def test_include_invalid_regions(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
data = """chr1\t1\t100000000000000000
chr10\t666\t66610000
chrY\t12345\t1234567"""
(s, a) = epidb.add_annotation("test annotation", "hg19", "testing",
data, "CHROMOSOME,START,END",
{"HI": "HOW ARE YOU?"}, self.admin_key)
self.assertFailure(s, a)
self.assertEquals(
a,
"Error while reading the BED file. Line: 0. - '100000000000000000 is not a valid end position'"
)
data = """chr1\t2147483647\t2147483648"""
(s, a) = epidb.add_annotation("test annotation", "hg19", "testing",
data, "CHROMOSOME,START,END",
{"HI": "HOW ARE YOU?"}, self.admin_key)
self.assertFailure(s, a)
self.assertEquals(
a,
"Invalid region: 2147483647 - 2147483648. It is beyond the length of the chromosome chr1 ."
)
def test_annotation_shuffle(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
cpg_island = ",".join([
"CHROMOSOME", "START", "END", "NAME", "LENGTH", "NUM_CPG",
"NUM_GC", "PER_CPG", "PER_CG", "OBS_EXP"
])
file_data = None
with open("data/cpgIslandExtFull.bed", 'r') as f:
file_data = f.read()
res = epidb.add_annotation(
"Cpg Islands", "hg19", "CpG islands are associated ...", file_data,
cpg_island, {
"url":
"genome.ucsc.edu/cgi-bin/hgTables?db=hg19&hgta_group=regulation&hgta_track=cpgIslandExt&hgta_table=cpgIslandExt&hgta_doSchema=describe+table+schema"
}, self.admin_key)
self.assertSuccess(res)
res, qid = epidb.select_annotations("Cpg Islands", "hg19", None, None,
None, self.admin_key)
self.assertSuccess(res, qid)
res, req = epidb.get_regions(qid, "CHROMOSOME,START,END",
self.admin_key)
self.assertSuccess(res, req)
regions = self.get_regions_request(req)
# ---
file_data = None
with open("data/cpgIslandExtShuffle.bed", 'r') as f:
file_data = f.read()
res = epidb.add_annotation(
"Cpg Islands Shuffle", "hg19", "CpG islands are associated ...",
file_data, cpg_island, {
"url":
"genome.ucsc.edu/cgi-bin/hgTables?db=hg19&hgta_group=regulation&hgta_track=cpgIslandExt&hgta_table=cpgIslandExt&hgta_doSchema=describe+table+schema"
}, self.admin_key)
self.assertSuccess(res)
res, qid_shuffle = epidb.select_annotations("Cpg Islands Shuffle",
"hg19", None, None, None,
self.admin_key)
self.assertSuccess(res, qid)
res, req_shuffle = epidb.get_regions(qid_shuffle,
"CHROMOSOME,START,END",
self.admin_key)
self.assertSuccess(res, req)
regions_shuffle = self.get_regions_request(req_shuffle)
self.assertEqual(regions_shuffle, regions)
self.assertEqual(regions, regions_shuffle)
def test_list_annotations(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init(epidb)
genome_info = None
with open("data/genomes/hg19", 'r') as f:
genome_info = f.read().replace(",", "")
file_data = None
with open("data/cpgIslandExt.txt", 'r') as f:
file_data = f.read()
res = epidb.add_genome("hg19", "Human genome 19", genome_info,
self.admin_key)
self.assertSuccess(res)
res = epidb.add_annotation(
"Cpg Islands", "hg19", "CpG islands are associated ...", file_data,
"", {
"url":
"genome.ucsc.edu/cgi-bin/hgTables?db=hg19&hgta_group=regulation&hgta_track=cpgIslandExt&hgta_table=cpgIslandExt&hgta_doSchema=describe+table+schema"
}, self.admin_key)
self.assertSuccess(res)
res = epidb.add_genome("hg19a", "Human genome 19a", genome_info,
self.admin_key)
self.assertSuccess(res)
res = epidb.add_annotation(
"Cpg Islands", "hg19a", "CpG islands are associated ...",
file_data, "", {
"url":
"genome.ucsc.edu/cgi-bin/hgTables?db=hg19&hgta_group=regulation&hgta_track=cpgIslandExt&hgta_table=cpgIslandExt&hgta_doSchema=describe+table+schema"
}, self.admin_key)
self.assertSuccess(res)
res = epidb.add_genome("hg19b", "Human genome 19b", genome_info,
self.admin_key)
self.assertSuccess(res)
res = epidb.add_annotation(
"Cpg Islands", "hg19b", "CpG islands are associated ...",
file_data, "", {
"url":
"genome.ucsc.edu/cgi-bin/hgTables?db=hg19&hgta_group=regulation&hgta_track=cpgIslandExt&hgta_table=cpgIslandExt&hgta_doSchema=describe+table+schema"
}, self.admin_key)
self.assertSuccess(res)
expected = [
'okay',
