):
"""
Check that the value of the 'identity' property is the same whether
or not the .pbi index was used to calculate it.
"""
fn1 = data.getAlignedBam()
fn2 = tempfile.NamedTemporaryFile(suffix=".bam").name
shutil.copyfile(fn1, fn2)
with IndexedBamReader(fn1) as bam_pbi:
with BamReader(fn2) as bam_noindex:
i1 = np.array([rec.identity for rec in bam_pbi])
i2 = np.array([rec.identity for rec in bam_noindex])
assert (i2 == i1).all()
class TestCCSBam:
@classmethod
def setup_class(cls):
cls.f = BamReader(data.getCCSBAM())
@pytest.mark.skip(reason="broken")
def testBasicOperations(self):
assert False == self.f.isEmpty
assert False == self.f.isSorted
assert 18 == len(self.f)
def testQStartEndUnavailable(self):
for aln in self.f:
with pytest.raises(UnavailableFeature):
aln.qStart
with pytest.raises(UnavailableFeature):
aln.qEnd
@pytest.mark.internal_data
class TestTranscriptBam:
BAM_FILE = "/pbi/dept/secondary/siv/testdata/isoseqs/TranscriptSet/unpolished.bam"
@classmethod
def setup_class(cls):
cls.f = IndexedBamReader(cls.BAM_FILE)
def test_transcript_set_support(self):
assert len(self.f) == 12218
class TestEmptyBam:
def test_empty_bam_reads_in_range(self):
with IndexedBamReader(data.getEmptyAlignedBam()) as bam:
reads = bam.readsInRange("lambda_NEB3011", 0, 50000,
justIndices=True)
assert len(reads) == 0
class TestMultipleReadGroups:
"""
Verify that BAM files with multiple read groups are handled sensibly - see
bug 26548.
"""
SAM_IN = """\
@HD\tVN:1.5\tSO:coordinate\tpb:3.0.7
@SQ\tSN:ecoliK12_pbi_March2013_2955000_to_2980000\tLN:25000\tM5:734d5f3b2859595f4bd87a2fe6b7389b
@RG\tID:19d45c63\tPL:PACBIO\tDS:READTYPE=SUBREAD;Ipd:CodecV1=ip;PulseWidth:CodecV1=pw;BINDINGKIT=101-789-500;SEQUENCINGKIT=101-789-300;BASECALLERVERSION=5.0.0;FRAMERATEHZ=100.000000\tPU:movie1\tPM:SEQUELII\tSM:test_sample1
@RG\tID:69995355\tPL:PACBIO\tDS:READTYPE=SUBREAD;Ipd:CodecV1=ip;PulseWidth:CodecV1=pw;BINDINGKIT=101-789-500;SEQUENCINGKIT=101-789-300;BASECALLERVERSION=5.0.0;FRAMERATEHZ=100.000000\tPU:m64012_181222_192540\tPM:SEQUELII\tSM:test_sample2
movie1/54130/0_10\t2\tecoliK12_pbi_March2013_2955000_to_2980000\t2\t10\t10=\t*\t0\t0\tAATGAGGAGA\t*\tRG:Z:19d45c63\tdq:Z:2222'$22'2\tdt:Z:NNNNAGNNGN\tip:B:C,255,2,0,10,22,34,0,2,3,0,16\tiq:Z:(+#1'$#*1&\tmq:Z:&1~51*5&~2\tnp:i:1\tqe:i:10\tqs:i:0\trq:f:0.854\tsn:B:f,2,2,2,2\tsq:Z:<32<4<<<<3\tzm:i:54130\tAS:i:-3020\tNM:i:134\tcx:i:2
m64012_181222_192540/1/10_20\t2\tecoliK12_pbi_March2013_2955000_to_2980000\t12\t10\t10=\t*\t0\t0\tAATGAGGAGA\t*\tRG:Z:69995355\tdq:Z:2222'$22'2\tdt:Z:NNNNAGNNGN\tip:B:C,255,2,0,10,22,34,0,2,3,0,16\tiq:Z:(+#1'$#*1&\tmq:Z:&1~51*5&~2\tnp:i:1\tqe:i:20\tqs:i:10\trq:f:0.854\tsn:B:f,2,2,2,2\tsq:Z:<32<4<<<<3\tzm:i:54130\tAS:i:-3020\tNM:i:134\tcx:i:2"""
@classmethod
def setup_class(cls):
f1 = tempfile.NamedTemporaryFile(suffix=".sam").name
f2 = tempfile.NamedTemporaryFile(suffix=".bam").name
with open(f1, "w") as f:
f.write(cls.SAM_IN)
with AlignmentFile(f1) as sam_in:
with AlignmentFile(f2, 'wb', template=sam_in) as bam_out:
for aln in sam_in:
bam_out.write(aln)
cls.bam_file = f2
def test_retrieve_read_group_properties(self):
movie_names = []
with BamReader(self.bam_file) as bam_in:
