def test_genes_location(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
data = gzip.open(
"data/gtf/gencode.v19.annotation.ONLY_GENES.gtf.gz").read()
(s, ss) = epidb.add_gene_model("Test One", "hg19",
"Test One Description", data, "GTF", {},
self.admin_key)
self.assertSuccess(s, ss)
(s, query_id) = epidb.select_genes(None, "", "Test One", ["chr1"],
1000, 15000, self.admin_key)
(s, r_id) = epidb.get_regions(query_id, "CHROMOSOME,START,END",
self.admin_key)
regions = self.get_regions_request(r_id)
self.assertEquals(regions, "chr1\t11869\t14412\nchr1\t14363\t29806")
(s, query_id) = epidb.select_genes(None, "", "Test One",
["chr1", "chr11", "chr21"], 10000,
2000000, self.admin_key)
(s, r_id) = epidb.count_regions(query_id, self.admin_key)
count = self.get_regions_request(r_id)
self.assertEquals(count, {'count': 269})
status, gene_models = epidb.list_gene_models(self.admin_key)
self.assertEquals(gene_models, [['gs1', 'Test One']])
(s, genes) = epidb.list_genes("", "", "chr21", 9683191, 9683272,
gene_models[0][1], self.admin_key)
self.assertEquals(genes, [{
'transcript_status': 'NOVEL',
'gene_name': 'CR381670.1',
'gene_type': 'miRNA',
'end': 9683272,
'source': 'ENSEMBL',
'frame': '.',
'level': '3',
'gene_id': 'ENSG00000238411.1',
'start': 9683191,
'transcript_id': 'ENSG00000238411.1',
'score': 0.0,
'strand': '+',
'transcript_name': 'CR381670.1',
'_id': 'gn52851',
'gene_status': 'NOVEL',
'transcript_type': 'miRNA',
'chromosome': 'chr21'
}])
(s, genes) = epidb.list_genes("", "", "chr21", 9683191, 9683272,
gene_models[0][1], self.admin_key)
self.assertEquals(genes, [{
'transcript_status': 'NOVEL',
'gene_name': 'CR381670.1',
'gene_type': 'miRNA',
'end': 9683272,
'source': 'ENSEMBL',
'frame': '.',
'level': '3',
'gene_id': 'ENSG00000238411.1',
'start': 9683191,
'transcript_id': 'ENSG00000238411.1',
'score': 0.0,
'strand': '+',
'transcript_name': 'CR381670.1',
'_id': 'gn52851',
'gene_status': 'NOVEL',
'transcript_type': 'miRNA',
'chromosome': 'chr21'
}])
(s, genes) = epidb.list_genes("CR381670.1", "", "chr21", None, None,
gene_models[0][1], self.admin_key)
self.assertEquals(genes, [{
'transcript_status': 'NOVEL',
'gene_name': 'CR381670.1',
'gene_type': 'miRNA',
'end': 9683272,
'source': 'ENSEMBL',
'frame': '.',
'level': '3',
'gene_id': 'ENSG00000238411.1',
'start': 9683191,
'transcript_id': 'ENSG00000238411.1',
'score': 0.0,
'strand': '+',
'transcript_name': 'CR381670.1',
'_id': 'gn52851',
'gene_status': 'NOVEL',
'transcript_type': 'miRNA',
'chromosome': 'chr21'
}])
(s, genes) = epidb.list_genes(None, "", "chr10", None, None,
gene_models[0][1], self.admin_key)
self.assertEquals(2260, len(genes))
def test_gene_retrieve(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
data = open("data/gtf/gencode.v23.basic.annotation_head.gtf").read()
(s, ss) = epidb.add_gene_model("Test One", "hg19",
"Test One Description", data, "GTF", {},
self.admin_key)
self.assertSuccess(s, ss)
(s, ss) = epidb.add_gene_ontology_term("GO:00001", "label 1",
"description",
"biological_process",
self.admin_key)
self.assertSuccess(s, ss)
(s, ss) = epidb.add_gene_ontology_term("GO:00002", "label 2",
"description 2",
"biological_process",
self.admin_key)
self.assertSuccess(s, ss)
(s, ss) = epidb.add_gene_ontology_term("GO:00003", "label 3",
"description 3",
"biological_process",
self.admin_key)
self.assertSuccess(s, ss)
(s, ss) = epidb.add_gene_ontology_term("GO:00004", "label 4",
"description 4",
"biological_process",
self.admin_key)
self.assertSuccess(s, ss)
(s, ss) = epidb.list_genes("", "", "chr1", 0, 1000000, "test one",
self.admin_key)
self.assertSuccess(s, ss)
(s, ss) = epidb.annotate_gene("ENSG00000238009", "GO:00001",
self.admin_key)
self.assertSuccess(s, ss)
(s, ss) = epidb.annotate_gene("ENSG00000239906", "GO:00002",
self.admin_key)
self.assertSuccess(s, ss)
(s, ss) = epidb.annotate_gene("ENSG00000239945", "GO:00003",
self.admin_key)
self.assertSuccess(s, ss)
(s, ss) = epidb.annotate_gene("ENSG00000238009", "GO:00001",
