def retriveDataForIds(ids,datasetCollectionName):
raise Exception, " Error: Not completed"
datasetsIndexFile = getMainDatasetIndexFileName(datasetCollectionName)
datasets = readDatasetDescriptions.readDatasets(datasetsIndexFile,datasetCollectionName)
for datasetKey in datasets.keys():
dataset = datasets[datasetKey]
if cgsAS.getFeatureDatasetProperty(datasetKey,"hasFeatures") == False:
continue
dataset.openDBDataConnection(cgsAS)
regionData = {}
for id in ids:
regionData[id] = {}
for datasetKey in datasets.keys():
dataset = datasets[datasetKey]
for id in ids:
raise Exception, "Error: Not completed"
def exportDataInitializeStructures(datasets,regionSet,exportGenome):
raise GDMException, "openDBDataConnection was changed"
initializadDatasets = {}
cgsAS = CGSAnnotationsSettings.CGSAnnotationsSettings(regionSet,exportGenome,{},{})
datasetsIndexFile = getMainDatasetIndexFileName(exportGenome)
defaultDatasets = readDatasetDescriptions.readDatasets(datasetsIndexFile)
#fullyProcessedDefaultDatasets = readSettingsFile(settings.fullyProcessedDefaultDatasetsFile)
for datasetKey in defaultDatasets.keys():
if not datasetKey in datasets or cgsAS.getFeatureDatasetProperty(datasetKey,"hasFeatures") == False:
log_CSEngine("exportDataInitializeStructures: Skipping "+datasetKey)
continue
log_CSEngine("exportDataInitializeStructures: Loading "+datasetKey)
defaultDatasets[datasetKey].init(False)
defaultDatasets[datasetKey].openDBDataConnection(cgsAS)
initializadDatasets[datasetKey] = defaultDatasets[datasetKey]
if datasetKey == regionSet:
cgsAS.addRegionDataset({datasetKey:{}})
cgsAS.addFeatureDataset({datasetKey:{}})
return initializadDatasets
genome = sys.argv[1]
directParam = "computeAll"
if len(sys.argv) > 2:
directParam = sys.argv[2]
print "Genome:", genome
datasetCollectionName = genome + "_ucsc_cpg_islands_test"
cgsAS = CGSAnnotationsSettings.CGSAnnotationsSettings(datasetCollectionName,
genome, {}, {})
if directParam == "computeAll":
datasetsIndexFile = getMainDatasetIndexFileName(cgsAS.genome + "_test")
#===============================================================================
# #Step 1 Read all datasets
#===============================================================================
import readDatasetDescriptions
datasets = readDatasetDescriptions.readDatasets(datasetsIndexFile)
#===============================================================================
# #Step 2 Download and process datasets
#===============================================================================
#datasets = {"broad_histones_CTCF":datasets["broad_histones_CTCF"],
# datasetCollectionName:datasets[datasetCollectionName]}
for dataset in datasets:
datasets[dataset].init()
cgsAS.addFeatureDataset(
{dataset: datasets[dataset].getDefaultAnnotationSettings()})
if dataset == "hg18_ensembl_gene_genes":
cgsAS.addFeatureDataset({
"hg18_ensembl_gene_genes": {
"includeGO": True,
"includeGeneDescriptions": True,
#===============================================================================
genome = sys.argv[1]
directParam = "computeAll"
if len(sys.argv) > 2:
directParam = sys.argv[2]
print "Genome:",genome
datasetCollectionName = genome+"_ucsc_cpg_islands_test"
cgsAS = CGSAnnotationsSettings.CGSAnnotationsSettings(datasetCollectionName,genome,{},{})
if directParam == "computeAll":
datasetsIndexFile = getMainDatasetIndexFileName(cgsAS.genome+"_test")
#===============================================================================
# #Step 1 Read all datasets
#===============================================================================
import readDatasetDescriptions
datasets = readDatasetDescriptions.readDatasets(datasetsIndexFile)
#===============================================================================
# #Step 2 Download and process datasets
#===============================================================================
#datasets = {"broad_histones_CTCF":datasets["broad_histones_CTCF"],
# datasetCollectionName:datasets[datasetCollectionName]}
for dataset in datasets:
datasets[dataset].init()
cgsAS.addFeatureDataset({dataset:datasets[dataset].getDefaultAnnotationSettings()})
if dataset == "hg18_ensembl_gene_genes":
cgsAS.addFeatureDataset({"hg18_ensembl_gene_genes":{"includeGO":True,
"includeGeneDescriptions": True,
"includeOMIM": True,
"includeGeneTranscripts":False,
"includeGenesUpTo":10000}})
