def test_export_nexus(self):
"""The 'export nexus-basic' and 'nexus-ogt' commands."""
cnr = cnvlib.read("formats/amplicon.cnr")
table_nb = export.export_nexus_basic(cnr)
self.assertEqual(len(table_nb), len(cnr))
varr = commands.load_het_snps("formats/na12878_na12882_mix.vcf", None,
None, 15, None)
table_ogt = export.export_nexus_ogt(cnr, varr, 0.05)
self.assertEqual(len(table_ogt), len(cnr))
def test_export_nexus(self):
"""The 'export nexus-basic' and 'nexus-ogt' commands."""
cnr = cnvlib.read("formats/amplicon.cnr")
table_nb = export.export_nexus_basic(cnr)
self.assertEqual(len(table_nb), len(cnr))
varr = commands.load_het_snps("formats/na12878_na12882_mix.vcf",
None, None, 15, None)
table_ogt = export.export_nexus_ogt(cnr, varr, 0.05)
self.assertEqual(len(table_ogt), len(cnr))
def test_export_theta(self):
"""The 'export theta' command."""
segarr = cnvlib.read("formats/tr95t.cns")
len_seg_auto = len(segarr.autosomes())
table_theta = export.export_theta(segarr, None)
self.assertEqual(len(table_theta), len_seg_auto)
ref = cnvlib.read("formats/reference-tr.cnn")
table_theta = export.export_theta(segarr, ref)
self.assertEqual(len(table_theta), len_seg_auto)
varr = commands.load_het_snps("formats/na12878_na12882_mix.vcf",
"NA12882", "NA12878", 15, None)
tumor_snps, normal_snps = export.export_theta_snps(varr)
self.assertLess(len(tumor_snps), len(varr))
self.assertGreater(len(tumor_snps), 0)
self.assertLess(len(normal_snps), len(varr))
self.assertGreater(len(normal_snps), 0)
def test_export_theta(self):
"""The 'export theta' command."""
segarr = cnvlib.read("formats/tr95t.cns")
len_seg_auto = len(segarr.autosomes())
table_theta = export.export_theta(segarr, None)
self.assertEqual(len(table_theta), len_seg_auto)
ref = cnvlib.read("formats/reference-tr.cnn")
table_theta = export.export_theta(segarr, ref)
self.assertEqual(len(table_theta), len_seg_auto)
varr = commands.load_het_snps("formats/na12878_na12882_mix.vcf",
"NA12882", "NA12878", 15, None)
tumor_snps, normal_snps = export.export_theta_snps(varr)
self.assertLess(len(tumor_snps), len(varr))
self.assertGreater(len(tumor_snps), 0)
self.assertLess(len(normal_snps), len(varr))
self.assertGreater(len(normal_snps), 0)
