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)
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)
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)
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))