def test_call(self):
"""The 'call' command."""
# Methods: clonal, threshold
tr_cns = cnvlib.read("formats/tr95t.cns")
tr_thresh = commands.do_call(tr_cns,
"threshold",
is_reference_male=True,
is_sample_female=True)
self.assertEqual(len(tr_cns), len(tr_thresh))
tr_clonal = commands.do_call(tr_cns,
"clonal",
purity=.65,
is_reference_male=True,
is_sample_female=True)
self.assertEqual(len(tr_cns), len(tr_clonal))
cl_cns = cnvlib.read("formats/cl_seq.cns")
cl_thresh = commands.do_call(cl_cns,
"threshold",
thresholds=np.log2(
(np.arange(12) + .5) / 6.),
is_reference_male=True,
is_sample_female=True)
self.assertEqual(len(cl_cns), len(cl_thresh))
cl_clonal = commands.do_call(cl_cns,
"clonal",
ploidy=6,
purity=.99,
is_reference_male=True,
is_sample_female=True)
self.assertEqual(len(cl_cns), len(cl_clonal))
def test_call_sex(self):
"""Test each 'call' method on allosomes."""
for (
fname,
sample_is_f,
ref_is_m,
chr1_expect,
chrx_expect,
chry_expect,
chr1_cn,
chrx_cn,
chry_cn,
) in (
("formats/f-on-f.cns", True, False, 0, 0, None, 2, 2, None),
("formats/f-on-m.cns", True, True, 0.585, 1, None, 3, 2, None),
("formats/m-on-f.cns", False, False, 0, -1, 0, 2, 1, 1),
("formats/m-on-m.cns", False, True, 0, 0, 0, 2, 1, 1),
):
cns = cnvlib.read(fname)
chr1_idx = (cns.chromosome == 'chr1')
chrx_idx = (cns.chromosome == 'chrX')
chry_idx = (cns.chromosome == 'chrY')
def test_chrom_means(segments):
self.assertEqual(chr1_cn, segments['cn'][chr1_idx].mean())
self.assertAlmostEqual(chr1_expect,
segments['log2'][chr1_idx].mean(), 0)
self.assertEqual(chrx_cn, segments['cn'][chrx_idx].mean())
self.assertAlmostEqual(chrx_expect,
segments['log2'][chrx_idx].mean(), 0)
if not sample_is_f:
self.assertEqual(chry_cn, segments['cn'][chry_idx].mean())
self.assertAlmostEqual(chry_expect,
segments['log2'][chry_idx].mean(),
0)
# Call threshold
cns_thresh = commands.do_call(cns,
None,
"threshold",
is_reference_male=ref_is_m,
is_sample_female=sample_is_f)
test_chrom_means(cns_thresh)
# Call clonal pure
cns_clone = commands.do_call(cns,
None,
"clonal",
is_reference_male=ref_is_m,
is_sample_female=sample_is_f)
test_chrom_means(cns_clone)
# Call clonal barely-mixed
cns_p99 = commands.do_call(cns,
None,
"clonal",
purity=0.99,
is_reference_male=ref_is_m,
is_sample_female=sample_is_f)
test_chrom_means(cns_p99)
def test_call(self):
# Methods: clonal, threshold
tr_cns = cnvlib.read("formats/tr95t.cns")
tr_thresh = commands.do_call(tr_cns, "threshold",
is_reference_male=True, is_sample_female=True)
self.assertEqual(len(tr_cns), len(tr_thresh))
tr_clonal = commands.do_call(tr_cns, "clonal",
purity=.65,
is_reference_male=True, is_sample_female=True)
self.assertEqual(len(tr_cns), len(tr_clonal))
cl_cns = cnvlib.read("formats/cl_seq.cns")
cl_thresh = commands.do_call(cl_cns, "threshold",
thresholds=np.log2((np.arange(12) + .5) / 6.),
is_reference_male=True, is_sample_female=True)
self.assertEqual(len(cl_cns), len(cl_thresh))
cl_clonal = commands.do_call(cl_cns, "clonal",
ploidy=6, purity=.99,
is_reference_male=True, is_sample_female=True)
self.assertEqual(len(cl_cns), len(cl_clonal))
def test_call_sex(self):
"""Test each 'call' method on allosomes."""
