def test_export(self):
"""Run the 'export' command with each format."""
# SEG
seg_rows = export.export_seg(["formats/tr95t.cns"])
self.assertGreater(len(seg_rows), 0)
seg2_rows = export.export_seg(["formats/tr95t.cns",
"formats/cl_seq.cns"])
self.assertGreater(len(seg2_rows), len(seg_rows))
# THetA2
cnr = cnvlib.read("formats/tr95t.cns")
theta_rows = export.export_theta(cnr, None)
self.assertGreater(len(theta_rows), 0)
ref = cnvlib.read("formats/reference-tr.cnn")
theta_rows = export.export_theta(cnr, ref)
self.assertGreater(len(theta_rows), 0)
# Formats that calculate absolute copy number
for fname, ploidy, is_f in [("tr95t.cns", 2, True),
("cl_seq.cns", 6, True),
("amplicon.cns", 2, False)]:
cns = cnvlib.read("formats/" + fname)
# BED
self.assertLess(len(export.export_bed(cns, ploidy, True, is_f,
cns.sample_id, "ploidy")),
len(cns))
self.assertLess(len(export.export_bed(cns, ploidy, True, is_f,
cns.sample_id, "variant")),
len(cns))
self.assertEqual(len(export.export_bed(cns, ploidy, True, is_f,
cns.sample_id, "all")),
len(cns))
# VCF
_vheader, vcf_body = export.export_vcf(cns, ploidy, True, is_f)
self.assertTrue(0 < len(vcf_body.splitlines()) < len(cns))
def test_export(self):
"""Run the 'export' command with each format."""
# SEG
seg_rows = export.export_seg(["formats/tr95t.cns"])
self.assertGreater(len(seg_rows), 0)
seg2_rows = export.export_seg(["formats/tr95t.cns",
"formats/cl_seq.cns"])
self.assertGreater(len(seg2_rows), len(seg_rows))
# THetA2
cnr = cnvlib.read("formats/tr95t.cns")
theta_rows = export.export_theta(cnr, None)
self.assertGreater(len(theta_rows), 0)
ref = cnvlib.read("formats/reference-tr.cnn")
theta_rows = export.export_theta(cnr, ref)
self.assertGreater(len(theta_rows), 0)
# Formats that calculate absolute copy number
for fname, ploidy, is_f in [("tr95t.cns", 2, True),
("cl_seq.cns", 6, True),
("amplicon.cns", 2, False)]:
cns = cnvlib.read("formats/" + fname)
# BED
self.assertLess(len(export.export_bed(cns, ploidy, True, is_f,
cns.sample_id, "ploidy")),
len(cns))
self.assertLess(len(export.export_bed(cns, ploidy, True, is_f,
cns.sample_id, "variant")),
len(cns))
self.assertEqual(len(export.export_bed(cns, ploidy, True, is_f,
cns.sample_id, "all")),
len(cns))
# VCF
_vheader, vcf_body = export.export_vcf(cns, ploidy, True, is_f)
self.assertTrue(0 < len(vcf_body.splitlines()) < len(cns))
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)
def test_export(self):
# SEG
seg_rows = export.export_seg(["formats/tr95t.cns"])
self.assertTrue(len(seg_rows) > 0)
seg2_rows = export.export_seg(["formats/tr95t.cns",
"formats/cl_seq.cns"])
self.assertTrue(len(seg2_rows) > len(seg_rows))
# THetA2
_header, theta_rows = export.export_theta("formats/tr95t.cns",
"formats/reference-tr.cnn")
self.assertTrue(len(theta_rows) > 0)
# VCF
tr_cns = cnvlib.read("formats/tr95t.cns")
_header, tr_vcf_body = export.export_vcf(tr_cns, 2, True, True)
self.assertTrue(0 < len(tr_vcf_body.splitlines()) < len(tr_cns))
cl_cns = cnvlib.read("formats/cl_seq.cns")
_header, cl_vcf_body = export.export_vcf(cl_cns, 6, True, True)
self.assertTrue(0 < len(cl_vcf_body.splitlines()) < len(cl_cns))