def test_filter_regions(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_full(epidb)
res, qid = epidb.select_regions("hg19_chr1_1", "hg19", None, None, None,
None, None, None, None, self.admin_key)
self.assertSuccess(res, qid)
res, qid2 = epidb.filter_regions(qid, "START", ">=", "875400 ", "number", self.admin_key)
self.assertSuccess(res, qid2)
res, req = epidb.get_regions(qid2, "CHROMOSOME,START,END", self.admin_key)
self.assertSuccess(res, req)
regions = self.get_regions_request(req)
# Test filter with string values
expected_regions = helpers.get_result("filter_ge_875400")
self.assertEqual(regions, expected_regions)
res, qid3 = epidb.filter_regions(qid, "STRAND", "==", "+", "string", self.admin_key)
self.assertSuccess(res, qid3)
res, req = epidb.get_regions(qid3, "CHROMOSOME,START,END,STRAND", self.admin_key)
self.assertSuccess(res, req)
regions = self.get_regions_request(req)
self.assertEqual(regions, 'chr1\t713240\t713390\t+\nchr1\t713900\t714050\t+\nchr1\t714160\t714310\t+\nchr1\t714540\t714690\t+\nchr1\t715060\t715210\t+\nchr1\t762060\t762210\t+\nchr1\t839540\t839690\t+\nchr1\t840080\t840230\t+\nchr1\t860240\t860390\t+\nchr1\t875400\t875550\t+\nchr1\t876180\t876330\t+')
res, qid3 = epidb.filter_regions(qid, "STRAND", "!=", "+", "string", self.admin_key)
self.assertSuccess(res, qid3)
res, req = epidb.get_regions(qid3, "CHROMOSOME,START,END,STRAND", self.admin_key)
self.assertSuccess(res, req)
regions = self.get_regions_request(req)
self.assertEqual(regions, 'chr1\t713520\t713670\t-\nchr1\t761180\t761330\t-\nchr1\t762420\t762570\t.\nchr1\t762820\t762970\t-\nchr1\t763020\t763170\t-\nchr1\t840600\t840750\t-\nchr1\t858880\t859030\t.\nchr1\t859600\t859750\t.\nchr1\t861040\t861190\t-\nchr1\t875900\t876050\t-')
def test_multiple_genomes_2(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base()
sample_id = self.sample_ids[0]
format = "CHROMOSOME,START,END"
self.insert_experiment(epidb, "hg18_chr1_1", sample_id)
self.insert_experiment(epidb, "hg19_chr1_1", sample_id)
self.insert_experiment(epidb, "hg19_chr1_2", sample_id)
# retrieve every paired combination
combinations = [(["hg18_chr1_1", "hg19_chr1_2"], "multiple_genomes"),
(["hg18_chr1_1", "hg19_chr1_1"], "multiple_genomes_2"),
(["hg19_chr1_1",
"hg19_chr1_2"], "multiple_experiments")]
for (experiments, result_regions) in combinations:
res, qid = epidb.select_regions(experiments, ["hg18", "hg19"],
None, None, None, None, None, None,
None, self.admin_key)
self.assertSuccess(res, qid)
res, req = epidb.get_regions(qid, format, self.admin_key)
self.assertSuccess(res, req)
regions = self.get_regions_request(req)
regions_expected = helpers.get_result(result_regions)
self.assertEqual(regions, regions_expected)
def test_merge_tiling(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_full(epidb)
res, qid1 = epidb.tiling_regions(10000, "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)
# limit the tilings on the range of the experiment
res, qid3 = epidb.filter_regions(qid1, "START", ">=", "713240", "number", self.admin_key)
self.assertSuccess(res, qid3)
res, qid4 = epidb.filter_regions(qid3, "END", "<=", "876330", "number", self.admin_key)
self.assertSuccess(res, qid4)
res, qid5 = epidb.merge_queries(qid4, qid2, self.admin_key)
self.assertSuccess(res, qid5)
res, req = epidb.get_regions(qid5, "CHROMOSOME,START,END", self.admin_key)
self.assertSuccess(res, req)
regions = self.get_regions_request(req)
expected_regions = helpers.get_result("merge_tiling")
self.assertEqual(regions, expected_regions)
def test_multiple_genomes(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base()
sample_id = self.sample_ids[0]
format = "CHROMOSOME,START,END"
self.insert_experiment(epidb, "hg18_chr1_1", sample_id)
self.insert_experiment(epidb, "hg19_chr1_2", sample_id)
