def test_multiple_overlap(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
sample_id = self.sample_ids[0]
self.insert_experiment(epidb, "hg19_chr1_1", sample_id)
self.insert_annotation(epidb, "Cpg Islands")
res, qid_1 = epidb.select_annotations("Cpg Islands", "hg19", None,
None, None, self.admin_key)
self.assertSuccess(res, qid_1)
res, req = epidb.count_regions(qid_1, self.admin_key)
self.assertSuccess(res, req)
count = self.count_request(req)
self.assertEqual(count, 14)
res, qid_2 = epidb.select_regions("hg19_chr1_1", "hg19", None, None,
None, None, None, None, None,
self.admin_key)
self.assertEqual(res, "okay")
res, req = epidb.count_regions(qid_2, self.admin_key)
self.assertSuccess(res, req)
count = self.count_request(req)
self.assertEqual(count, 21)
res, i_id = epidb.intersection(qid_1, qid_2, self.admin_key)
self.assertEqual(res, "okay")
res, req = epidb.count_regions(i_id, self.admin_key)
self.assertSuccess(res, req)
count = self.count_request(req)
self.assertEqual(count, 3)
res, i_id = epidb.intersection(qid_2, qid_2, self.admin_key)
self.assertSuccess(res, i_id)
res, req = epidb.count_regions(i_id, self.admin_key)
self.assertSuccess(res, req)
count = self.count_request(req)
self.assertEqual(count, 21)
res, i_id = epidb.intersection(qid_1, qid_1, self.admin_key)
self.assertSuccess(res, i_id)
res, req = epidb.count_regions(i_id, self.admin_key)
self.assertSuccess(res, req)
count = self.count_request(req)
self.assertEqual(count, 14)
res, i_id = epidb.intersection(i_id, i_id, self.admin_key)
self.assertSuccess(res, i_id)
res, req = epidb.count_regions(i_id, self.admin_key)
self.assertSuccess(res, req)
count = self.count_request(req)
self.assertEqual(count, 14)
def test_load_bedgraph(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
sample_id = self.sample_ids[0]
regions_data = gzip.open("data/bedgraph/chr19.txt.gz").read()
# adding two experiments with the same data should work
res = epidb.add_experiment(
"S0022IH2.ERX300681.H3K36me3.bwa.GRCh38.20150528.bedgraph", "hg19",
"Methylation", sample_id, "tech1", "ENCODE", "desc1", regions_data,
"bedgraph", {"md5sum": "afd4af5afd5afd4af5afd5afd4af5afd5"},
self.admin_key)
self.assertSuccess(res)
(status, query_id) = epidb.select_regions(
"#afd4af5afd5afd4af5afd5afd4af5afd5", None, None, None, None, None,
"chr19", 49388217, 49417994, self.admin_key)
self.assertSuccess(status, query_id)
(status, input) = epidb.input_regions("hg19",
"chr19\t49388217\t49417994",
self.admin_key)
self.assertSuccess(status, input)
(status, query_overlap) = epidb.intersection(query_id, input,
self.admin_key)
self.assertSuccess(status, query_overlap)
(status, request_id) = epidb.get_regions(query_id,
"CHROMOSOME,START,END,VALUE",
self.admin_key)
self.assertSuccess(status, request_id)
(status,
overlap_request_id) = epidb.get_regions(query_id,
"CHROMOSOME,START,END,VALUE",
self.admin_key)
self.assertSuccess(status, overlap_request_id)
by_select = self.get_regions_request(request_id)
by_overlap = self.get_regions_request(overlap_request_id)
self.assertEqual(by_overlap, by_select)
self.assertTrue(len(by_select) > 0)
(status, info) = epidb.info("#afd4af5afd5afd4af5afd5afd4af5afd5",
self.admin_key)
self.assertEquals(info[0]["_id"], "e1")
def test_intersect_tiling(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_full(epidb)
res, qid1 = epidb.tiling_regions(1000, "hg19", "chr1", self.admin_key)
self.assertSuccess(res, qid1)
res, qid2 = epidb.select_regions("hg19_chr1_1", "hg19", None, None, None, None, None, None, None, self.admin_key)
self.assertSuccess(res, qid2)
res, qid3 = epidb.intersection(qid1, qid2, self.admin_key)
self.assertSuccess(res, qid3)
res, req = epidb.get_regions(qid3, "CHROMOSOME,START,END", self.admin_key)
self.assertSuccess(res, req)
