def test_select_only_peaks_cached(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
sample_id = self.sample_ids[0]
files = ["reference_example", "test1"]
for filename in files:
wig_data = helpers.load_bedgraph(filename)
res = epidb.add_experiment(filename, "hg19", "Methylation",
sample_id, "tech1", "ENCODE", "desc1",
wig_data, "bedgraph", None,
self.admin_key)
(s, q) = epidb.select_experiments(files, "", None, None,
self.admin_key)
(s, q_cache) = epidb.query_cache(q, True, self.admin_key)
(s, req) = epidb.count_regions(q_cache, self.admin_key)
count = self.count_request(req)
self.assertEqual(1009, count)
(s, req2) = epidb.count_regions(q_cache, self.admin_key)
count = self.count_request(req2)
self.assertEqual(1009, count)
self.assertEqual(req, req2)
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)
def test_aggregation(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
sample_id = self.sample_ids[0]
cpg_island = ",".join([
"CHROMOSOME", "START", "END", "NAME", "LENGTH", "NUM_CPG",
"NUM_GC", "PER_CPG", "PER_CG", "OBS_EXP"
])
with open("data/cpgIslandExtFull.txt", 'r') as f:
file_data = f.read()
(res, a_1) = epidb.add_annotation("Cpg Islands", "hg19",
"Complete CpG islands",
file_data, cpg_island, None,
self.admin_key)
self.assertSuccess(res, a_1)
res, q_cgi = epidb.select_annotations("Cpg Islands", "hg19", None,
None, None, self.admin_key)
self.assertSuccess(res, q_cgi)
res, qid_2 = epidb.tiling_regions(1000000, "hg19", None,
self.admin_key)
self.assertSuccess(res, qid_2)
res, req = epidb.count_regions(qid_2, self.admin_key)
self.assertSuccess(res, req)
count = self.count_request(req)
self.assertEquals(count, 3118)
res, _qid_3 = epidb.aggregate(q_cgi, qid_2, "@LENGTH", self.admin_key)
self.assertSuccess(res, _qid_3)
res, qid_3 = epidb.query_cache(_qid_3, True, self.admin_key)
self.assertSuccess(res, qid_3)
res, qid_4 = epidb.filter_regions(qid_3, "@AGG.COUNT", ">", "0",
"number", self.admin_key)
res, req = epidb.count_regions(qid_4, self.admin_key)
count = self.count_request(req)
self.assertEquals(count, 2574)
res, qid_4 = epidb.filter_regions(qid_2, "@AGG.COUNT", "<", "0",
"number", self.admin_key)
res, req = epidb.count_regions(qid_4, self.admin_key)
count = self.count_request(req)
self.assertEquals(count, 0)
res, qid_4 = epidb.filter_regions(qid_3, "@AGG.COUNT", ">=", "100",
"number", self.admin_key)
(res, req) = epidb.get_regions(
qid_4,
"CHROMOSOME,START,END,@AGG.MIN,@AGG.MAX,@AGG.MEDIAN,@AGG.MEAN,@AGG.VAR,@AGG.SD,@AGG.COUNT,@AGG.SUM",
self.admin_key)
self.assertSuccess(res, req)
regions = self.get_regions_request(req)
expected = 'chr1\t1000000\t2000000\t201.0000\t5585.0000\t469.0000\t766.0082\t589695.4375\t767.9163\t122\t93453.0000\nchr16\t0\t1000000\t201.0000\t6377.0000\t484.0000\t746.6083\t674998.0625\t821.5826\t120\t89593.0000\nchr16\t1000000\t2000000\t201.0000\t5449.0000\t398.0000\t666.6393\t630197.3125\t793.8497\t122\t81330.0000\nchr16\t2000000\t3000000\t201.0000\t4843.0000\t533.0000\t780.4951\t559994.2500\t748.3276\t101\t78830.0000\nchr16\t88000000\t89000000\t202.0000\t3785.0000\t347.0000\t553.3461\t295400.6875\t543.5078\t104\t57548.0000\nchr19\t0\t1000000\t201.0000\t7814.0000\t424.0000\t776.2705\t944608.4375\t971.9097\t122\t94705.0000\nchr19\t1000000\t2000000\t201.0000\t6035.0000\t430.0000\t738.8853\t625527.1250\t790.9027\t183\t135216.0000\nchr19\t2000000\t3000000\t201.0000\t3978.0000\t395.0000\t673.9907\t444749.5000\t666.8954\t107\t72117.0000\nchr19\t3000000\t4000000\t201.0000\t2753.0000\t387.0000\t531.0648\t172512.1094\t415.3458\t108\t57355.0000\nchr20\t62000000\t63000000\t202.0000\t5019.0000\t501.0000\t716.2427\t427763.9375\t654.0366\t103\t73773.0000\nchr7\t0\t1000000\t201.0000\t6234.0000\t348.0000\t556.3500\t475220.5625\t689.3624\t100\t55635.0000\nchr9\t139000000\t140000000\t202.0000\t6342.0000\t406.0000\t777.3303\t817548.5625\t904.1839\t109\t84729.0000'
self.assertEquals(regions, expected)
(s, req) = epidb.count_regions(qid_4, self.admin_key)
self.assertSuccess(s, req)
count = self.count_request(req)
self.assertEquals(count, 12)
