def test_remap_invalid_assembly(self):
s = SNPs("tests/input/GRCh37.csv")
chromosomes_remapped, chromosomes_not_remapped = s.remap(-1)
self.assertEqual(s.build, 37)
self.assertEqual(s.assembly, "GRCh37")
self.assertEqual(len(chromosomes_remapped), 0)
self.assertEqual(len(chromosomes_not_remapped), 2)
def f():
s = SNPs("tests/input/GRCh37.csv")
chromosomes_remapped, chromosomes_not_remapped = s.remap(36)
self.assertEqual(s.build, 36)
self.assertEqual(s.assembly, "NCBI36")
self.assertEqual(len(chromosomes_remapped), 2)
self.assertEqual(len(chromosomes_not_remapped), 0)
pd.testing.assert_frame_equal(s.snps, self.snps_NCBI36(), check_exact=True)
def test_remap_37_to_37(self):
s = SNPs("tests/input/GRCh37.csv")
chromosomes_remapped, chromosomes_not_remapped = s.remap(37)
self.assertEqual(s.build, 37)
self.assertEqual(s.assembly, "GRCh37")
self.assertEqual(len(chromosomes_remapped), 0)
self.assertEqual(len(chromosomes_not_remapped), 2)
pd.testing.assert_frame_equal(s.snps, self.snps_GRCh37(), check_exact=True)
def f():
s = SNPs("tests/input/NCBI36.csv", parallelize=True)
chromosomes_remapped, chromosomes_not_remapped = s.remap(37)
self.assertEqual(s.build, 37)
self.assertEqual(s.assembly, "GRCh37")
self.assertEqual(len(chromosomes_remapped), 2)
self.assertEqual(len(chromosomes_not_remapped), 0)
pd.testing.assert_frame_equal(s.snps, self.snps_GRCh37(), check_exact=True)
def test_remap_no_snps(self):
s = SNPs()
chromosomes_remapped, chromosomes_not_remapped = s.remap(38)
self.assertFalse(s.build)
self.assertEqual(len(chromosomes_remapped), 0)
self.assertEqual(len(chromosomes_not_remapped), 0)