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()
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 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_movie_filter(self):
# unaligned bam
bam0 = ("/pbi/dept/secondary/siv/testdata/"
"SA3-DS/ecoli/2590956/0003/"
"Analysis_Results/m140913_222218_42240_c10069"
"9952400000001823139203261564_s1_p0.all.subreadset.xml")
bam1 = ("/pbi/dept/secondary/siv/testdata/"
"SA3-DS/ecoli/2590953/0001/"
"Analysis_Results/m140913_005018_42139_c10071"
"3652400000001823152404301534_s1_p0.all.subreadset.xml")
aln = SubreadSet(bam0, bam1)
assert len(set(aln.readGroupTable['ID'])) == len(
aln.readGroupTable['ID'])
assert len(set(aln.readGroupTable['ID'])) == 2
assert len(set(aln.readGroupTable['ID'])) == len(set(aln.index.qId))
assert len(aln) == 178570
aln.filters.addRequirement(movie=[(
'=',
'm140913_005018_42139_c100713652400000001823152404301534_s1_p0')])
assert len(SubreadSet(bam1)) == len(aln)
# aligned bam
# bam0 = ("/pbi/dept/secondary/siv/testdata/"
# "SA3-DS/ecoli/2590956/0003/Alignment_Results/"
# "m140913_222218_42240_c1006999524000000018231"
# "39203261564_s1_p0.all.alignmentset.xml")
bam0 = upstreamdata.getAlignedBam()
bam1 = ("/pbi/dept/secondary/siv/testdata/"
"SA3-DS/ecoli/2590953/0001/Alignment_Results/"
"m140913_005018_42139_c1007136524000000018231"
"52404301534_s1_p0.all.alignmentset.xml")
aln = AlignmentSet(bam0, bam1)
assert len(set(aln.readGroupTable['ID'])) == len(
aln.readGroupTable['ID'])
assert len(set(aln.readGroupTable['ID'])) == 2
assert len(set(aln.readGroupTable['ID'])) == len(set(aln.index.qId))
assert len(aln) == 103144
aln.filters.addRequirement(movie=[(
'=',
'm140913_005018_42139_c100713652400000001823152404301534_s1_p0')])
assert len(AlignmentSet(bam1)) == len(aln)