[['a1', 'Chromosomes size for hg19'], ['a2', 'Cpg Islands'],
['a3', 'Chromosomes size for hg19a'], ['a4', 'Cpg Islands'],
['a5', 'Chromosomes size for hg19b'], ['a6', 'Cpg Islands']]
]
result = epidb.list_annotations("", self.admin_key)
self.assertEqual(expected, result)
def test_annotation_full_cpg_islands(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
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()
regions_count = len(file_data.split("\n"))
(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, qid_1 = epidb.select_annotations("Cpg Islands", "hg19", None,
None, None, self.admin_key)
self.assertSuccess(res, qid_1)
(s, req) = epidb.count_regions(qid_1, self.admin_key)
count = self.count_request(req)
self.assertEqual(regions_count, count)
def test_long_sequence_content(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
sequence = open("data/genomes/chromosomes/hg19.chr19").read()
res = epidb.upload_chromosome("hg19", "chr19", sequence,
self.admin_key)
self.assertSuccess(res)
join_seq = "".join(sequence.split("\n"))
data = "chr19\t0\t59128983"
ann_name = "Full chr19"
(s, aid) = epidb.add_annotation(ann_name, "hg19", None, data, None,
None, self.admin_key)
(s, sid) = epidb.select_annotations(ann_name, "hg19", None, None, None,
self.admin_key)
fmt = "@SEQUENCE"
(s, req) = epidb.get_regions(sid, fmt, self.admin_key)
self.assertSuccess(res, req)
regions = self.get_regions_request(req)
self.assertEqual(len(regions), len(join_seq))
self.assertEqual(regions, join_seq)
def test_get_sequences(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
sequence = open("data/genomes/chromosomes/chrM.fa").read()
res = epidb.upload_chromosome("hg19", "chrM", sequence, self.admin_key)
data = """chrM\t1\t30
chrM\t2\t31
chrM\t2340\t2377"""
ann_name = "Interesting Regions at chrM"
(s, aid) = epidb.add_annotation(ann_name, "hg19", None, data, None,
None, self.admin_key)
self.assertSuccess(s, aid)
(s, sid) = epidb.select_annotations(ann_name, "hg19", None, None, None,
self.admin_key)
self.assertSuccess(s, sid)
fmt = "CHROMOSOME,START,END,@NAME,@SEQUENCE,@LENGTH"
(s, req) = epidb.get_regions(sid, fmt, self.admin_key)
self.assertSuccess(res, req)
regions = self.get_regions_request(req)
expected = """chrM\t1\t30\tInteresting Regions at chrM\tATCACAGGTCTATCACCCTATTAACCACT\t29
chrM\t2\t31\tInteresting Regions at chrM\tTCACAGGTCTATCACCCTATTAACCACTC\t29
chrM\t2340\t2377\tInteresting Regions at chrM\tGCCTGCGTCAGATCAAAACACTGAACTGACAATTAAC\t37"""
self.assertEqual(regions, expected)
def test_include_annotations(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
user_id, user_key = self.get_new_user(epidb)
ann = helpers.data.ANNOTATIONS["Cpg Islands"]
with open(ann["data_file"], 'r') as f:
annotation_data = f.read()
s = epidb.add_annotation("Cpg Islands", ann["genome"],
ann["description"], annotation_data,
ann["format"], ann["metadata"], user_key)
self.assertFailure(s)
self.modify_user_permission(epidb, user_id, "INCLUDE_ANNOTATIONS")
s = epidb.add_annotation("Cpg Islands", ann["genome"],
ann["description"], annotation_data,
ann["format"], ann["metadata"], user_key)
self.assertSuccess(s)
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_no_start_position(self):
file_content = """1036\t1146\t43\t0\t18\tchr19\t59118819\t1000\t-10000\t+\t(TTAGGG)n\tSimple_repeat\tSimple_repeat\t5\t165\t0\t1\n585\t1080\t161\t1\t0\tchr19_gl000208_random\t0\t719\t-91970\t-\tALR/Alpha\tSatellite\tcentr\t-41\t719\t1\t4"""
rmsk = [
"BIN", "swSCORE", "MILLI_DIV", "MILLI_DEL", "MILLI_INS", "NAME",
"START", "END", "GENO_LEFT", "STRAND", "repNAME", "REP_CLASS",
"REP_FAMILY", "REP_START", "REP_END", "REP_LEFT", "ID"
]
format = ",".join(rmsk)
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
(r, a) = epidb.add_annotation("repeat_masker", "hg19", None,
file_content, format, None,
self.admin_key)
self.assertFailure(r, a)
self.assertEquals(
a,
"120002:The CHROMOSOME is missing in the format. Please, inform the CHROMOSOME column in the Format."