for (fname, sample_is_f, ref_is_m,
chr1_expect, chrx_expect, chry_expect,
chr1_cn, chrx_cn, chry_cn,
) in (
("formats/f-on-f.cns", True, False, 0, 0, None, 2, 2, None),
("formats/f-on-m.cns", True, True, 0.585, 1, None, 3, 2, None),
("formats/m-on-f.cns", False, False, 0, -1, 0, 2, 1, 1),
("formats/m-on-m.cns", False, True, 0, 0, 0, 2, 1, 1),
):
cns = cnvlib.read(fname)
chr1_idx = (cns.chromosome == 'chr1')
chrx_idx = (cns.chromosome == 'chrX')
chry_idx = (cns.chromosome == 'chrY')
def test_chrom_means(segments):
self.assertEqual(chr1_cn, segments['cn'][chr1_idx].mean())
self.assertAlmostEqual(chr1_expect,
segments['log2'][chr1_idx].mean(), 0)
self.assertEqual(chrx_cn, segments['cn'][chrx_idx].mean())
self.assertAlmostEqual(chrx_expect,
segments['log2'][chrx_idx].mean(), 0)
if not sample_is_f:
self.assertEqual(chry_cn, segments['cn'][chry_idx].mean())
self.assertAlmostEqual(chry_expect,
segments['log2'][chry_idx].mean(), 0)
# Call threshold
cns_thresh = commands.do_call(cns, None, "threshold",
is_reference_male=ref_is_m,
is_sample_female=sample_is_f)
test_chrom_means(cns_thresh)
# Call clonal pure
cns_clone = commands.do_call(cns, None, "clonal",
is_reference_male=ref_is_m,
is_sample_female=sample_is_f)
test_chrom_means(cns_clone)
# Call clonal barely-mixed
cns_p99 = commands.do_call(cns, None, "clonal", purity=0.99,
is_reference_male=ref_is_m,
is_sample_female=sample_is_f)
test_chrom_means(cns_p99)
def test_call_filter(self):
segments = cnvlib.read("formats/tr95t.segmetrics.cns")
variants = tabio.read("formats/na12878_na12882_mix.vcf", "vcf")
# Each filter individually, then all filters together
for filters in (['ampdel'], ['cn'], ['ci'], ['sem'],
['sem', 'cn', 'ampdel'],
['ci', 'cn', 'ampdel']):
result = commands.do_call(segments, variants, method="threshold",
purity=.9, is_reference_male=True,
is_sample_female=True, filters=filters)
self.assertLessEqual(len(result), len(segments))
self.assertLessEqual(len(segments.chromosome.unique()), len(result))
for colname in 'baf', 'cn', 'cn1', 'cn2':
self.assertIn(colname, result)
def test_call_filter(self):
segments = cnvlib.read("formats/tr95t.segmetrics.cns")
variants = tabio.read("formats/na12878_na12882_mix.vcf", "vcf")
# Each filter individually, then all filters together
for filters in (['ampdel'], ['cn'], ['ci'], ['sem'],
['sem', 'cn', 'ampdel'],
['ci', 'cn']):
result = commands.do_call(segments, variants, method="threshold",
purity=.9, is_reference_male=True,
is_sample_female=True, filters=filters)
self.assertLessEqual(len(result), len(segments))
if 'ampdel' not in filters:
# At least 1 segment per chromosome remains
self.assertLessEqual(len(segments.chromosome.unique()),
len(result))
for colname in 'baf', 'cn', 'cn1', 'cn2':
self.assertIn(colname, result)