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']])