)
rmsk2 = [
"BIN", "swSCORE", "MILLI_DIV", "MILLI_DEL", "MILLI_INS",
"CHROMOSOME", "START", "END", "GENO_LEFT", "STRAND", "repNAME",
"REP_CLASS", "REP_FAMILY", "REP_START", "REP_END", "REP_LEFT", "ID"
]
format2 = ",".join(rmsk2)
(r, a) = epidb.add_annotation("repeat_masker2", "hg19", None,
file_content, format2, None,
self.admin_key)
self.assertSuccess(r, a)
def test_output_format(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
file_data = open("data/cpgIslandAllFields.txt").read()
cpg_island = ",".join([
"CHROMOSOME", "START", "END", "NAME", "LENGTH", "NUM_CPG",
"NUM_GC", "PER_CPG", "PER_CG", "OBS_EXP"
])
res = epidb.add_annotation("Cpg Islands", "hg19", "CpG islands",
file_data, cpg_island, None, self.admin_key)
self.assertSuccess(res)
res, qid_1 = epidb.select_annotations("Cpg Islands", "hg19", None,
None, None, self.admin_key)
self.assertSuccess(res, qid_1)
self.assertEqual(qid_1, 'q1')
res, req = epidb.count_regions(qid_1, self.admin_key)
self.assertSuccess(res, req)
count = self.count_request(req)
self.assertEqual(10, count)
res, req = epidb.get_regions(
qid_1,
"chr:start:end:name:length:cpgNum:gcNum:perCpg:perGc:obsExp",
self.admin_key)
self.assertEquals(
req,
"125000:Column name 'chr:start:end:name:length:cpgNum:gcNum:perCpg:perGc:obsExp' does not exist."
)
res, req = epidb.get_regions(
qid_1,
"CHROMOSOME,START,END,NAME,LENGTH,NUM_CPG,NUM_GC,PER_CPG,PER_CG,OBS_EXP",
self.admin_key)
regions = self.get_regions_request(req)
expected = 'chr1\t28735\t29810\tCpG: 116\t1075\t116\t787\t21.6000\t73.2000\t0.8300\nchr1\t135124\t135563\tCpG: 30\t439\t30\t295\t13.7000\t67.2000\t0.6400\nchr1\t327790\t328229\tCpG: 29\t439\t29\t295\t13.2000\t67.2000\t0.6200\nchr1\t437151\t438164\tCpG: 84\t1013\t84\t734\t16.6000\t72.5000\t0.6400\nchr1\t449273\t450544\tCpG: 99\t1271\t99\t777\t15.6000\t61.1000\t0.8400\nchr1\t533219\t534114\tCpG: 94\t895\t94\t570\t21.0000\t63.7000\t1.0400\nchr1\t544738\t546649\tCpG: 171\t1911\t171\t1405\t17.9000\t73.5000\t0.6700\nchr1\t713984\t714547\tCpG: 60\t563\t60\t385\t21.3000\t68.4000\t0.9200\nchr1\t762416\t763445\tCpG: 115\t1029\t115\t673\t22.4000\t65.4000\t1.0700\nchr1\t788863\t789211\tCpG: 28\t348\t28\t192\t16.1000\t55.2000\t1.0600'
self.assertSuccess(res, regions)
self.assertEquals(expected, regions)
def test_annotation_signal_bedgraph(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
sample_id = self.sample_ids[0]
files = ["test1"]
for filename in files:
wig_data = helpers.load_bedgraph(filename)
res = epidb.add_annotation(filename, "hg19", "Test data", wig_data,
"bedgraph", None, self.admin_key)
self.assertSuccess(res)
(s, q) = epidb.select_annotations(files, "hg19", None, None, None,
self.admin_key)
(s, req) = epidb.count_regions(q, self.admin_key)
self.assertSuccess(s, req)
count = self.count_request(req)
self.assertEqual(1000, count)
(s, q_filtered_down) = epidb.filter_regions(q, "VALUE", ">", "0.75",
"number", self.admin_key)
(s, q_filtered_up) = epidb.filter_regions(q_filtered_down, "VALUE",
"<", "0.8", "number",
self.admin_key)
(s, q_chr_x) = epidb.filter_regions(q_filtered_up, "CHROMOSOME", "!=",
"chrX", "string", self.admin_key)
(s, q_chr_7) = epidb.filter_regions(q_chr_x, "CHROMOSOME", "!=",
"chr7", "string", self.admin_key)
(s, req) = epidb.get_regions(
q_chr_7, "CHROMOSOME,START,END,VALUE,@NAME,@EPIGENETIC_MARK",
self.admin_key)
regions = self.get_regions_request(req)
self.assertEqual(
regions,
'chr1\t104372258\t104372293\t0.7767\ttest1\t\nchr10\t126498141\t126498176\t0.7695\ttest1\t\nchr11\t66110277\t66110312\t0.7613\ttest1\t\nchr15\t38653026\t38653061\t0.7720\ttest1\t\nchr15\t87725326\t87725361\t0.7727\ttest1\t\nchr16\t2119419\t2119454\t0.7696\ttest1\t\nchr16\t63360719\t63360754\t0.7740\ttest1\t\nchr19\t46369215\t46369250\t0.7727\ttest1\t\nchr8\t21923667\t21923702\t0.7930\ttest1\t'
)
def test_annotation_info(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
aid = None
with open("data/cpgIslandExt.txt") as f:
res, aid = epidb.add_annotation("Cpg Islands", "hg19", "CpG islands are associated ...",
f.read(), "", {"url":"genome.ucsc.edu...", "meta":"data"},
self.admin_key)
self.assertSuccess(res, aid)
res, data = epidb.info(aid, self.admin_key)
self.assertEqual(res, 'okay')
self.assertEqual(data[0]['name'], "Cpg Islands")
self.assertEqual(data[0]['description'], "CpG islands are associated ...")
