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 TestIndexedBam(_IndexedAlnFileReaderTests):
READER_CONSTRUCTOR = IndexedBamReader
CONSTRUCTOR_ARGS = (data.getBamAndCmpH5()[0], data.getLambdaFasta())
def test_empty_bam(self):
fn = data.getEmptyBam()
bam = IndexedBamReader(fn)
EQ(len(bam), 0)
class TestBasicBam(_BasicAlnFileReaderTests):
READER_CONSTRUCTOR = BamReader
CONSTRUCTOR_ARGS = (data.getBamAndCmpH5()[0], data.getLambdaFasta())
def testSpecVersion(self):
EQ("3.0.1", self.f.version)
def testReadScore(self):
EQISH(0.904, self.fwdAln.readScore, 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_merged_contigset(self):
fn = tempfile.NamedTemporaryFile(suffix=".contigset.xml").name
with ContigSet(upstreamData.getLambdaFasta(),
upstreamData.getFasta()) as cset:
self.assertEqual(len(list(cset)), 49)
self.assertEqual(len(cset), 49)
cset.consolidate()
cset.write(fn)
log.debug("Writing to {f}".format(f=fn))
self.assertEqual(len(list(cset)), 49)
self.assertEqual(len(cset), 49)
with ContigSet(fn) as cset:
self.assertEqual(len(list(cset)), 49)
self.assertEqual(len(cset), 49)
def test_merged_contigset(self):
fn = tempfile.NamedTemporaryFile(suffix=".contigset.xml").name
with ContigSet(upstreamData.getLambdaFasta(),
upstreamData.getFasta()) as cset:
assert len(list(cset)) == 49
assert len(cset) == 49
cset.consolidate()
cset.write(fn)
log.debug("Writing to {f}".format(f=fn))
assert len(list(cset)) == 49
assert len(cset) == 49
with ContigSet(fn) as cset:
assert len(list(cset)) == 49
assert len(cset) == 49
def test_contigset_write(self):
fasta = upstreamData.getLambdaFasta()
ds = ContigSet(fasta)
assert isinstance(ds.resourceReaders()[0], IndexedFastaReader)
outdir = tempfile.mkdtemp(suffix="dataset-unittest")
outfn = os.path.join(outdir, 'test.fasta')
w = FastaWriter(outfn)
for rec in ds:
w.writeRecord(rec)
w.close()
fas = FastaReader(outfn)
for rec in fas:
# make sure a __repr__ didn't slip through:
assert not rec.sequence.startswith('<')
def test_contigset_write(self):
fasta = upstreamData.getLambdaFasta()
ds = ContigSet(fasta)
self.assertTrue(isinstance(ds.resourceReaders()[0],
IndexedFastaReader))
outdir = tempfile.mkdtemp(suffix="dataset-unittest")
outfn = os.path.join(outdir, 'test.fasta')
w = FastaWriter(outfn)
for rec in ds:
w.writeRecord(rec)
w.close()
fas = FastaReader(outfn)
for rec in fas:
# make sure a __repr__ didn't slip through:
self.assertFalse(rec.sequence.startswith('<'))
def __init__(self):
bamFname, cmpFname = D.getBamAndCmpH5()
lambdaFasta = D.getLambdaFasta()
self.b = PacBioBamReader(bamFname, lambdaFasta)
self.c = CmpH5Reader(cmpFname)
self.bBasic = BamReader(bamFname)
# Note that sorting orders are not generally the same... BAM
# sorts + alns before - alns, when there is a tie on tStart;
# we don't do this in cmp.h5 (we next sort on tEnd). However
# in this file there are no ties on tStart.
self.bAlns = list(self.b)
self.bFwd = self.bAlns[0]
self.bRev = self.bAlns[1]
self.cAlns = list(self.c)
self.cFwd = self.cAlns[0]
self.cRev = self.cAlns[1]
self.cFwdClipped = self.cFwd.clippedTo(10, 60)
self.bFwdClipped = self.bFwd.clippedTo(10, 60)
self.cRevClipped = self.cRev.clippedTo(310, 360)
self.bRevClipped = self.bRev.clippedTo(310, 360)
def test_contigset_index(self):
fasta = upstreamData.getLambdaFasta()
ds = ContigSet(fasta)
self.assertEqual(ds[0].name, "lambda_NEB3011")
class TestIndexedBam(_IndexedAlnFileReaderTests):
READER_CONSTRUCTOR = IndexedBamReader
CONSTRUCTOR_ARGS = (data.getBamAndCmpH5()[0], data.getLambdaFasta())
class TestBasicBam(_BasicAlnFileReaderTests):
READER_CONSTRUCTOR = BamReader
CONSTRUCTOR_ARGS = (data.getBamAndCmpH5()[0], data.getLambdaFasta())
def testSpecVersion(self):
EQ("3.0b7", self.f.version)
def test_contigset_index(self):
fasta = upstreamData.getLambdaFasta()
ds = ContigSet(fasta)
assert ds[0].name == "lambda_NEB3011"
def test_contigset_index(self):
fasta = upstreamData.getLambdaFasta()
ds = ContigSet(fasta)
self.assertEqual(ds[0].name, "lambda_NEB3011")