regions = self.get_regions_request(req)
expected_regions = helpers.get_result("intersect_tiling")
self.assertEqual(regions, expected_regions)
def test_intersection_two_genomes(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_full(epidb)
res, qid_1 = epidb.select_regions("hg19_chr1_1", ["hg19", "hg18"], None, None, None,
None, None, None, None, self.admin_key)
self.assertSuccess(res, qid_1)
res, qid_2 = epidb.select_regions("hg18_chr1_1", ["hg18", "hg19"], None, None, None,
None, None, None, None, self.admin_key)
self.assertSuccess(res, qid_2)
res, qid_3 = epidb.intersection(qid_1, qid_2, self.admin_key)
self.assertSuccess(res, qid_3)
res, req = epidb.get_regions(qid_3, "CHROMOSOME,START,END", self.admin_key)
self.assertSuccess(res, req)
regions = self.get_regions_request(req)
expected_regions = helpers.get_result("intersection_multiple_genomes")
self.assertEqual(regions, expected_regions)
def test_complex1(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_full(epidb)
res, qid_1_1 = epidb.select_regions("hg19_chr1_1", "hg19", None, None,
None, None, None, None, None,
self.admin_key)
#server.get_regions(qid_1_1, )
self.assertSuccess(res, qid_1_1)
res, qid_1_2 = epidb.select_regions("hg19_chr1_2", "hg19", None, None,
None, None, None, None, None,
self.admin_key)
self.assertSuccess(res, qid_1_2)
res, qid_2 = epidb.merge_queries(qid_1_1, qid_1_2, self.admin_key)
self.assertSuccess(res, qid_2)
res, regions = epidb.get_regions(qid_2, "CHROMOSOME,START,END",
self.admin_key)
self.assertSuccess(res, regions)
res, qid_1_3 = epidb.select_regions("hg19_chr1_3", "hg19", None, None,
None, None, None, None, None,
self.admin_key)
self.assertSuccess(res, qid_1_3)
res, qid_5 = epidb.intersection(qid_2, qid_1_3, self.admin_key)
self.assertSuccess(res, qid_5)
res, req = epidb.get_regions(
qid_5,
"CHROMOSOME,START,END,NAME,SCORE,STRAND,SIGNAL_VALUE,P_VALUE,Q_VALUE,PEAK",
self.admin_key)
self.assertSuccess(res, req)
regions = self.get_regions_request(req)
expected_regions = helpers.get_result("complex1")
self.assertEqual(
regions.split("\n").sort(),
expected_regions.split("\n").sort())
def test_overlap_simple(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
# Test the intersect command
data_one = "chr1\t3049996\t3050022\nchr1\t3050022\t3050040\nchr1\t3050040\t3050051\nchr1\t3050051\t3050126"
region = "chr1\t3050022\t3050100"
(s, q1) = epidb.input_regions("hg19", data_one, self.admin_key)
self.assertSuccess(s, q1)
(s, q_input) = epidb.input_regions("hg19", region, self.admin_key)
self.assertSuccess(s, q_input)
(s, q3) = epidb.intersection(q1, q_input, self.admin_key)
self.assertSuccess(s, q3)
(s, req) = epidb.get_regions(q3, "CHROMOSOME,START,END",
self.admin_key)
self.assertSuccess(s, req)
regions = self.get_regions_request(req)
self.assertEqual(
regions,
'chr1\t3050022\t3050040\nchr1\t3050040\t3050051\nchr1\t3050051\t3050126'
)
# Test the select annotation
sample_id = self.sample_ids[0]
res = epidb.add_annotation("exp1", "hg19", "desc1", data_one,
"CHROMOSOME,START,END", None,
self.admin_key)
self.assertSuccess(res)
(s, q1) = epidb.select_annotations("exp1", "hg19", "chr1", 3050022,
3050100, self.admin_key)
self.assertSuccess(s, q1)
(s, req) = epidb.get_regions(q1, "CHROMOSOME,START,END",
self.admin_key)
self.assertSuccess(s, req)
regions = self.get_regions_request(req)
self.assertEqual(
regions,
'chr1\t3050022\t3050040\nchr1\t3050040\t3050051\nchr1\t3050051\t3050126'
)
# Test the select experiment
sample_id = self.sample_ids[0]
res = epidb.add_experiment("exp1", "hg19", "Methylation", sample_id,
"tech1", "ENCODE", "desc1", data_one,
"CHROMOSOME,START,END", None,
self.admin_key)
self.assertSuccess(res)
(s, q1) = epidb.select_experiments("exp1", "chr1", 3050022, 3050100,
