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(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)