def test_build_index_with_force_merged_nodups_with_no_preset(self): ## recognizing custom parameters
pypairix.build_index(TEST_FILE_2D_SPACE, delimiter=' ', sc=2, bc=3, ec=3, sc2=6, bc2=7, ec2=7, force=1)
pr2 = pypairix.open(TEST_FILE_2D_SPACE)
query = '{}:{}-{}|{}:{}-{}'.format(self.chrom, self.start, self.end, self.chrom2, self.start2, self.end2)
it2 = pr2.querys2D(query)
pr2_result = build_it_result(it2, self.f_type)
self.assertEqual(self.result, pr2_result)
def test_build_index_with_force(self): ## recognizing file extension pairs.gz
pypairix.build_index(TEST_FILE_LARGE_CHR, force=1)
pr2 = pypairix.open(TEST_FILE_LARGE_CHR)
query = '{}:{}-{}|{}:{}-{}'.format(self.chrom, self.start, self.end, self.chrom2, self.start2, self.end2)
it2 = pr2.querys2D(query)
pr2_result = build_it_result(it2, self.f_type)
self.assertEqual(self.result, pr2_result)
def test_build_index_with_force_merged_nodups(self): ## recognizing preset merged_nodups
pypairix.build_index(TEST_FILE_2D_SPACE, "merged_nodups", force=1)
pr2 = pypairix.open(TEST_FILE_2D_SPACE)
query = '{}:{}-{}|{}:{}-{}'.format(self.chrom, self.start, self.end, self.chrom2, self.start2, self.end2)
it2 = pr2.querys2D(query)
pr2_result = build_it_result(it2, self.f_type)
self.assertEqual(self.result, pr2_result)
def test_build_index_with_force_vcf(self): ## recognizing file extension vcf.gz
pypairix.build_index(TEST_FILE_1D, force=1)
pr2 = pypairix.open(TEST_FILE_1D)
query = '{}:{}-{}'.format(self.chrom, self.start, self.end)
it2 = pr2.querys(query)
pr2_result = [[x[0], x[1], x[1]] for x in it2]
self.assertEqual(self.result, pr2_result)
def test_build_index_with_region_split_character(self):
pypairix.build_index(TEST_FILE_LARGE_CHR, region_split_character="^", force=1)
pr2 = pypairix.open(TEST_FILE_LARGE_CHR)
query = '{}:{}-{}^{}:{}-{}'.format(self.chrom, self.start, self.end, self.chrom2, self.start2, self.end2)
it2 = pr2.querys2D(query)
pr2_result = build_it_result(it2, self.f_type)
pypairix.build_index(TEST_FILE_LARGE_CHR, force=1) # revert
self.assertEqual(self.result, pr2_result)
def test_build_index_with_force_merged_nodups_tab(self): ## recognizing custom set
pypairix.build_index(TEST_FILE_2D, sc=2, bc=3, ec=3, sc2=6, bc2=7, ec2=7, force=1)
# test with reindex
pr2 = pypairix.open(TEST_FILE_2D)
query = '{}:{}-{}|{}:{}-{}'.format(self.chrom, self.start, self.end, self.chrom2, self.start2, self.end2)
it2 = pr2.querys2D(query)
pr2_result = build_it_result(it2, self.f_type)
self.assertEqual(self.result, pr2_result)
def test_build_index_without_force(self):
# expect an error here... the px2 file already exists
with self.assertRaises(pypairix.PairixError) as error:
pypairix.build_index(TEST_FILE_LARGE_CHR)
# errors are handled differently in python 2 and python 3
if sys.version_info > (3,0):
self.assertEqual(error.exception.__str__(), "The index file exists. Please use force=1 to overwrite.")
else:
self.assertEqual(error.exception.message, "The index file exists. Please use force=1 to overwrite.")