multiple_genomes_regions = helpers.get_result("multiple_genomes")
# there was a bug in internal merge procedure triggered by the order of genomes
for genomes in [["hg19", "hg18"], ["hg18", "hg19"]]:
res, qid = epidb.select_regions(["hg18_chr1_1", "hg19_chr1_2"],
genomes, None, None, None, None,
None, None, None, self.admin_key)
self.assertSuccess(res, qid)
res, req = epidb.get_regions(qid, format, self.admin_key)
self.assertSuccess(res, req)
regions = self.get_regions_request(req)
self.assertEqual(regions, multiple_genomes_regions)
def test_experiment_name_metacolumn2(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base()
self.insert_experiment(epidb, "hg19_chr1_1")
self.insert_experiment(epidb, "hg19_chr1_2")
res, qid1 = epidb.select_regions("hg19_chr1_2", "hg19", None, None,
None, None, None, 750000, 770000,
self.admin_key)
self.assertSuccess(res, qid1)
res, qid2 = epidb.select_regions("hg19_chr1_1", "hg19", None, None,
None, None, None, 750000, 770000,
self.admin_key)
self.assertSuccess(res, qid2)
res, qid3 = epidb.merge_queries(qid1, qid2, self.admin_key)
self.assertSuccess(res, qid3)
expected = helpers.get_result("experiment_name_multiple_experiments")
res, req = epidb.get_regions(qid3, "CHROMOSOME,START,END,@NAME",
self.admin_key)
self.assertSuccess(res, req)
regions = self.get_regions_request(req)
l_regions = regions.split("\n")
l_expected = expected.split("\n")
self.assertEqual(set(l_regions), set(l_expected))
def test_chromosome_explicit(self):
# regression test: chromosome was put in the first column no matter
# what the format string specified
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base()
self.insert_experiment(epidb, "hg19_chr1_1")
(s, m) = epidb.create_column_type_simple("foobar", "", "string",
self.admin_key)
self.assertSuccess(s, m)
full_experiment_regions = helpers.get_result("full_experiment_regions")
res, qid = epidb.select_regions("hg19_chr1_1", "hg19", None, None,
None, None, None, None, None,
self.admin_key)
self.assertSuccess(res, qid)
fmt = "foobar,START,END,NAME,SCORE,STRAND,SIGNAL_VALUE,P_VALUE,Q_VALUE,PEAK"
res, req = epidb.get_regions(qid, fmt, self.admin_key)
self.assertSuccess(res, req)
regions = self.get_regions_request(req)
self.assertNotEqual(regions, full_experiment_regions)
fmt = "START,START,END,NAME,SCORE,STRAND,SIGNAL_VALUE,P_VALUE,Q_VALUE,PEAK"
res, req = epidb.get_regions(qid, fmt, self.admin_key)
self.assertSuccess(res, req)
regions = self.get_regions_request(req)
self.assertNotEqual(regions, full_experiment_regions)
# leave out chromosome entirely
regions_wo_chr = helpers.get_result("full_experiment_regions_wo_chr")
# Creating another column, named NAME, that in the experiment is name.
# This column should return empty.
(s, m) = epidb.create_column_type_simple("COISA", "", "string",
self.admin_key)
self.assertSuccess(s, m)
fmt = "START,END,COISA,SCORE,STRAND,SIGNAL_VALUE,P_VALUE,Q_VALUE,PEAK"
res, req = epidb.get_regions(qid, fmt, self.admin_key)
regions = self.get_regions_request(req)
self.assertSuccess(res, regions)
self.assertEqual(regions, regions_wo_chr)
def test_minimum_parameters(self):
# select_regions needs at least one of
# experiment name, epigenetic_mark, sample, technique or project
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base()
sample_id = self.sample_ids[0]
self.insert_experiment(epidb, "hg19_chr1_1", sample_id)
# none of them: should fail
res = epidb.select_regions(None, None, None, None, None, None, None,
None, None, self.admin_key)
self.assertFailure(res)
res = epidb.select_regions(None, None, "Methylation", None, None, None,
None, None, None, self.admin_key)
self.assertFailure(res)
res = epidb.select_regions(None, None, None, sample_id, None, None,
None, None, None, self.admin_key)
