Python do_reference Examples

Example #1

File: test_cnvlib.py Project: WinterLi1993/cnvkit

 def test_reference(self):
     """The 'reference' command."""
     # Empty/unspecified antitargets
     nlines = linecount("formats/amplicon.cnr") - 1
     ref = commands.do_reference(["formats/amplicon.cnr"], ["formats/empty"])
     self.assertEqual(len(ref), nlines)
     ref = commands.do_reference(["formats/amplicon.cnr"])
     self.assertEqual(len(ref), nlines)
     # Empty/unspecified antitargets, flat reference
     nlines = linecount("formats/amplicon.bed")
     ref = commands.do_reference_flat("formats/amplicon.bed",
                                      "formats/empty")
     self.assertEqual(len(ref), nlines)
     ref = commands.do_reference_flat("formats/amplicon.bed")
     self.assertEqual(len(ref), nlines)

Example #2

File: test_cnvlib.py Project: zengfengbo/cnvkit

 def test_reference(self):
     # Empty antitargets
     ref = commands.do_reference(["formats/amplicon.cnr"], ["formats/empty"])
     self.assertTrue(len(ref) > 0)
     # Empty antitargets, flat reference
     ref = commands.do_reference_flat("formats/amplicon.bed",
                                      "formats/empty")
     self.assertTrue(len(ref) > 0)

Example #3

File: test_cnvlib.py Project: xtmgah/cnvkit

 def test_reference(self):
     """The 'reference' command."""
     # Empty antitargets
     ref = commands.do_reference(["formats/amplicon.cnr"], ["formats/empty"])
     self.assertGreater(len(ref), 0)
     # Empty antitargets, flat reference
     ref = commands.do_reference_flat("formats/amplicon.bed",
                                      "formats/empty")
     self.assertGreater(len(ref), 0)

Example #4

File: test_cnvlib.py Project: kyleabeauchamp/cnvkit

 def test_reference(self):
     """The 'reference' command."""
     # Empty antitargets
     ref = commands.do_reference(["formats/amplicon.cnr"], ["formats/empty"])
     self.assertGreater(len(ref), 0)
     # Empty antitargets, flat reference
     ref = commands.do_reference_flat("formats/amplicon.bed",
                                      "formats/empty")
     self.assertGreater(len(ref), 0)

Example #5

File: test_cnvlib.py Project: weizhiting/cnvkit

 def test_reference(self):
     """The 'reference' command."""
     # Empty/unspecified antitargets
     nlines = linecount("formats/amplicon.cnr") - 1
     ref = commands.do_reference(["formats/amplicon.cnr"], ["formats/empty"])
     self.assertEqual(len(ref), nlines)
     ref = commands.do_reference(["formats/amplicon.cnr"])
     self.assertEqual(len(ref), nlines)
     # Empty/unspecified antitargets, flat reference
     nlines = linecount("formats/amplicon.bed")
     ref = commands.do_reference_flat("formats/amplicon.bed",
                                      "formats/empty")
     self.assertEqual(len(ref), nlines)
     ref = commands.do_reference_flat("formats/amplicon.bed")
     self.assertEqual(len(ref), nlines)
     # Misc
     ref = cnvlib.read('formats/reference-tr.cnn')
     targets, antitargets = reference.reference2regions(ref)
     self.assertLess(0, len(antitargets))
     self.assertEqual(len(antitargets), (ref['gene'] == 'Background').sum())
     self.assertEqual(len(targets), len(ref) - len(antitargets))

Example #6

File: test_cnvlib.py Project: JimmyLiJing/cnvkit

 def test_reference(self):
     """The 'reference' command."""
     # Empty/unspecified antitargets
     nlines = linecount("formats/amplicon.cnr") - 1
     ref = commands.do_reference(["formats/amplicon.cnr"], ["formats/empty"])
     self.assertEqual(len(ref), nlines)
     ref = commands.do_reference(["formats/amplicon.cnr"])
     self.assertEqual(len(ref), nlines)
     # Empty/unspecified antitargets, flat reference
     nlines = linecount("formats/amplicon.bed")
     ref = commands.do_reference_flat("formats/amplicon.bed",
                                      "formats/empty")
     self.assertEqual(len(ref), nlines)
     ref = commands.do_reference_flat("formats/amplicon.bed")
     self.assertEqual(len(ref), nlines)
     # Misc
     ref = cnvlib.read('formats/reference-tr.cnn')
     targets, antitargets = reference.reference2regions(ref)
     self.assertLess(0, len(antitargets))
     self.assertEqual(len(antitargets), (ref['gene'] == 'Background').sum())
     self.assertEqual(len(targets), len(ref) - len(antitargets))