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
_header, theta_rows = export.export_theta("formats/tr95t.cns",
"formats/reference-tr.cnn")
self.assertGreater(len(theta_rows), 0)
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
_header, theta_rows = export.export_theta("formats/tr95t.cns",
"formats/reference-tr.cnn")
self.assertGreater(len(theta_rows), 0)
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):
# 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))
def test_export_bed_vcf(self):
"""The 'export' command for formats with 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
for show in ("ploidy", "variant", "all"):
tbl_bed = export.export_bed(cns, ploidy, True, is_f,
cns.sample_id, show)
if show == "all":
self.assertEqual(len(tbl_bed), len(cns),
"{} {}".format(fname, ploidy))
else:
self.assertLess(len(tbl_bed), 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_bed_vcf(self):
"""The 'export' command for formats with 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
for show in ("ploidy", "variant", "all"):
tbl_bed = export.export_bed(cns, ploidy, True, is_f,
cns.sample_id, show)
if show == "all":
self.assertEqual(len(tbl_bed), len(cns),
"{} {}".format(fname, ploidy))
else:
self.assertLess(len(tbl_bed), len(cns))
# VCF
_vheader, vcf_body = export.export_vcf(cns, ploidy, True, is_f)
self.assertTrue(0 < len(vcf_body.splitlines()) < len(cns))