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_not_find_genome_and_in_order_chromosoms(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
genome_data = """chr1 1000000
chr2 900000
chr3 500000
chrX 100000"""
epidb.add_genome("Genome Example", "Example of Genome for the Manual",
genome_data, self.admin_key)
x = epidb.chromosomes("Genome Example", self.admin_key)
self.assertEquals(x, [
'okay',
[['chr1', 1000000], ['chr2', 900000], ['chr3', 500000],
['chrX', 100000]]
])
def test_chromosomes(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)
(r, chroms) = epidb.chromosomes("hg19", self.admin_key)
expected = [['chr1', 249250621], ['chr10', 135534747],
['chr11', 135006516], ['chr11_gl000202_random', 40103],
['chr12', 133851895], ['chr13', 115169878],
['chr14', 107349540], ['chr15', 102531392],
['chr16', 90354753], ['chr17', 81195210],
['chr17_ctg5_hap1', 1680828],
['chr17_gl000203_random', 37498],
['chr17_gl000204_random', 81310],
['chr17_gl000205_random', 174588],
['chr17_gl000206_random', 41001], ['chr18', 78077248],
['chr18_gl000207_random', 4262], ['chr19', 59128983],
['chr19_gl000208_random', 92689],
['chr19_gl000209_random', 159169],
['chr1_gl000191_random', 106433],
['chr1_gl000192_random', 547496], ['chr2', 243199373],
['chr20', 63025520], ['chr21', 48129895],
['chr21_gl000210_random', 27682], ['chr22', 51304566],
['chr3', 198022430], ['chr4', 191154276],
['chr4_ctg9_hap1', 590426],
['chr4_gl000193_random', 189789],
['chr4_gl000194_random', 191469], ['chr5', 180915260],
['chr6', 171115067], ['chr6_apd_hap1', 4622290],
['chr6_cox_hap2', 4795371], ['chr6_dbb_hap3', 4610396],
['chr6_mann_hap4', 4683263], ['chr6_mcf_hap5', 4833398],
['chr6_qbl_hap6', 4611984], ['chr6_ssto_hap7', 4928567],
['chr7', 159138663], ['chr7_gl000195_random', 182896],
['chr8', 146364022], ['chr8_gl000196_random', 38914],
['chr8_gl000197_random', 37175], ['chr9', 141213431],
['chr9_gl000198_random', 90085],
['chr9_gl000199_random', 169874],
['chr9_gl000200_random', 187035],
['chr9_gl000201_random', 36148], ['chrM', 16571],
['chrUn_gl000211', 166566], ['chrUn_gl000212', 186858],
['chrUn_gl000213', 164239], ['chrUn_gl000214', 137718],
['chrUn_gl000215', 172545], ['chrUn_gl000216', 172294],
['chrUn_gl000217', 172149], ['chrUn_gl000218', 161147],
['chrUn_gl000219', 179198], ['chrUn_gl000220', 161802],
['chrUn_gl000221', 155397], ['chrUn_gl000222', 186861],
['chrUn_gl000223', 180455], ['chrUn_gl000224', 179693],
['chrUn_gl000225', 211173], ['chrUn_gl000226', 15008],
['chrUn_gl000227', 128374], ['chrUn_gl000228', 129120],
['chrUn_gl000229', 19913], ['chrUn_gl000230', 43691],
['chrUn_gl000231', 27386], ['chrUn_gl000232', 40652],
['chrUn_gl000233', 45941], ['chrUn_gl000234', 40531],
['chrUn_gl000235', 34474], ['chrUn_gl000236', 41934],
['chrUn_gl000237', 45867], ['chrUn_gl000238', 39939],
['chrUn_gl000239', 33824], ['chrUn_gl000240', 41933],
['chrUn_gl000241', 42152], ['chrUn_gl000242', 43523],
['chrUn_gl000243', 43341], ['chrUn_gl000244', 39929],
['chrUn_gl000245', 36651], ['chrUn_gl000246', 38154],
['chrUn_gl000247', 36422], ['chrUn_gl000248', 39786],
['chrUn_gl000249', 38502], ['chrX', 155270560],
['chrY', 59373566]]
self.assertEqual(chroms, expected)
hg18_genome_info = None
with open("data/genomes/hg18", 'r') as f:
hg18_genome_info = f.read().replace(",", "")
res = epidb.add_genome("hg18", "Human genome 18", hg18_genome_info,
self.admin_key)
self.assertSuccess(res)
(r, chroms) = epidb.chromosomes("hg18", self.admin_key)
expected = [['chr1', 247249719], ['chr10', 135374737],
['chr10_random', 113275], ['chr11', 134452384],
['chr11_random', 215294], ['chr12', 132349534],
['chr13', 114142980], ['chr13_random', 186858],
['chr14', 106368585], ['chr15', 100338915],
['chr15_random', 784346], ['chr16', 88827254],
['chr16_random', 105485], ['chr17', 78774742],
['chr17_random', 2617613], ['chr18', 76117153],
['chr18_random', 4262], ['chr19', 63811651],
['chr19_random', 301858], ['chr1_random', 1663265],
['chr2', 242951149], ['chr20', 62435964],
['chr21', 46944323], ['chr21_random', 1679693],
['chr22', 49691432], ['chr22_h2_hap1', 63661],
['chr22_random', 257318], ['chr2_random', 185571],
['chr3', 199501827], ['chr3_random', 749256],
['chr4', 191273063], ['chr4_random', 842648],
['chr5', 180857866], ['chr5_h2_hap1', 1794870],
['chr5_random', 143687], ['chr6', 170899992],
['chr6_cox_hap1', 4731698], ['chr6_qbl_hap2', 4565931],
['chr6_random', 1875562], ['chr7', 158821424],
['chr7_random', 549659], ['chr8', 146274826],
['chr8_random', 943810], ['chr9', 140273252],
['chr9_random', 1146434], ['chrM', 16571],
['chrX', 154913754], ['chrX_random', 1719168],
['chrY', 57772954]]
self.assertEqual(chroms, expected)
mm9_genome_info = None
with open("data/genomes/mm9", 'r') as f:
mm9_genome_info = f.read().replace(",", "")
res = epidb.add_genome("mm9", "Mouse genome 9", mm9_genome_info,
self.admin_key)
self.assertSuccess(res)
(r, chroms) = epidb.chromosomes("mm9", self.admin_key)
expected = [['chr1', 197195432], ['chr10', 129993255],
['chr11', 121843856], ['chr12', 121257530],
['chr13', 120284312], ['chr13_random', 400311],
['chr14', 125194864], ['chr15', 103494974],
['chr16', 98319150], ['chr16_random', 3994],
['chr17', 95272651], ['chr17_random', 628739],
['chr18', 90772031], ['chr19', 61342430],
['chr1_random', 1231697], ['chr2', 181748087],
['chr3', 159599783], ['chr3_random', 41899],
['chr4', 155630120], ['chr4_random', 160594],
['chr5', 152537259], ['chr5_random', 357350],
['chr6', 149517037], ['chr7', 152524553],
['chr7_random', 362490], ['chr8', 131738871],
['chr8_random', 849593], ['chr9', 124076172],
['chr9_random', 449403], ['chrM', 16299],
['chrUn_random', 5900358], ['chrX', 166650296],
['chrX_random', 1785075], ['chrY', 15902555],
['chrY_random', 58682461]]
self.assertEqual(chroms, expected)
