def test_big_file(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
f = gzip.open("data/bedgraph/bigwig.bg.gz")
data = f.read()
(status, a1) = epidb.add_annotation("exp_wig", "hg19", "bla", data,
"bedgraph", None, self.admin_key)
(status, q1) = epidb.select_annotations("exp_wig", "hg19", None, None,
None, self.admin_key)
status, r1 = epidb.binning(q1, "VALUE", 5, self.admin_key)
binning = self.get_regions_request(r1)
self.assertEqual(
binning, {
'binning': {
'ranges': [
-1126.72, -726.6238, -326.5276, 73.5686, 473.6648,
873.761
],
'counts': [8, 5, 3992582, 3489, 13]
}
})
to_filter_low = binning["binning"]["ranges"][2]
status, filtered = epidb.filter_regions(q1, "VALUE", ">",
str(to_filter_low), "number",
self.admin_key)
to_filter_high = binning["binning"]["ranges"][4]
status, filtered = epidb.filter_regions(q1, "VALUE", "<",
str(to_filter_high), "number",
self.admin_key)
status, r_filtered = epidb.binning(filtered, "VALUE", 10,
self.admin_key)
binning = self.get_regions_request(r_filtered)
self.assertEqual(
binning, {
'binning': {
'counts': [4, 4, 1, 2, 2, 17, 1, 3932813, 772, 119],
'ranges': [
-1126.72, -967.0013, -807.2826, -647.5638, -487.8452,
-328.1265, -168.4077, -8.689, 151.0297, 310.7484,
470.4671
]
}
})
def test_basic_binning(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
sample_id = self.sample_ids[0]
self.insert_experiment(epidb, "hg19_big_2", sample_id)
res, qid = epidb.select_regions("hg19_big_2", "hg19", None, None, None,
None, None, None, None, self.admin_key)
self.assertSuccess(res, qid)
status, req = epidb.binning(qid, "P_VALUE", 5, self.admin_key)
self.assertSuccess(status, req)
binning = self.get_regions_request(req)
self.assertEquals(
binning, {
'binning': {
'ranges':
[2.0006, 37.8473, 73.6939, 109.5406, 145.3873, 181.234],
'counts': [63506, 2632, 3111, 6626, 1668]
}
})
sample_id = self.sample_ids[0]
self.insert_experiment(epidb, "hg19_big_1", sample_id)
res, qid = epidb.select_regions("hg19_big_1", "hg19", None, None, None,
None, None, None, None, self.admin_key)
self.assertSuccess(res, qid)
status, req = epidb.binning(qid, "P_VALUE", 5, self.admin_key)
self.assertSuccess(status, req)
binning = self.get_regions_request(req)
self.assertEquals(
binning, {
'binning': {
'ranges':
[2.0017, 41.3178, 80.6338, 119.9499, 159.2659, 198.582],
'counts': [39349, 2824, 2510, 5325, 4299]
}
})
status, req = epidb.binning(qid, "P_VALUE", 0, self.admin_key)
self.assertFailure(status, req)
status, req = epidb.binning(qid, "P_VALUE", -1, self.admin_key)
self.assertFailure(status, req)
status, req = epidb.binning(qid, "P_VALUE", 66666, self.admin_key)
self.assertFailure(status, req)
res, qid = epidb.select_regions("hg19_big_1", "hg19", None, None, None,
None, None, None, None, self.admin_key)
self.assertSuccess(res, qid)
status, req = epidb.binning(qid, "QEERR", 5, self.admin_key)
self.assertSuccess(status, req)
msg = self.get_regions_request_error(req)
status, msg = epidb.get_request_data(req, self.admin_key)
self.assertEqual(
msg,
"101007:The experiment 'hg19_big_1' does not have the column 'QEERR'."
)
