def test_genome_empty(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init(epidb)
hg18_genome_info = None
with open("data/genomes/hg18", 'r') as f:
hg18_genome_info = f.read().replace(",", "")
mm9_genome_info = None
with open("data/genomes/mm9", 'r') as f:
mm9_genome_info = f.read().replace(",", "")
res = epidb.add_genome("hg18", "Human genome 18", hg18_genome_info,
self.admin_key)
self.assertSuccess(res)
res = epidb.add_genome("mm9", "Mouse genome 9", mm9_genome_info,
self.admin_key)
self.assertSuccess(res)
(res, genomes) = epidb.list_genomes(self.admin_key)
self.assertEqual(len(genomes), 2)
genome_names = [x[1] for x in genomes]
self.assertTrue("hg18" in genome_names)
self.assertTrue("mm9" in genome_names)
def test_remove_genome(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(",", "")
res = epidb.add_genome("A1", "ANGELICA", genome_info, self.admin_key)
self.assertSuccess(res)
genome_id = res[1]
res, user = epidb.add_user("user1", "*****@*****.**", "test",
self.admin_key)
self.assertSuccess(res, user)
res = epidb.remove(genome_id, user[1])
self.assertFailure(res)
res = epidb.add_genome("A1", "XUXA", genome_info, self.admin_key)
self.assertFailure(res)
(res, genomes) = epidb.list_genomes(self.admin_key)
self.assertEqual(len(genomes), 1)
self.assertEqual(genomes[0][0], genome_id)
self.assertEqual(genomes[0][1], "A1")
res = epidb.remove(genome_id, self.admin_key)
self.assertSuccess(res)
res = epidb.add_genome("A1", "XUXA", genome_info, self.admin_key)
self.assertSuccess(res)
status, found = epidb.search("XUXA", "", self.admin_key)
self.assertEqual(len(found), 2)
status, found = epidb.search("ANGELICA", "", self.admin_key)
self.assertEqual(len(found), 0)
status, genomes = epidb.list_genomes(self.admin_key)
self.assertSuccess(status, genomes)
for genome in genomes:
res = epidb.remove(genome[0], self.admin_key)
self.assertSuccess(res)
res, anns = epidb.list_annotations(genome[1], self.admin_key)
self.assertEqual(len(anns), 0)
def test_misc_formats(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
files = ["chr_s_e_name.bed", "chr_s_e_score.bed", "bed10.bed"]
print epidb.list_genomes(self.admin_key)
for f in files:
print f
content = open("data/bed/" + f).read()
res, q1 = epidb.input_regions("hg19", content, self.admin_key)
print epidb.info(q1, self.admin_key)
fmt = epidb.info(q1, self.admin_key)[1][0]['args']['format']
self.assertSuccess(res, q1)
print fmt
r, r1 = epidb.get_regions(q1, fmt, self.admin_key)
self.assertSuccess(r, r1)
for l in self.get_regions_request(r1).split("\n"):
print l
print len(l.split("\t"))
def test_genome_hg19(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(",", "")
res = epidb.add_genome("hg19", "Human genome 19", genome_info,
self.admin_key)
self.assertSuccess(res)
(res, genomes) = epidb.list_genomes(self.admin_key)
self.assertEqual(len(genomes), 1)
self.assertEqual(genomes[0][1], "hg19")
r1 = epidb.chromosomes("hg19", self.admin_key)
r2 = epidb.chromosomes("g1", self.admin_key)
self.assertEqual(len(r1[1]), 93)
self.assertEqual(r1[1][0][0], "chr1")
self.assertEqual(r1[1][0][1], 249250621)
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)
