Exemple #1
0
 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))
Exemple #2
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 def test_export_seg(self):
     """The 'export seg' command."""
     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))
Exemple #3
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 def test_export_seg(self):
     """The 'export seg' command."""
     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))
Exemple #4
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 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))
Exemple #5
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 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))