self.assertFailure(res)
res = epidb.select_regions(None, None, None, None, "ENCODE", None,
None, None, None, self.admin_key)
self.assertFailure(res)
res = epidb.select_regions(None, None, None, None, None, "tech1", None,
None, None, self.admin_key)
self.assertFailure(res)
# at least one: should pass
expected_regions = helpers.get_result("hg19_chr1_1_output")
format = "CHROMOSOME,START,END,NAME,SCORE,STRAND,SIGNAL_VALUE,P_VALUE,Q_VALUE,PEAK"
argument_combinations = [
(None, "hg19", None, sample_id, None, None, None, None, None),
("hg19_chr1_1", "hg19", None, None, None, None, None, None, None),
(None, "hg19", None, None, None, "ENCODE", None, None, None),
(None, "hg19", None, None, "tech1", None, None, None, None),
(None, "hg19", "Methylation", None, None, None, None, None, None)
]
for args in argument_combinations:
args = args + (self.admin_key, )
res, qid = epidb.select_regions(*args)
self.assertSuccess(res, qid)
res, req = epidb.get_regions(qid, format, self.admin_key)
self.assertSuccess(res, req)
regions = self.get_regions_request(req)
self.assertEqual(regions, expected_regions)
def test_metacolumn_sequence(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base()
sequence = open("data/genomes/chromosomes/chrM.fa").read()
res = epidb.upload_chromosome("hg19", "chrM", sequence, self.admin_key)
self.assertSuccess(res)
res, qid = epidb.tiling_regions(10000, "hg19", "chrM", self.admin_key)
self.assertSuccess(res, qid)
expected = helpers.get_result("experiment_name_custom_sequence")
res, req = epidb.get_regions(qid, "CHROMOSOME,START,END,@NAME,@LENGTH,@SEQUENCE", self.admin_key)
self.assertSuccess(res, req)
regions = self.get_regions_request(req)
self.assertEqual(regions, expected)
def test_filter_tiling(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base()
res, qid = epidb.tiling_regions(10000, "hg19", "chr1", self.admin_key)
self.assertSuccess(res, qid)
res, qid2 = epidb.filter_regions(qid, "END", "<=", "100000", "number", self.admin_key)
self.assertSuccess(res, qid2)
res, req = epidb.get_regions(qid2, "CHROMOSOME,START,END", self.admin_key)
self.assertSuccess(res, req)
regions = self.get_regions_request(req)
expected_regions = helpers.get_result("filter_tiling")
self.assertEqual(regions, expected_regions)
def test_select_full_experiment(self, format=None):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base()
sample_id = self.sample_ids[0]
self.insert_experiment(epidb, "hg19_chr1_1", sample_id)
full_experiment_regions = helpers.get_result("hg19_chr1_1_output")
region_count = len(full_experiment_regions.split("\n"))
format = "CHROMOSOME,START,END,NAME,SCORE,STRAND,SIGNAL_VALUE,P_VALUE,Q_VALUE,PEAK"
# test to retrieve the whole data with all parameters of the experiment
# set or not set
argument_combinations = [
("hg19_chr1_1", "hg19", "Methylation", sample_id, "tech1",
"ENCODE", "chr1", 713240, 876330),
("hg19_chr1_1", "hg19", "Methylation", sample_id, "tech1",
"ENCODE", "chr1", 713240, None),
("hg19_chr1_1", "hg19", "Methylation", sample_id, "tech1",
"ENCODE", "chr1", None, None),
("hg19_chr1_1", "hg19", "Methylation", sample_id, "tech1",
"ENCODE", None, None, None),
("hg19_chr1_1", "hg19", "Methylation", sample_id, "tech1", None,
None, None, None),
("hg19_chr1_1", "hg19", "Methylation", sample_id, None, None, None,
None, None),
("hg19_chr1_1", "hg19", "Methylation", None, None, None, None,
None, None),
("hg19_chr1_1", "hg19", None, None, None, None, None, None, None)
]
for args in argument_combinations:
args = args + (self.admin_key, )
res, qid = epidb.select_regions(*args)
self.assertSuccess(res, qid)
res, req = epidb.count_regions(qid, self.admin_key)
self.assertSuccess(res, req)
count = self.count_request(req)
self.assertEqual(count, region_count)