self.assertEqual(data[0]['genome'], "hg19")
self.assertEqual(data[0]['extra_metadata'], {"url":"genome.ucsc.edu...", "meta":"data"})
self.assertEqual(data[0]['upload_info']['user'], "test_admin")
self.assertEqual(data[0]['format'], "CHROMOSOME,START,END")
self.assertEqual(data[0]['_id'], aid)
def test_annotation(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
file_data = None
with open("data/cpgIslandExt.txt", 'r') as f:
file_data = f.read()
res = epidb.add_annotation(
"Cpg Islands", "hg19", "CpG islands are associated ...", file_data,
"", {
"url":
"genome.ucsc.edu/cgi-bin/hgTables?db=hg19&hgta_group=regulation&hgta_track=cpgIslandExt&hgta_table=cpgIslandExt&hgta_doSchema=describe+table+schema"
}, self.admin_key)
self.assertSuccess(res)
res, annotations = epidb.list_annotations("hg19", self.admin_key)
self.assertSuccess(res, annotations)
self.assertEqual(len(annotations), 2)
self.assertEqual(annotations[0][1], "Chromosomes size for hg19")
self.assertEqual(annotations[1][1], "Cpg Islands")
size = len(file_data.split("\n"))
res, qid = epidb.select_annotations("Cpg Islands", "hg19", None, None,
None, self.admin_key)
self.assertSuccess(res, qid)
res, req = epidb.count_regions(qid, self.admin_key)
self.assertSuccess(res, req)
count = self.count_request(req)
self.assertEqual(size, count)
res, req = epidb.get_regions(qid, "CHROMOSOME,START,END",
self.admin_key)
self.assertSuccess(res, req)
regions = self.get_regions_request(req)
self.assertEqual(regions, file_data)
def test_annotation_signal_wig(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
sample_id = self.sample_ids[0]
files = [
"scores1", "scores2", "scores3", "scores4", "scores5", "scores6",
"scores7", "yeast_pol2", "yeast_rap1"
]
for filename in files:
wig_data = helpers.load_wig(filename)
res = epidb.add_annotation(filename, "hg19", "Test data", wig_data,
"wig", None, self.admin_key)
self.assertSuccess(res)
(s, r) = epidb.select_annotations(files, "hg19", None, None, None,
self.admin_key)
(s, req) = epidb.count_regions(r, self.admin_key)
count = self.count_request(req)
self.assertEqual(5667, count)
def test_wrong_chromosomes_usage(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
cpg_island = ",".join([
"CHROMOSOME", "START", "END", "NAME", "LENGTH", "NUM_CPG",
"NUM_GC", "PER_CPG", "PER_CG", "OBS_EXP"
])
file_data = None
with open("data/cpgIslandExtFull.txt", 'r') as f:
file_data = f.read()
res = epidb.add_annotation("Cpg Islands", "hg19",
"Complete CpG islands", file_data,
cpg_island, None, self.admin_key)
self.assertSuccess(res)
size_total = len(file_data.split("\n"))
(status, qid_cpg) = epidb.select_annotations("Cpg Islands", "hg19",
"chr1", None, None,
self.admin_key)
(s, req) = epidb.count_regions(qid_cpg, self.admin_key)
self.assertSuccess(s, req)
c = self.count_request(req)
self.assertEquals(2462, c)
total = 0
(status, cq1) = epidb.select_annotations("Cpg Islands", "hg19", "chr1",
None, None, self.admin_key)
(s, req1) = epidb.count_regions(cq1, self.admin_key)
c1 = self.count_request(req1)
(status, cq2) = epidb.select_annotations("Cpg Islands", "hg19", "chr7",
None, None, self.admin_key)
(s, req2) = epidb.count_regions(cq2, self.admin_key)
c2 = self.count_request(req2)
(status, cq3) = epidb.select_annotations("Cpg Islands", "hg19",
"chr18", None, None,
self.admin_key)
(s, req3) = epidb.count_regions(cq3, self.admin_key)
c3 = self.count_request(req3)
(status, cq4) = epidb.select_annotations("Cpg Islands", "hg19", "chrX",
None, None, self.admin_key)
(s, req4) = epidb.count_regions(cq4, self.admin_key)
c4 = self.count_request(req4)
total = int(c1) + int(c2) + int(c3) + int(c4)
(status, qid_count) = epidb.select_annotations(
"Cpg Islands", "hg19", ["chr1", "chr7", "chr18", "chrX"], None,
None, self.admin_key)
(s, req) = epidb.count_regions(qid_count, self.admin_key)
c = self.count_request(req)
self.assertEquals(c, total)
