def test_gene_case_insensitive(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, 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)
status, gene_models = epidb.list_gene_models(self.admin_key)
self.assertEquals(gene_models, [['gs1', 'Test One']])
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_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']])