res, req = epidb.get_regions(qid, format, self.admin_key)
self.assertSuccess(res, req)
regions = self.get_regions_request(req)
self.assertEqual(regions, full_experiment_regions)
def test_filter_two_genomes(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_full(epidb)
res, qid = epidb.select_regions(["hg19_chr1_1", "hg18_chr1_1"], ["hg19", "hg18"], None, None, None,
None, None, None, None, self.admin_key)
self.assertSuccess(res, qid)
res, qid2 = epidb.filter_regions(qid, "START", ">=", "875400 ", "number", self.admin_key)
self.assertSuccess(res, qid2)
res, req = epidb.get_regions(qid2, "CHROMOSOME,START,END", self.admin_key)
self.assertSuccess(res, req)
regions = self.get_regions_request(req)
expected_regions = helpers.get_result("filter_multiple_genomes_ge_875400")
self.assertEqual(regions, expected_regions)
def test_retrieve_with_defaults(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base()
self.insert_experiment(epidb, "hg19_chr1_1")
expected_regions = helpers.get_result("hg19_chr1_1_output")
format = "CHROMOSOME,START,END,NAME,SCORE,STRAND,SIGNAL_VALUE,P_VALUE,Q_VALUE,PEAK"
res, qid = epidb.select_regions("hg19_chr1_1", "hg19", None, None,
None, None, None, None, None,
self.admin_key)
self.assertSuccess(res, qid)
res, req = epidb.get_regions(qid, format, self.admin_key)
self.assertSuccess(res, req)
regions = self.get_regions_request(req)
self.assertEqual(regions, expected_regions)
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_experiment_name_metacolumn(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base()
self.insert_experiment(epidb, "hg19_chr1_1")
expected_regions = helpers.get_result("experiment_name_metacolumn")
format = "CHROMOSOME,START,END,@NAME"
res, qid = epidb.select_regions("hg19_chr1_1", "hg19", None, None,
None, None, None, None, None,
self.admin_key)
self.assertSuccess(res, qid)
res, req = epidb.get_regions(qid, format, self.admin_key)
self.assertSuccess(res, req)
regions = self.get_regions_request(req)
self.assertEqual(regions, expected_regions)
def test_argument_normalization(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base()
sample_id = self.sample_ids[0]
self.insert_experiment(epidb, "hg19_chr1_1", sample_id)
full_experiment_regions = helpers.get_result("full_experiment_regions")
format = "CHROMOSOME,START,END,NAME,SCORE,STRAND,SIGNAL_VALUE,P_VALUE,Q_VALUE,PEAK"
res, qid = epidb.select_regions("HG19_CHR1_1", "hg19", "methylation",
sample_id, " Tech1", "ENCode ", "chr1",
713240, 876330, self.admin_key)
self.assertSuccess(res, qid)
res, req = epidb.get_regions(qid, format, self.admin_key)
self.assertSuccess(res, req)
regions = self.get_regions_request(req)
self.assertEqual(regions, full_experiment_regions)
def test_select_range(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base()
sample_id = self.sample_ids[0]
format = "CHROMOSOME,START,END"
self.insert_experiment(epidb, "hg19_chr1_1", sample_id)
range_regions = helpers.get_result("range_760k_875k")
res, qid = epidb.select_regions("hg19_chr1_1", "hg19", None, None,
None, None, None, 760000, 875000,
self.admin_key)
self.assertSuccess(res, qid)
res, req = epidb.get_regions(qid, format, self.admin_key)
self.assertSuccess(res, req)
regions = self.get_regions_request(req)
self.assertEqual(regions, range_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_multiple_experiments(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base()
sample_id = self.sample_ids[0]
format = "CHROMOSOME,START,END"
self.insert_experiment(epidb, "hg19_chr1_1", sample_id)
self.insert_experiment(epidb, "hg19_chr1_2", sample_id)
multiple_experiments_regions = helpers.get_result(
"multiple_experiments")
res, qid = epidb.select_experiments(["hg19_chr1_1", "hg19_chr1_2"],
None, None, None, self.admin_key)
self.assertSuccess(res, qid)
