def test_segment_parallel(self):
"""The 'segment' command, in parallel."""
cnarr = cnvlib.read("formats/amplicon.cnr")
psegments = segmentation.do_segmentation(cnarr, "haar", processes=2)
ssegments = segmentation.do_segmentation(cnarr, "haar", processes=1)
self.assertEqual(psegments.data.shape, ssegments.data.shape)
self.assertEqual(len(psegments.meta), len(ssegments.meta))
def test_segment(self):
"""The 'segment' command."""
# R methods are in another script
segments = segmentation.do_segmentation("formats/amplicon.cnr", "haar")
self.assertTrue(len(segments) > 0)
segments = segmentation.do_segmentation("formats/amplicon.cnr", "haar",
threshold=.001, skip_low=True)
self.assertTrue(len(segments) > 0)
def test_segment(self):
"""The 'segment' command."""
cnarr = cnvlib.read("formats/amplicon.cnr")
# R methods are in another script
segments = segmentation.do_segmentation(cnarr, "haar")
self.assertGreater(len(segments), 0)
segments = segmentation.do_segmentation(cnarr, "haar", threshold=.001,
skip_low=True)
self.assertGreater(len(segments), 0)
def test_segment(self):
cnarr = cnvlib.read("formats/amplicon.cnr")
# Each method
for method in ("cbs", "flasso"):
cns = segmentation.do_segmentation(cnarr, method)
self.assertGreater(len(cns), 0)
# With the R dataframe
cns, dframe = segmentation.do_segmentation(cnarr, "flasso", 0.01,
save_dataframe=True)
self.assertGreater(len(cns), 0)
self.assertGreater(len(dframe), 0)
def test_segment_hmm(self):
"""The 'segment' command with HMM methods."""
for fname in ("formats/amplicon.cnr", "formats/p2-20_1.cnr"):
cnarr = cnvlib.read(fname)
n_chroms = cnarr.chromosome.nunique()
# NB: R methods are in another script; haar is pure-Python
segments = segmentation.do_segmentation(cnarr, "hmm")
self.assertGreater(len(segments), n_chroms)
segments = segmentation.do_segmentation(cnarr, "hmm-tumor",
skip_low=True)
self.assertGreater(len(segments), n_chroms)
segments = segmentation.do_segmentation(cnarr, "hmm-germline")
self.assertGreater(len(segments), n_chroms)
def test_segment(self):
"""The 'segment' command."""
cnarr = cnvlib.read("formats/amplicon.cnr")
n_chroms = cnarr.chromosome.nunique()
# NB: R methods are in another script; haar is pure-Python
segments = segmentation.do_segmentation(cnarr, "haar")
self.assertGreater(len(segments), n_chroms)
segments = segmentation.do_segmentation(cnarr, "haar", threshold=.0001,
skip_low=True)
self.assertGreater(len(segments), n_chroms)
varr = tabio.read("formats/na12878_na12882_mix.vcf", "vcf")
segments = segmentation.do_segmentation(cnarr, "haar", variants=varr)
self.assertGreater(len(segments), n_chroms)
def _test_method(self, method):
for cnr in (self.tas_cnr,
# self.wgs_cnr
):
cns, raw_str = segmentation.do_segmentation(cnr, method, processes=1,
save_dataframe=True)
self.assertGreater(len(cns), 0)
self.assertGreater(len(raw_str), 0)
# Parallel should produce the same results
p_cns, p_raw_str = segmentation.do_segmentation(cnr, method,
processes=2,
save_dataframe=True)
self.assertEqual(cns.data.shape, p_cns.data.shape)
self.assertEqual(len(cns.meta), len(p_cns.meta))
self.assertEqual(raw_str, p_raw_str)
def test_gainloss(self):
probes = cnvlib.read("formats/amplicon.cnr")
rows = commands.do_gainloss(probes, male_reference=True)
self.assertTrue(len(rows) > 0)
segs = segmentation.do_segmentation("formats/amplicon.cnr", False,
"haar")
rows = commands.do_gainloss(probes, segs, True, 0.3, 4)
self.assertTrue(len(rows) > 0)
def test_segment(self):
"""The 'segment' command."""
cnarr = cnvlib.read("formats/amplicon.cnr")
n_chroms = cnarr.chromosome.nunique()
# NB: R methods are in another script; haar is pure-Python
segments = segmentation.do_segmentation(cnarr, "haar")
self.assertGreater(len(segments), n_chroms)
self.assertTrue((segments.start < segments.end).all())
segments = segmentation.do_segmentation(cnarr,
"haar",
threshold=.0001,
skip_low=True)
self.assertGreater(len(segments), n_chroms)
self.assertTrue((segments.start < segments.end).all())
varr = tabio.read("formats/na12878_na12882_mix.vcf", "vcf")
segments = segmentation.do_segmentation(cnarr, "haar", variants=varr)
self.assertGreater(len(segments), n_chroms)
self.assertTrue((segments.start < segments.end).all())
def test_segment_hmm(self):
"""The 'segment' command with HMM methods."""
for fname in ("formats/amplicon.cnr", "formats/p2-20_1.cnr"):
cnarr = cnvlib.read(fname)
n_chroms = cnarr.chromosome.nunique()
# NB: R methods are in another script; haar is pure-Python
segments = segmentation.do_segmentation(cnarr, "hmm")
self.assertGreater(len(segments), n_chroms)
self.assertTrue((segments.start < segments.end).all())
segments = segmentation.do_segmentation(cnarr, "hmm-tumor",
skip_low=True)
self.assertGreater(len(segments), n_chroms)
self.assertTrue((segments.start < segments.end).all())
segments = segmentation.do_segmentation(cnarr, "hmm-germline")
self.assertGreater(len(segments), n_chroms)
self.assertTrue((segments.start < segments.end).all())
varr = tabio.read("formats/na12878_na12882_mix.vcf", "vcf")
segments = segmentation.do_segmentation(cnarr, "hmm", variants=varr)
self.assertGreater(len(segments), n_chroms)
def test_segment_hmm(self):
"""The 'segment' command with HMM methods."""
for fname in ("formats/amplicon.cnr", "formats/p2-20_1.cnr"):
cnarr = cnvlib.read(fname)
n_chroms = cnarr.chromosome.nunique()
# NB: R methods are in another script; haar is pure-Python
segments = segmentation.do_segmentation(cnarr, "hmm")
self.assertGreater(len(segments), n_chroms)
self.assertTrue((segments.start < segments.end).all())
segments = segmentation.do_segmentation(cnarr,
"hmm-tumor",
skip_low=True)
self.assertGreater(len(segments), n_chroms)
self.assertTrue((segments.start < segments.end).all())
segments = segmentation.do_segmentation(cnarr, "hmm-germline")
self.assertGreater(len(segments), n_chroms)
self.assertTrue((segments.start < segments.end).all())
varr = tabio.read("formats/na12878_na12882_mix.vcf", "vcf")
segments = segmentation.do_segmentation(cnarr,
"hmm",
variants=varr)
self.assertGreater(len(segments), n_chroms)
def test_segment(self):
# R methods are in another script
cns = segmentation.do_segmentation("formats/amplicon.cnr", False,
"haar")
self.assertTrue(len(cns) > 0)
def test_breaks(self):
probes = cnvlib.read("formats/amplicon.cnr")
segs = segmentation.do_segmentation("formats/amplicon.cnr", False,
"haar")
rows = commands.do_breaks(probes, segs, 4)
self.assertTrue(len(rows) > 0)