for aln in bam_in:
assert aln.sequencingChemistry == 'S/P4-C2/5.0-8M'
movie_names.extend([rg.MovieName for rg in bam_in.readGroupTable])
assert movie_names == ['movie1', 'm64012_181222_192540']
def test_sample_names(self):
with BamReader(self.bam_file) as bam:
samples = {rg.MovieName: rg.SampleName for rg in bam.readGroupTable}
assert samples == {
"movie1": "test_sample1",
"m64012_181222_192540": "test_sample2"}
class TestMissingHeaderM5:
"""
Verify that BAM files no M5 for SQ can still be processed
"""
SAM_IN = """\
@HD\tVN:1.5\tSO:coordinate\tpb:3.0.7
@SQ\tSN:ecoliK12_pbi_March2013_2955000_to_2980000\tLN:25000
@RG\tID:19d45c63\tPL:PACBIO\tDS:READTYPE=SUBREAD;Ipd:CodecV1=ip;PulseWidth:CodecV1=pw;BINDINGKIT=101-789-500;SEQUENCINGKIT=101-789-300;BASECALLERVERSION=5.0.0;FRAMERATEHZ=100.000000\tPU:movie1\tPM:SEQUELII
@RG\tID:69995355\tPL:PACBIO\tDS:READTYPE=SUBREAD;Ipd:CodecV1=ip;PulseWidth:CodecV1=pw;BINDINGKIT=101-789-500;SEQUENCINGKIT=101-789-300;BASECALLERVERSION=5.0.0;FRAMERATEHZ=100.000000\tPU:m64012_181222_192540\tPM:SEQUELII
movie1/54130/0_10\t2\tecoliK12_pbi_March2013_2955000_to_2980000\t2\t10\t10=\t*\t0\t0\tAATGAGGAGA\t*\tRG:Z:19d45c63\tdq:Z:2222'$22'2\tdt:Z:NNNNAGNNGN\tip:B:C,255,2,0,10,22,34,0,2,3,0,16\tiq:Z:(+#1'$#*1&\tmq:Z:&1~51*5&~2\tnp:i:1\tqe:i:10\tqs:i:0\trq:f:0.854\tsn:B:f,2,2,2,2\tsq:Z:<32<4<<<<3\tzm:i:54130\tAS:i:-3020\tNM:i:134\tcx:i:2
m64012_181222_192540/1/10_20\t2\tecoliK12_pbi_March2013_2955000_to_2980000\t12\t10\t10=\t*\t0\t0\tAATGAGGAGA\t*\tRG:Z:69995355\tdq:Z:2222'$22'2\tdt:Z:NNNNAGNNGN\tip:B:C,255,2,0,10,22,34,0,2,3,0,16\tiq:Z:(+#1'$#*1&\tmq:Z:&1~51*5&~2\tnp:i:1\tqe:i:20\tqs:i:10\trq:f:0.854\tsn:B:f,2,2,2,2\tsq:Z:<32<4<<<<3\tzm:i:54130\tAS:i:-3020\tNM:i:134\tcx:i:2"""
def test_retrieve_read_group_properties(self):
f1 = tempfile.NamedTemporaryFile(suffix=".sam").name
f2 = tempfile.NamedTemporaryFile(suffix=".bam").name
with open(f1, "w") as f:
f.write(self.SAM_IN)
with AlignmentFile(f1) as sam_in:
with AlignmentFile(f2, 'wb', template=sam_in) as bam_out:
for aln in sam_in:
bam_out.write(aln)
movie_names = []
with BamReader(f2) as bam_in:
for aln in bam_in:
assert aln.sequencingChemistry == 'S/P4-C2/5.0-8M'
movie_names.append(aln.movieName)
assert movie_names == ['movie1', 'm64012_181222_192540']
class TestUpdatedChemistryMapping:
"""
Verify we load the mapping from the updated chemistry mapping.xml
from SMRT_CHEMISTRY_BUNDLE_DIR
"""
def test_load_updated_mapping(self):
import os
from os.path import dirname
from pbcore.chemistry.chemistry import _loadBarcodeMappings
os.environ["SMRT_CHEMISTRY_BUNDLE_DIR"] = dirname(data.getMappingXml())
mappings = _loadBarcodeMappings()
assert mappings.get(("1", "2", "3.4"), None) == "FOUND"
del os.environ["SMRT_CHEMISTRY_BUNDLE_DIR"]
mappings = _loadBarcodeMappings()
assert mappings.get(("1", "2", "3.4"), None) is None
class TestBarcodedBam:
@pytest.mark.internal_data
def test_read_lima_demultiplexed_bam(self):
fn = "/pbi/dept/secondary/siv/testdata/pbcore-unittest/data/demultiplex.lbc1--lbc1.bam"
bam = IndexedBamReader(fn)
assert str(bam[0]) == "Unmapped BAM record: m54008_160219_003234/74056024/1184_3910"
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