cpg_island_chrs = """chr1
chr10
chr11
chr11_gl000202_random
chr12
chr13
chr14
chr15
chr16
chr17
chr17_ctg5_hap1
chr17_gl000204_random
chr17_gl000205_random
chr18
chr19
chr1_gl000191_random
chr1_gl000192_random
chr2
chr20
chr21
chr22
chr3
chr4
chr4_ctg9_hap1
chr4_gl000193_random
chr4_gl000194_random
chr5
chr6
chr6_apd_hap1
chr6_cox_hap2
chr6_dbb_hap3
chr6_mann_hap4
chr6_mcf_hap5
chr6_qbl_hap6
chr6_ssto_hap7
chr7
chr8
chr8_gl000197_random
chr9
chr9_gl000199_random
chr9_gl000200_random
chr9_gl000201_random
chrUn_gl000211
chrUn_gl000212
chrUn_gl000213
chrUn_gl000214
chrUn_gl000215
chrUn_gl000216
chrUn_gl000217
chrUn_gl000218
chrUn_gl000219
chrUn_gl000220
chrUn_gl000221
chrUn_gl000222
chrUn_gl000223
chrUn_gl000224
chrUn_gl000225
chrUn_gl000228
chrUn_gl000229
chrUn_gl000231
chrUn_gl000235
chrUn_gl000236
chrUn_gl000237
chrUn_gl000240
chrUn_gl000241
chrUn_gl000242
chrUn_gl000243
chrX
chrY"""
(status,
qid_count) = epidb.select_annotations("Cpg Islands", "hg19",
cpg_island_chrs.split("\n"),
None, None, self.admin_key)
(s, req) = epidb.count_regions(qid_count, self.admin_key)
c = self.count_request(req)
self.assertEquals(size_total, c)
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)
def test_aggregation_bug_on_normalfields_better_data(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
res = epidb.add_technique("ChIP-seq", "ChIP-sequencing", {},
self.admin_key)
self.assertSuccess(res)
sample_id = self.sample_ids[0]
broad_peak_format = ",".join([
"CHROMOSOME",
"START",
"END",
"NAME",
"SCORE",
"STRAND",
"SIGNAL_VALUE",
"P_VALUE",
"Q_VALUE",
])
with open("data/wgEncodeBroadHistoneH1hescH3k27me3StdPk.bed",
'r') as f:
file_data = f.read()
(res, a_1) = epidb.add_experiment(
"wgEncodeBroadHistoneH1hescH3k27me3StdPk.bed", "hg19",
"H3k4me3", "s1", "ChIPseq", "ENCODE",
"wgEncodeBroadHistoneH1hescH3k27me3StdPk.bed from ENCODE",
file_data, broad_peak_format, None, self.admin_key)
self.assertSuccess(res, a_1)
res, q_exp = epidb.select_experiments(
"wgEncodeBroadHistoneH1hescH3k27me3StdPk.bed", "chr1", None,
None, self.admin_key)
self.assertSuccess(res, q_exp)
# Insert annotation
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_3 = epidb.aggregate(q_exp, q_cgi, "SCORE", self.admin_key)
self.assertSuccess(res, qid_3)
res, chr_sizes = epidb.select_annotations("Chromosomes size for hg19",
"hg19", None, None, None,
self.admin_key)
res, qid_5 = epidb.aggregate(qid_3, chr_sizes, "@AGG.COUNT",
self.admin_key)
status, req = epidb.get_regions(
qid_5,
"CHROMOSOME,@AGG.MIN,@AGG.MAX,@AGG.MEDIAN,@AGG.MEAN,@AGG.VAR,@AGG.SD,@AGG.COUNT",
self.admin_key)
rs = self.get_regions_request(req)
expected = 'chr1\t0.0000\t8.0000\t0.0000\t0.5142\t0.5301\t0.7281\t2462'
self.assertEquals(rs, expected)
def test_coverage(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
file_data = None
with open("data/cpgIslandExtFull.txt", 'r') as f:
file_data = f.read()
cpg_island = ",".join([
"CHROMOSOME", "START", "END", "NAME", "LENGTH", "NUM_CPG",
"NUM_GC", "PER_CPG", "PER_CG", "OBS_EXP"
])
res = epidb.add_annotation(
"Cpg Islands", "hg19", "CpG islands are associated ...", file_data,
cpg_island, {
"url":
"genome.ucsc.edu/cgi-bin/hgTables?db=hg19&hgta_group=regulation&hgta_track=cpgIslandExt&hgta_table=cpgIslandExt&hgta_doSchema=describe+table+schema"
}, self.admin_key)
self.assertSuccess(res)
res, qid = epidb.select_annotations("Cpg Islands", "hg19", None, None,
None, self.admin_key)
self.assertSuccess(res, qid)
status, req = epidb.coverage(qid, "HG19", self.admin_key)
coverage = self.get_regions_request(req)
self.assertEqual(
coverage, {
'coverages': {
'chr8_gl000197_random': {
'total': 3140,
'coverage': 8.4465,
'size': 37175
},
'chrUn_gl000229': {
'total': 1962,
'coverage': 9.8529,
'size': 19913
},
'chr6_apd_hap1': {
'total': 39175,
'coverage': 0.8475,
'size': 4622290
},
'chrUn_gl000223': {
'total': 2949,
'coverage': 1.6342,