self.admin_key)
self.assertSuccess(s, ss)
(s, ss) = epidb.annotate_gene("ENSG00000239945", "GO:00002",
self.admin_key)
self.assertSuccess(s, ss)
(s, ss) = epidb.annotate_gene("ENSG00000239906", "GO:00003",
self.admin_key)
self.assertSuccess(s, ss)
(s, ss) = epidb.annotate_gene("ENSG00000223972", "GO:00001",
self.admin_key)
self.assertSuccess(s, ss)
(s, ss) = epidb.annotate_gene("ENSG00000223972", "GO:00004",
self.admin_key)
self.assertSuccess(s, ss)
(s, ss) = epidb.list_genes("ENSG00000239906.1", None, "chr1", 0,
1000000, "Test One", self.admin_key)
self.assertSuccess(s, ss)
(s, ss) = epidb.list_genes("", "GO:00001", "chr1", 0, 1000000,
"Test One", self.admin_key)
self.assertSuccess(s, ss)
(s, ss) = epidb.list_genes("", ["GO:00001", "GO:00002"], "chr1", 0,
1000000, "Test One", self.admin_key)
self.assertSuccess(s, ss)
(s, query_id) = epidb.select_genes(None, "", "Test One", None, None,
None, self.admin_key)
(s, r_id) = epidb.get_regions(
query_id,
"@GENE_ID(Test One),@GENE_NAME(Test One),@GO_IDS(Test One),@GO_LABELS(Test One)",
self.admin_key)
regions = self.get_regions_request(r_id)
self.assertEquals(
"ENSG00000223972.5\tDDX11L1\tGO:00001,GO:00004\tlabel 1,label 4\nENSG00000227232.5\tWASH7P\t\t\nENSG00000278267.1\tMIR6859-1\t\t\nENSG00000243485.3\tRP11-34P13.3\t\t\nENSG00000274890.1\tMIR1302-2\t\t\nENSG00000237613.2\tFAM138A\t\t\nENSG00000268020.3\tOR4G4P\t\t\nENSG00000240361.1\tOR4G11P\t\t\nENSG00000186092.4\tOR4F5\t\t\nENSG00000238009.6\tRP11-34P13.7\tGO:00001\tlabel 1\nENSG00000239945.1\tRP11-34P13.8\tGO:00003,GO:00002\tlabel 3,label 2\nENSG00000233750.3\tCICP27\t\t\nENSG00000268903.1\tRP11-34P13.15\t\t\nENSG00000269981.1\tRP11-34P13.16\t\t\nENSG00000239906.1\tRP11-34P13.14\tGO:00002,GO:00003\tlabel 2,label 3\nENSG00000241860.6\tRP11-34P13.13\t\t\nENSG00000222623.1\tRNU6-1100P\t\t\nENSG00000241599.1\tRP11-34P13.9\t\t\nENSG00000279928.1\tFO538757.3\t\t\nENSG00000279457.3\tFO538757.2\t\t",
regions)
def test_select_genes(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
data = open("data/gtf/gencode.v23.basic.annotation_head.gtf").read()
(s, ss) = epidb.add_gene_model("Test One", "hg19",
"Test One Description", data, "GTF", {},
self.admin_key)
self.assertSuccess(s, ss)
(s, ss) = epidb.list_genes(["ENSG00000279457.3"], "", None, None, None,
"Test One", self.admin_key)
self.assertEquals(ss, [{
'gene_name': 'FO538757.2',
'gene_type': 'protein_coding',
'end': 200322,
'source': 'ENSEMBL',
'frame': '.',
'level': '3',
'tag': 'ncRNA_host',
'gene_id': 'ENSG00000279457.3',
'start': 184923,
'score': 0.0,
'strand': '-',
'_id': 'gn20',
'gene_status': 'KNOWN',
'chromosome': 'chr1'
}])
(s, ss) = epidb.list_genes("ENSG00000279457", "", "chr1", None, None,
"Test One", self.admin_key)
self.assertEquals(ss, [])
(s, ss) = epidb.list_genes(None, None, None, None, None, "Test One",
self.admin_key)
self.assertEquals(20, len(ss))
(s, query_id) = epidb.select_genes(["RP11-34P13.7"], "", "Test One",
None, None, None, self.admin_key)
(s, req) = epidb.count_regions(query_id, self.admin_key)
count = self.count_request(req)
self.assertEquals(count, 1)
(s, new_query_id) = epidb.select_genes(["RP11-34P13.7"], "",
"Test One", None, None, None,
self.admin_key)
self.assertEquals(query_id, new_query_id)
(s, new_query_id) = epidb.select_genes("RP11-34P13.7", "", "Test One",
None, None, None,
self.admin_key)
self.assertEquals(query_id, new_query_id)
(s, query_id) = epidb.select_genes(["RP11-34P13.234"], "", "Test One",
None, None, None, self.admin_key)
(s, req) = epidb.count_regions(query_id, self.admin_key)
count = self.count_request(req)
self.assertEquals(count, 0)
(s, query_id) = epidb.select_genes(["RP11-34P13"], "", "Test One",
None, None, None, self.admin_key)
(s, req) = epidb.count_regions(query_id, self.admin_key)
count = self.count_request(req)
self.assertEquals(count, 0)
status, gene_models = epidb.list_gene_models(self.admin_key)
self.assertEquals(gene_models, [['gs1', 'Test One']])
