def test_shitty_deep_file(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
eid1 = self.insert_experiment(epidb, "deepshitty")
res, qid1 = epidb.select_regions("deepshitty", "hg18", None, None,
None, None, None, None, None,
self.admin_key)
self.assertSuccess(res, qid1)
res, req = epidb.get_experiments_by_query(qid1, self.admin_key)
exps = self.get_regions_request(req)
self.assertEqual(len(exps), 1)
(res, req) = epidb.get_regions(qid1, "CHROMOSOME,START,END",
self.admin_key)
exps = self.get_regions_request(req)
self.assertEqual(exps, "chr1\t62125\t62154")
def test_get_by_query(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
eid1 = self.insert_experiment(epidb, "hg18_chr1_1")
eid2 = self.insert_experiment(epidb, "hg19_chr1_1")
eid3 = self.insert_experiment(epidb, "hg19_chr1_2")
eid4 = self.insert_experiment(epidb, "hg19_chr1_3")
res, qid1 = epidb.select_regions("hg18_chr1_1", "hg18", None, None,
None, None, None, None, None,
self.admin_key)
self.assertSuccess(res, qid1)
res, req = epidb.get_experiments_by_query(qid1, self.admin_key)
exps = self.get_regions_request(req)
self.assertEqual(len(exps), 1)
self.assertEqual(exps, {eid1: "hg18_chr1_1"})
(res, req) = epidb.get_regions(qid1, "CHROMOSOME,START,END",
self.admin_key)
exps = self.get_regions_request(req)
self.assertEqual(
exps,
'chr1\t683240\t690390\nchr1\t697520\t697670\nchr1\t702900\t703050\nchr1\t714160\t714310\nchr1\t714540\t714690\nchr1\t715060\t715210\nchr1\t761180\t761330\nchr1\t762060\t762210\nchr1\t762420\t762570\nchr1\t762820\t762970\nchr1\t763020\t763170\nchr1\t839540\t839690\nchr1\t840080\t840230\nchr1\t840600\t840750\nchr1\t858880\t859030\nchr1\t859600\t859750\nchr1\t860240\t860390\nchr1\t861040\t861190\nchr1\t875400\t875550\nchr1\t875900\t876050\nchr1\t876400\t876650\nchr1\t877900\t878050\nchr1\t879180\t880330'
)
(res, req) = epidb.get_regions(qid1, "CHROMOSOME,START,END,@STRAND",
self.admin_key)
exps = self.get_regions_request(req)
self.assertEqual(
exps,
'chr1\t683240\t690390\t+\nchr1\t697520\t697670\t-\nchr1\t702900\t703050\t+\nchr1\t714160\t714310\t+\nchr1\t714540\t714690\t+\nchr1\t715060\t715210\t+\nchr1\t761180\t761330\t-\nchr1\t762060\t762210\t+\nchr1\t762420\t762570\t.\nchr1\t762820\t762970\t-\nchr1\t763020\t763170\t-\nchr1\t839540\t839690\t+\nchr1\t840080\t840230\t+\nchr1\t840600\t840750\t-\nchr1\t858880\t859030\t.\nchr1\t859600\t859750\t.\nchr1\t860240\t860390\t+\nchr1\t861040\t861190\t-\nchr1\t875400\t875550\t+\nchr1\t875900\t876050\t-\nchr1\t876400\t876650\t+\nchr1\t877900\t878050\t-\nchr1\t879180\t880330\t-'
)
res, qid2 = epidb.select_regions(None, "hg19", "Methylation", None,
None, None, None, None, None,
self.admin_key)
self.assertSuccess(res, qid1)
res, req = epidb.get_experiments_by_query(qid2, self.admin_key)
self.assertSuccess(res, req)
exps = self.get_regions_request(req)
self.assertSuccess(res, exps)
self.assertEqual(len(exps), 3)
self.assertEqual(
{
'e4': 'hg19_chr1_3',
'e3': 'hg19_chr1_2',
'e2': 'hg19_chr1_1'
}, exps)
self.assertTrue(eid2 in exps)
self.assertTrue(eid3 in exps)
self.assertTrue(eid4 in exps)
(res, req) = epidb.get_regions(qid2, "CHROMOSOME,START,END",
self.admin_key)
x = self.get_regions_request(req)
self.assertEqual(
x,
'chr1\t567500\t567650\nchr1\t713000\t713070\nchr1\t713240\t713390\nchr1\t713280\t713430\nchr1\t713520\t713670\nchr1\t713520\t713670\nchr1\t713900\t714050\nchr1\t713920\t714070\nchr1\t714160\t714310\nchr1\t714200\t714350\nchr1\t714300\t714350\nchr1\t714460\t714590\nchr1\t714540\t714690\nchr1\t714540\t714690\nchr1\t715060\t715210\nchr1\t715080\t715230\nchr1\t719100\t719330\nchr1\t761180\t761330\nchr1\t762060\t762210\nchr1\t762060\t762210\nchr1\t762100\t762250\nchr1\t762420\t762570\nchr1\t762440\t762590\nchr1\t762460\t762500\nchr1\t762620\t762790\nchr1\t762820\t762970\nchr1\t762820\t762970\nchr1\t763020\t763170\nchr1\t839540\t839690\nchr1\t840000\t840150\nchr1\t840080\t840230\nchr1\t840100\t840310\nchr1\t840600\t840750\nchr1\t840640\t840790\nchr1\t840850\t840990\nchr1\t857740\t857890\nchr1\t858740\t858890\nchr1\t858880\t859030\nchr1\t859600\t859750\nchr1\t859640\t859790\nchr1\t859650\t859790\nchr1\t860220\t860370\nchr1\t860240\t860390\nchr1\t860600\t860750\nchr1\t861040\t861190\nchr1\t861040\t861190\nchr1\t875220\t875370\nchr1\t875400\t875550\nchr1\t875900\t876050\nchr1\t875920\t876070\nchr1\t876180\t876330\nchr1\t876420\t876570\nchr1\t877000\t877150'
)
