本文整理汇总了Python中oncotator.DatasourceFactory.DatasourceFactory.createDatasourceFromConfigParser方法的典型用法代码示例。如果您正苦于以下问题：Python DatasourceFactory.createDatasourceFromConfigParser方法的具体用法？Python DatasourceFactory.createDatasourceFromConfigParser怎么用？Python DatasourceFactory.createDatasourceFromConfigParser使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类oncotator.DatasourceFactory.DatasourceFactory的用法示例。
在下文中一共展示了DatasourceFactory.createDatasourceFromConfigParser方法的1个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: testCreateDatasource
# 需要导入模块: from oncotator.DatasourceFactory import DatasourceFactory [as 别名]
# 或者: from oncotator.DatasourceFactory.DatasourceFactory import createDatasourceFromConfigParser [as 别名]
def testCreateDatasource(self):
"""
"""
dsFile = os.path.join("testdata", "ESP6500SI-V2.chr1.snps_indels.head.25.txt")
# Never specify "out/"
destDir = "out/create_ds_test/"
if os.path.exists(destDir):
shutil.rmtree(destDir)
os.makedirs(destDir)
datasourceFilename = "ESP6500SI-V2.chr1.snps_indels.head.25.tabix_indexed.txt.gz"
indexColumnNames = "CHROM,POS,POS,REF,ALT"
columnNames = "CHROM,POS,REF,ALT,DBSNP,EA_AC,AA_AC,TAC,MAF,GTS,EA_GTC,AA_GTC,GTC,DP,FG,GM,AA,AAC,PP,CDP,PH,CP,CG,GL,GS,CA,EXOME_CHIP,GWAS_PUBMED"
configFilename = "out/esp_coverage.config"
dataSourceType = "indexed_tsv"
dataSourceName = "ESP"
dataSourceVersion = "6500SI-V2"
dataSourceMatchMode = "overlap"
annotationColumnNames = "DBSNP,EA_GTC,DP"
datasourceBuilder = TabixIndexedTsvDatasourceCreator()
datasourceBuilder.createDatasource(destDir, dsFile, indexColumnNames, configFilename, dataSourceType,
dataSourceName, dataSourceVersion, dataSourceMatchMode,
annotationColumnNames, DatasourceInstallUtils.getIndexCols(dataSourceType,
indexColumnNames))
self.assertTrue(os.path.exists(destDir + datasourceFilename))
self.assertTrue(os.path.exists(destDir + datasourceFilename + ".tbi"))
configParser = ConfigUtils.createConfigParser(configFilename)
self.assertTrue(configParser.has_section("general"), "general section is missing.")
self.assertTrue(configParser.has_section("data_types"), "data_types section is missing.")
self.assertTrue(configParser.has_option("general", "type"), "type option is missing in general section.")
self.assertTrue(configParser.has_option("general", "src_file"),
"src_file option is missing in general section.")
self.assertTrue(configParser.has_option("general", "title"), "title option is missing in general section.")
self.assertTrue(configParser.has_option("general", "version"), "version option is missing in general section.")
self.assertTrue(configParser.has_option("general", "column_names"),
"column_names option is missing in general section.")
self.assertTrue(configParser.has_option("general", "annotation_column_names"),
"annotation_column_names option is missing in general section.")
self.assertTrue(configParser.has_option("general", "match_mode"),
"match_mode option is missing in general section")
self.assertTrue(configParser.has_option("general", "index_column_names"),
"index_column_names option is missing in general section.")
self.assertEqual(configParser.get("general", "type"), dataSourceType,
"Expected data source type is %s but was %s."
% (dataSourceType, configParser.get("general", "type")))
self.assertEqual(configParser.get("general", "src_file"), datasourceFilename,
"Expected data source src_file is %s but was %s."
% (datasourceFilename, configParser.get("general", "src_file")))
self.assertEqual(configParser.get("general", "title"), dataSourceName,
"Expected data source title is %s but was %s."
% (dataSourceName, configParser.get("general", "title")))
self.assertEqual(configParser.get("general", "version"), dataSourceVersion,
"Expected data source version is %s but was %s."
% (dataSourceVersion, configParser.get("general", "version")))
self.assertEqual(configParser.get("general", "column_names"), columnNames,
"Expected data source column names is %s but was %s."
% (columnNames, configParser.get("general", "column_names")))
self.assertEqual(configParser.get("general", "annotation_column_names"), annotationColumnNames,
"Expected data source annotation column names is %s but was %s."
% (annotationColumnNames, configParser.get("general", "annotation_column_names")))
self.assertEqual(configParser.get("general", "match_mode"), dataSourceMatchMode,
"Expected data source match mode is %s but was %s."
% (dataSourceMatchMode, configParser.get("general", "match_mode")))
self.assertEqual(configParser.get("general", "index_column_names"), indexColumnNames,
"Expected data source index column names is %s but was %s."
% (indexColumnNames, configParser.get("general", "index_column_names")))
self.assertEqual(configParser.get("data_types", "EA_GTC"), "String",
"Expected EA_GTC data type is %s but was %s."
% ("String", configParser.get("data_types", "EA_GTC")))
self.assertEqual(configParser.get("data_types", "DP"), "Integer",
"Expected DP data type is %s but was %s."
% ("Integer", configParser.get("data_types", "DP")))
ds = DatasourceFactory.createDatasourceFromConfigParser(configParser, "out/create_ds_test/")
mut = MutationData(chr="1", start="69428", end="69428", ref_allele="T", alt_allele="G")
mut2 = ds.annotate_mutation(mut)
self.assertEquals(mut2["ESP_DBSNP"], "dbSNP_134")
self.assertEquals(mut2["ESP_EA_GTC"], "92,129,3203")
self.assertEquals(mut2["ESP_DP"], "110")