self.admin_key)
self.assertSuccess(s, q1)
(s, req) = epidb.get_regions(q1, "CHROMOSOME,START,END",
self.admin_key)
self.assertSuccess(s, req)
regions = self.get_regions_request(req)
self.assertEqual(
regions,
'chr1\t3050022\t3050040\nchr1\t3050040\t3050051\nchr1\t3050051\t3050126'
)
(s, q1) = epidb.select_experiments("exp1", "chr1", None, None,
self.admin_key)
self.assertSuccess(s, q1)
(s, q2) = epidb.aggregate(q1, q_input, "START", self.admin_key)
self.assertSuccess(s, q2)
(s, req) = epidb.get_regions(q2, "@AGG.MIN,@AGG.MAX,@AGG.COUNT",
self.admin_key)
self.assertSuccess(s, req)
regions = self.get_regions_request(req)
self.assertEqual(regions, '3050022.0000\t3050051.0000\t3')
def test_complex2(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_full(epidb)
self.insert_experiment(epidb, "hg19_big_1")
self.insert_experiment(epidb, "hg19_big_2")
res, qid_1_1 = epidb.select_regions("hg19_big_1", "hg19", None, None,
None, None, None, 1000000, 3000000,
self.admin_key)
self.assertSuccess(res, qid_1_1)
res, req = epidb.count_regions(qid_1_1, self.admin_key)
self.assertSuccess(res, req)
c = self.count_request(req)
res, qid_1_2 = epidb.select_regions(
"hg19_big_1", "hg19", None, None, None, None,
["chr1", "chr3", "chr11", "chrX", "chr9"], None, None,
self.admin_key)
self.assertSuccess(res, qid_1_2)
res, req = epidb.count_regions(qid_1_2, self.admin_key)
self.assertSuccess(res, req)
c = self.count_request(req)
# this gives us regions from 1,000,000 to 3,000,000 on chromosomes chr1, chr3, chr9, chr11, chrY
res, qid_2_1 = epidb.intersection(qid_1_1, qid_1_2, self.admin_key)
self.assertSuccess(res, qid_2_1)
res, req = epidb.count_regions(qid_2_1, self.admin_key)
self.assertSuccess(res, req)
c = self.count_request(req)
self.assertEqual(c, 247)
res, qid_2_2 = epidb.tiling_regions(1000, "hg19",
["chr1", "chr2", "chr15", "chrX"],
self.admin_key)
self.assertSuccess(res, qid_2_2)
res, req = epidb.count_regions(qid_2_2, self.admin_key)
self.assertSuccess(res, req)
c = self.count_request(req)
res, qid_3_1 = epidb.merge_queries(qid_2_1, qid_2_2, self.admin_key)
self.assertSuccess(res, qid_3_1)
res, req = epidb.count_regions(qid_3_1, self.admin_key)
self.assertSuccess(res, req)
c = self.count_request(req)
res, qid_4_1 = epidb.filter_regions(qid_3_1, "START", ">=", "2000000",
"number", self.admin_key)
self.assertSuccess(res, qid_4_1)
res, req = epidb.count_regions(qid_4_1, self.admin_key)
self.assertSuccess(res, req)
c = self.count_request(req)
res, qid_4_2 = epidb.select_regions("hg19_big_2", "hg19", None, None,
None, None, ["chr1", "chrX"], None,
None, self.admin_key)
self.assertSuccess(res, qid_4_2)
(res, qid_4_2_cached) = epidb.query_cache(qid_4_2, True,
self.admin_key)
res, req = epidb.count_regions(qid_4_2_cached, self.admin_key)
self.assertSuccess(res, req)
c = self.count_request(req)
self.assertEqual(c, 8961)
res, qid_5_1 = epidb.intersection(qid_4_1, qid_4_2_cached,
self.admin_key)
self.assertSuccess(res, qid_5_1)
res, req = epidb.count_regions(qid_5_1, self.admin_key)
self.assertSuccess(res, req)
count = self.count_request(req)
self.assertEqual(count, 14356)
res, qid_6_1 = epidb.filter_regions(qid_5_1, "END", "<", "2200000",
"number", self.admin_key)
self.assertSuccess(res, qid_6_1)
(res, qid_6_1_cached) = epidb.query_cache(qid_6_1, True,
self.admin_key)
res, req = epidb.count_regions(qid_6_1, self.admin_key)
self.assertSuccess(res, req)
count = self.count_request(req)
self.assertEqual(count, 52)
res, req = epidb.get_regions(
qid_6_1,
"CHROMOSOME,START,END,NAME,SCORE,STRAND,SIGNAL_VALUE,P_VALUE,Q_VALUE,PEAK,@NAME",
self.admin_key)
self.assertSuccess(res, req)
regions = self.get_regions_request(req)
expected_regions = helpers.get_result("complex2")
self.assertEqual(regions, expected_regions)