'size': 180455
},
'chrUn_gl000236': {
'total': 1060,
'coverage': 2.5278,
'size': 41934
},
'chr13': {
'total': 453125,
'coverage': 0.3934,
'size': 115169878
},
'chr12': {
'total': 851919,
'coverage': 0.6365,
'size': 133851895
},
'chr11': {
'total': 1036273,
'coverage': 0.7676,
'size': 135006516
},
'chr10': {
'total': 966963,
'coverage': 0.7134,
'size': 135534747
},
'chr17': {
'total': 1274581,
'coverage': 1.5698,
'size': 81195210
},
'chr16': {
'total': 1081705,
'coverage': 1.1972,
'size': 90354753
},
'chr15': {
'total': 665790,
'coverage': 0.6494,
'size': 102531392
},
'chr14': {
'total': 622989,
'coverage': 0.5803,
'size': 107349540
},
'chr19': {
'total': 1624580,
'coverage': 2.7475,
'size': 59128983
},
'chr18': {
'total': 439689,
'coverage': 0.5631,
'size': 78077248
},
'chrUn_gl000228': {
'total': 49978,
'coverage': 38.7066,
'size': 129120
},
'chrUn_gl000243': {
'total': 296,
'coverage': 0.683,
'size': 43341
},
'chr9_gl000200_random': {
'total': 223,
'coverage': 0.1192,
'size': 187035
},
'chr6_mann_hap4': {
'total': 74514,
'coverage': 1.5911,
'size': 4683263
},
'chrUn_gl000237': {
'total': 312,
'coverage': 0.6802,
'size': 45867
},
'chrUn_gl000213': {
'total': 4465,
'coverage': 2.7186,
'size': 164239
},
'chrUn_gl000235': {
'total': 406,
'coverage': 1.1777,
'size': 34474
},
'chrUn_gl000211': {
'total': 1413,
'coverage': 0.8483,
'size': 166566
},
'chr17_gl000204_random': {
'total': 2683,
'coverage': 3.2997,
'size': 81310
},
'chrUn_gl000212': {
'total': 4931,
'coverage': 2.6389,
'size': 186858
},
'chrUn_gl000215': {
'total': 5660,
'coverage': 3.2803,
'size': 172545
},
'chrUn_gl000214': {
'total': 636,
'coverage': 0.4618,
'size': 137718
},
'chrUn_gl000217': {
'total': 3354,
'coverage': 1.9483,
'size': 172149
},
'chrUn_gl000216': {
'total': 1341,
'coverage': 0.7783,
'size': 172294
},
'chr6_dbb_hap3': {
'total': 83010,
'coverage': 1.8005,
'size': 4610396
},
'chrUn_gl000218': {
'total': 2063,
'coverage': 1.2802,
'size': 161147
},
'chr6_cox_hap2': {
'total': 92751,
'coverage': 1.9342,
'size': 4795371
},
'chrUn_gl000219': {
'total': 1778,
'coverage': 0.9922,
'size': 179198
},
'chr7': {
'total': 1147864,
'coverage': 0.7213,
'size': 159138663
},
'chr1_gl000191_random': {
'total': 1570,
'coverage': 1.4751,
'size': 106433
},
'chr4_ctg9_hap1': {
'total': 617,
'coverage': 0.1045,
'size': 590426
},
'chrUn_gl000222': {
'total': 4795,
'coverage': 2.5661,
'size': 186861
},
'chr17_ctg5_hap1': {
'total': 30127,
'coverage': 1.7924,
'size': 1680828
},
'chr11_gl000202_random': {
'total': 257,
'coverage': 0.6408,
'size': 40103
},
'chr6_qbl_hap6': {
'total': 90147,
'coverage': 1.9546,
'size': 4611984
},
'chr22': {
'total': 562123,
'coverage': 1.0957,
'size': 51304566
},
'chrY': {
'total': 115810,
'coverage': 0.1951,
'size': 59373566
},
'chr20': {
'total': 612174,
'coverage': 0.9713,
'size': 63025520
},
'chr21': {
'total': 268220,
'coverage': 0.5573,
'size': 48129895
},
'chr6_mcf_hap5': {
'total': 76009,
'coverage': 1.5726,
'size': 4833398
},
'chr17_gl000205_random': {
'total': 301,
'coverage': 0.1724,
'size': 174588
},
'chrX': {
'total': 732552,
'coverage': 0.4718,
'size': 155270560
},
'chr2': {
'total': 1379397,
'coverage': 0.5672,
'size': 243199373
},
'chr4_gl000193_random': {
'total': 602,
'coverage': 0.3172,
'size': 189789
},
'chr6': {
'total': 942464,
'coverage': 0.5508,
'size': 171115067
},
'chr5': {
'total': 966173,
'coverage': 0.534,
'size': 180915260
},
'chr4': {
'total': 837951,
'coverage': 0.4384,
'size': 191154276
},
'chr3': {
'total': 882783,
'coverage': 0.4458,
'size': 198022430
},
'chr1': {
'total': 1881629,
'coverage': 0.7549,
'size': 249250621
},
'chr1_gl000192_random': {
'total': 2945,
'coverage': 0.5379,
'size': 547496
},
'chr9_gl000199_random': {
'total': 246,
'coverage': 0.1448,
'size': 169874
},
'chrUn_gl000224': {
'total': 287,
'coverage': 0.1597,
'size': 179693
},
'chr4_gl000194_random': {