res, req = epidb.get_regions(qid, format, self.admin_key)
self.assertSuccess(res, req)
regions = self.get_regions_request(req)
self.assertEqual(regions, multiple_experiments_regions)
def test_merge_queries(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_full(epidb)
res, qid_1 = epidb.select_experiments("hg19_chr1_1", None, 760000,
860000, self.admin_key)
self.assertSuccess(res, qid_1)
res, qid_2 = epidb.select_regions("hg19_chr1_2", "hg19", None, None,
None, None, None, 760000, 860000,
self.admin_key)
self.assertSuccess(res, qid_2)
res, qid_3 = epidb.merge_queries(qid_1, qid_2, self.admin_key)
self.assertSuccess(res, qid_3)
expected_regions = helpers.get_result("merge_760k_860k")
res, req = epidb.get_regions(qid_3, "CHROMOSOME,START,END",
self.admin_key)
self.assertSuccess(res, req)
regions = self.get_regions_request(req)
self.assertEqual(regions, expected_regions)
def test_overlap(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_full(epidb)
##### SET 1 ######
res, qid_1 = epidb.select_regions("hg19_chr1_1", "hg19", None, None, None,
None, None, None, None, self.admin_key)
self.assertSuccess(res, qid_1)
res, qid_2 = epidb.select_regions("hg19_chr1_2", "hg19", None, None, None,
None, None, None, None, self.admin_key)
self.assertSuccess(res, qid_2)
res, qid_3 = epidb.overlap(qid_1, qid_2, True, 0, "bp", 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")
self.assertEqual(regions, expected_regions)
res, qid_31 = epidb.overlap(qid_1, qid_2, True, 165, "bp", self.admin_key)
self.assertSuccess(res, qid_31)
res, req = epidb.get_regions(qid_31, "CHROMOSOME,START,END", self.admin_key)
self.assertSuccess(res, req)
regions = self.get_regions_request(req)
expected_regions = """chr1\t713240\t713390
chr1\t713900\t714050
chr1\t714160\t714310
chr1\t715060\t715210
chr1\t762420\t762570
chr1\t840080\t840230
chr1\t840600\t840750
chr1\t858880\t859030
chr1\t859600\t859750
chr1\t860240\t860390
chr1\t875900\t876050"""
self.assertEqual(regions, expected_regions)
res, qid_4 = epidb.overlap(qid_1, qid_2, False, 0, "bp", self.admin_key)
self.assertSuccess(res, qid_4)
res, req = epidb.get_regions(qid_4, "CHROMOSOME,START,END", self.admin_key)
self.assertSuccess(res, req)
regions2 = self.get_regions_request(req)
expected = """chr1 761180 761330
chr1 763020 763170
chr1 839540 839690
chr1 875400 875550
chr1 876180 876330"""
self.assertEquals(regions2, expected)
res, qid_41 = epidb.overlap(qid_1, qid_2, False, 0, "bp", self.admin_key)
self.assertSuccess(res, qid_41)
res, req = epidb.get_regions(qid_41, "CHROMOSOME,START,END", self.admin_key)
self.assertSuccess(res, req)
regions2 = self.get_regions_request(req)
expected = """chr1 761180 761330
chr1 763020 763170
chr1 839540 839690
chr1 875400 875550
chr1 876180 876330"""
res, qid_41 = epidb.overlap(qid_1, qid_2, False, 0, "%", self.admin_key)
self.assertSuccess(res, qid_41)
res, req = epidb.get_regions(qid_41, "CHROMOSOME,START,END", self.admin_key)
self.assertSuccess(res, req)
regions2 = self.get_regions_request(req)
expected = """chr1 761180 761330
chr1 763020 763170
chr1 839540 839690
chr1 875400 875550
chr1 876180 876330"""
self.assertEquals(regions2, expected)
res, qid_5 = epidb.overlap(qid_1, qid_2, False, 350, "bp", self.admin_key)
self.assertSuccess(res, qid_5)
res, req = epidb.get_regions(qid_5, "CHROMOSOME,START,END", self.admin_key)
self.assertSuccess(res, req)
regions = self.get_regions_request(req)
expected = """chr1 761180 761330
chr1 763020 763170
chr1 875400 875550"""
self.assertEquals(regions, expected)
res, qid_6 = epidb.overlap(qid_1, qid_2, False, 500, "%", self.admin_key)
self.assertSuccess(res, qid_6)
res, req = epidb.get_regions(qid_6, "CHROMOSOME,START,END", self.admin_key)
self.assertSuccess(res, req)
regions = self.get_regions_request(req)