'total': 1920,
'coverage': 1.0028,
'size': 191469
},
'chr9_gl000201_random': {
'total': 1834,
'coverage': 5.0736,
'size': 36148
},
'chrUn_gl000220': {
'total': 17252,
'coverage': 10.6624,
'size': 161802
},
'chrUn_gl000221': {
'total': 303,
'coverage': 0.195,
'size': 155397
},
'chr9': {
'total': 941315,
'coverage': 0.6666,
'size': 141213431
},
'chr8': {
'total': 864319,
'coverage': 0.5905,
'size': 146364022
},
'chrUn_gl000225': {
'total': 9599,
'coverage': 4.5456,
'size': 211173
},
'chr6_ssto_hap7': {
'total': 70928,
'coverage': 1.4391,
'size': 4928567
},
'chrUn_gl000242': {
'total': 257,
'coverage': 0.5905,
'size': 43523
},
'chrUn_gl000231': {
'total': 1240,
'coverage': 4.5279,
'size': 27386
},
'chrUn_gl000240': {
'total': 206,
'coverage': 0.4913,
'size': 41933
},
'chrUn_gl000241': {
'total': 812,
'coverage': 1.9264,
'size': 42152
}
}
})
self.insert_experiment(epidb, "hg19_big_1")
res, qid = epidb.select_experiments("hg19_big_1", None, None, None,
self.admin_key)
self.assertSuccess(res, qid)
status, req = epidb.coverage(qid, "hg19", self.admin_key)
coverage = self.get_regions_request(req)
self.assertEqual(
coverage, {
'coverages': {
'chrX': {
'total': 1483495,
'coverage': 0.9554,
'size': 155270560
},
'chr13': {
'total': 1132457,
'coverage': 0.9833,
'size': 115169878
},
'chr12': {
'total': 2964677,
'coverage': 2.2149,
'size': 133851895
},
'chr11': {
'total': 2899893,
'coverage': 2.148,
'size': 135006516
},
'chr10': {
'total': 2420026,
'coverage': 1.7855,
'size': 135534747
},
'chr17': {
'total': 3111151,
'coverage': 3.8317,
'size': 81195210
},
'chr16': {
'total': 2134123,
'coverage': 2.3619,
'size': 90354753
},
'chr15': {
'total': 1820040,
'coverage': 1.7751,
'size': 102531392
},
'chr14': {
'total': 1692055,
'coverage': 1.5762,
'size': 107349540
},
'chr19': {
'total': 3237248,
'coverage': 5.4749,
'size': 59128983
},
'chr18': {
'total': 1012202,
'coverage': 1.2964,
'size': 78077248
},
'chr22': {
'total': 1204818,
'coverage': 2.3484,
'size': 51304566
},
'chr20': {
'total': 1436177,
'coverage': 2.2787,
'size': 63025520
},
'chr21': {
'total': 589069,
'coverage': 1.2239,
'size': 48129895
},
'chr7': {
'total': 2623790,
'coverage': 1.6487,
'size': 159138663
},
'chr6': {
'total': 3309649,
'coverage': 1.9342,
'size': 171115067
},
'chr5': {
'total': 2737174,
'coverage': 1.513,
'size': 180915260
},
'chr4': {
'total': 2204447,
'coverage': 1.1532,
'size': 191154276
},
'chr3': {
'total': 3096812,
'coverage': 1.5639,
'size': 198022430
},
'chr2': {
'total': 3900776,
'coverage': 1.6039,
'size': 243199373
},
'chr1': {
'total': 5292444,
'coverage': 2.1233,
'size': 249250621
},
'chr9': {
'total': 2336737,
'coverage': 1.6548,
'size': 141213431
},
'chr8': {
'total': 2050838,
'coverage': 1.4012,
'size': 146364022
}
}
})
def test_cancel_aggregation(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)
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_count = epidb.count_regions(qid_2, self.admin_key)
self.assertSuccess(res, req_count)
count = self.count_request(req_count)
self.assertEquals(count, 3118)
res, qid_3 = epidb.aggregate(q_cgi, qid_2, "@LENGTH", self.admin_key)
self.assertSuccess(res, qid_3)
res, qid_4 = epidb.filter_regions(qid_3, "@AGG.COUNT", ">=", "100",
"number", self.admin_key)
(res, req_regions) = epidb.get_regions(
qid_4,
"CHROMOSOME,START,END,@AGG.MIN,@AGG.MAX,@AGG.MEDIAN,@AGG.MEAN,@AGG.VAR,@AGG.SD,@AGG.COUNT",
self.admin_key)
self.assertSuccess(res, req_regions)
(s, user_two) = epidb.add_user("ANOTHER NAME", "ANOTHER EMAIL",
"INSTITUTE", self.admin_key)
s, tmp_user = epidb.modify_user_admin(user_two[0], "permission_level",
"GET_DATA", self.admin_key)
s, msg = epidb.cancel_request(req_regions, user_two[1])
self.assertEquals(msg, "130003:The request ID 'r2' is invalid.")
s, msg = epidb.cancel_request(req_count, user_two[1])
self.assertEquals(msg, "130003:The request ID 'r1' is invalid.")
(s, m) = epidb.cancel_request(req_regions, self.admin_key)
self.assertSuccess(s, m)
(s, m) = epidb.cancel_request(req_count, self.admin_key)
self.assertSuccess(s, m)
(s, user_ass) = epidb.add_user("ASS NAME", "ASS EMAIL", "INSTITUTE",
self.admin_key)
s, tmp_user = epidb.modify_user_admin(user_ass[0], "permission_level",
"GET_DATA", self.admin_key)
res, q_cgi_other = epidb.select_annotations("Cpg Islands", "hg19",
None, None, None,
user_two[1])
self.assertSuccess(res, q_cgi)
(res, req_other) = epidb.get_regions(q_cgi_other,
"CHROMOSOME,START,END",
user_two[1])
self.assertSuccess(res, req_regions)
(s, msg) = epidb.cancel_request(req_other, user_ass[1])
self.assertEquals(msg, "130003:The request ID 'r3' is invalid.")
(s, m) = epidb.cancel_request(req_other, self.admin_key)
self.assertSuccess(s, m)
(s, ss) = epidb.info(req_other, self.admin_key)
self.assertEquals(ss[0]['state'], 'canceled')
(s, ss_count) = epidb.info(req_count, self.admin_key)
self.assertEquals(ss_count[0]["state"], "removed")
(s, ss_regions) = epidb.info(req_regions, self.admin_key)
self.assertEquals(ss_regions[0]["state"], "canceled")
s, e1 = epidb.get_request_data(req_count, self.admin_key)
self.assertEqual(
e1, "Request ID r1 was not finished. Please, check its status.")
s, e2 = epidb.get_request_data(req_regions, self.admin_key)
self.assertEqual(
e2, "Request ID r2 was not finished. Please, check its status.")
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_remove_annotation(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
file_data = None
with open("data/cpgIslandExt.txt", 'r') as f:
file_data = f.read()
res = epidb.add_annotation(
"Cpg Islands", "hg19", "CpG islands are associated ...", file_data,
"", {
"url":
"genome.ucsc.edu/cgi-bin/hgTables?db=hg19&hgta_group=regulation&hgta_track=cpgIslandExt&hgta_table=cpgIslandExt&hgta_doSchema=describe+table+schema"
}, self.admin_key)
self.assertSuccess(res)
annotation_id = res[1]
res, user = epidb.add_user("user1", "*****@*****.**", "test",
self.admin_key)
self.assertSuccess(res, user)
res = epidb.remove(annotation_id, user[1])
self.assertFailure(res)
res = epidb.remove(annotation_id, self.admin_key)
self.assertSuccess(res)
res = epidb.add_annotation(
"Cpg Islands", "hg19", "CpG islands are associated ...", file_data,
"", {
"url":
"genome.ucsc.edu/cgi-bin/hgTables?db=hg19&hgta_group=regulation&hgta_track=cpgIslandExt&hgta_table=cpgIslandExt&hgta_doSchema=describe+table+schema"
}, self.admin_key)
self.assertSuccess(res)
annotation_id = res[1]
res, genomes = epidb.search("hg19", "genomes", self.admin_key)
res, anns = epidb.remove(genomes[0][0], self.admin_key)
self.assertFailure(res, anns)
self.assertEqual(anns, "This genome is being used by annotations.")
res = epidb.add_annotation(
"Cpg Islands", "hg19", "CpG islands are associated ...", file_data,
"", {
"url":
"genome.ucsc.edu/cgi-bin/hgTables?db=hg19&hgta_group=regulation&hgta_track=cpgIslandExt&hgta_table=cpgIslandExt&hgta_doSchema=describe+table+schema"
}, self.admin_key)
self.assertFailure(res)
res = epidb.remove(annotation_id, self.admin_key)
self.assertSuccess(res)
res = epidb.add_annotation(
"Cpg Islands", "hg19", "CpG islands are associated ...", file_data,
"", {
"url":
"genome.ucsc.edu/cgi-bin/hgTables?db=hg19&hgta_group=regulation&hgta_track=cpgIslandExt&hgta_table=cpgIslandExt&hgta_doSchema=describe+table+schema"
}, self.admin_key)
self.assertSuccess(res)
res = epidb.remove(res[1], self.admin_key)
self.assertSuccess(res)
res, genomes = epidb.list_genomes(self.admin_key)
for genome in genomes:
res = epidb.remove(genome[0], self.admin_key)
self.assertSuccess(res)
res, anns = epidb.list_annotations("hg18", self.admin_key)
self.assertSuccess(res, anns)
self.assertEqual(len(anns), 0)
res, anns = epidb.list_annotations("hg19", self.admin_key)
self.assertSuccess(res, anns)
self.assertEqual(len(anns), 0)