self.assertEquals(regions, "chr1\t763020\t763170")
##### SET 2 ######
res, q1 = epidb.input_regions("hg19", "chr1\t1000\t1010\nchr1\t1100\t1110\nchr1\t1200\t1210\nchr1\t1300\t1310\nchr1\t1400\t1410\nchr1\t1500\t1510", self.admin_key)
self.assertSuccess(res, q1)
res, q2 = epidb.input_regions("hg19", "chr1\t1011\t1020\nchr1\t1111\t1120\nchr1\t1211\t1220\nchr1\t1311\t1320\nchr1\t1411\t1420\nchr1\t1511\t1520", self.admin_key)
self.assertSuccess(res, q2)
res, q3 = epidb.overlap(q1, q2, False, 0, "bp", self.admin_key)
self.assertSuccess(res, q3)
res, req = epidb.get_regions(q3, "CHROMOSOME,START,END", self.admin_key)
self.assertSuccess(res, req)
regions = self.get_regions_request(req)
expected = 'chr1\t1000\t1010\nchr1\t1100\t1110\nchr1\t1200\t1210\nchr1\t1300\t1310\nchr1\t1400\t1410\nchr1\t1500\t1510'
self.assertEquals(regions, expected)
res, q3 = epidb.overlap(q1, q2, False, 20, "%", self.admin_key)
self.assertSuccess(res, q3)
res, req = epidb.get_regions(q3, "CHROMOSOME,START,END", self.admin_key)
self.assertSuccess(res, req)
regions = self.get_regions_request(req)
expected = ''
self.assertEquals(regions, expected)
res, q3 = epidb.overlap(q1, q2, False, 1, "%", self.admin_key)
self.assertSuccess(res, q3)
res, req = epidb.get_regions(q3, "CHROMOSOME,START,END", self.admin_key)
self.assertSuccess(res, req)
regions = self.get_regions_request(req)
expected = 'chr1\t1000\t1010\nchr1\t1100\t1110\nchr1\t1200\t1210\nchr1\t1300\t1310\nchr1\t1400\t1410\nchr1\t1500\t1510'
self.assertEquals(regions, expected)
res, q3 = epidb.overlap(q2, q1, False, 0, "bp", self.admin_key)
self.assertSuccess(res, q3)
res, req = epidb.get_regions(q3, "CHROMOSOME,START,END", self.admin_key)
self.assertSuccess(res, req)
regions = self.get_regions_request(req)
self.assertEquals(regions, 'chr1\t1011\t1020\nchr1\t1111\t1120\nchr1\t1211\t1220\nchr1\t1311\t1320\nchr1\t1411\t1420\nchr1\t1511\t1520')
res, q4 = epidb.input_regions("hg19", "chr1\t1000\t1010\nchr1\t1200\t1210\nchr1\t1300\t1310", self.admin_key)
self.assertSuccess(res, q4)
res, q5 = epidb.input_regions("hg19", "chr1\t1011\t1020\nchr1\t1111\t1120\nchr1\t1211\t1220\nchr1\t1311\t1320\nchr1\t1411\t1420\nchr1\t1511\t1520", self.admin_key)
self.assertSuccess(res, q5)
res, q6 = epidb.overlap(q4, q5, False, 0, "bp", self.admin_key)
self.assertSuccess(res, q6)
res, req = epidb.get_regions(q6, "CHROMOSOME,START,END", self.admin_key)
self.assertSuccess(res, req)
regions = self.get_regions_request(req)
self.assertEquals(regions, 'chr1\t1000\t1010\nchr1\t1200\t1210\nchr1\t1300\t1310')
res, q4 = epidb.input_regions("hg19", "chr1\t1000\t1010", self.admin_key)
self.assertSuccess(res, q4)
res, q5 = epidb.input_regions("hg19", "chr1\t1011\t1020\nchr1\t1111\t1120\nchr1\t1211\t1220\nchr1\t1311\t1320\nchr1\t1411\t1420\nchr1\t1511\t1520", self.admin_key)
self.assertSuccess(res, q5)
res, q6 = epidb.overlap(q4, q5, False, 0, "bp", self.admin_key)
self.assertSuccess(res, q6)
res, req = epidb.get_regions(q6, "CHROMOSOME,START,END", self.admin_key)
self.assertSuccess(res, req)
regions = self.get_regions_request(req)
self.assertEqual(regions, "chr1\t1000\t1010")
res, q7 = epidb.overlap(q5, q4, False, 0, "bp", self.admin_key)
self.assertSuccess(res, q7)
res, req = epidb.get_regions(q7, "CHROMOSOME,START,END", self.admin_key)
self.assertSuccess(res, req)
regions = self.get_regions_request(req)
self.assertEqual(regions, "chr1\t1011\t1020\nchr1\t1111\t1120\nchr1\t1211\t1220\nchr1\t1311\t1320\nchr1\t1411\t1420\nchr1\t1511\t1520")
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 get_result():
data = json.loads(request.data.decode("utf-8"))
result = helpers.get_result(data["id"])
app.logger.info('new result, id %s', data["id"])
return jsonify({"id": result['id'], "status": result['result']}), 200
