def persistNewProfileName(domainConfigurationDirectory, profileName): from oracle.fabric.profiles.impl import ProfileConstants; fileName = domainConfigurationDirectory + File.separatorChar + 'server-profile-mbean-config.xml' profileProperties = Properties() profileProperties.loadFromXML(FileInputStream(fileName)) profileProperties.setProperty(ProfileConstants.CURRENT_SOA_PROFILE_PROPERTY_NAME, profileName) profileProperties.storeToXML(FileOutputStream(fileName), None)
sys.path.append(jarName) # import the java classes from java.util import Properties from java.io import FileInputStream, File from de.hu.berlin.wbi.objects import DatabaseConnection, dbSNP, UniprotFeature from seth import SETH print("init'ing seth") # get some mutations from text seth = SETH(mutName) # setup db connection print("setup mysql connection") property = Properties() property.loadFromXML(FileInputStream(File(propName))) db = DatabaseConnection(property) db.connect() dbSNP.init(db, "PSM", "hgvs") UniprotFeature.init(db, "uniprot") def test(): gene = 1312 potentialSNPs = dbSNP.getSNP(gene) features = UniprotFeature.getFeatures(gene) mutations = seth.findMutations("p.A123T and Val158Met") for mut in mutations: start, end = mut.getStart(), mut.getEnd() wtRes, mutRes = mut.getWtResidue(), mut.getMutResidue() pos, text = mut.getPosition(), mut.getText()
def getCurrentProfileName(domainConfigurationDirectory): from oracle.fabric.profiles.impl import ProfileConstants; fileName = domainConfigurationDirectory + File.separatorChar + 'server-profile-mbean-config.xml' profileProperties = Properties() profileProperties.loadFromXML(FileInputStream(fileName)) return profileProperties.getProperty(ProfileConstants.CURRENT_SOA_PROFILE_PROPERTY_NAME)
sys.path.append(jarName) # import the java classes from java.util import Properties from java.io import FileInputStream, File from de.hu.berlin.wbi.objects import DatabaseConnection, dbSNP, UniprotFeature from seth import SETH print "init'ing seth" # get some mutations from text seth = SETH(mutName) # setup db connection print "setup mysql connection" property = Properties() property.loadFromXML(FileInputStream(File(propName))) db = DatabaseConnection(property) db.connect() dbSNP.init(db, "PSM", "hgvs") UniprotFeature.init(db, "uniprot") def test(): gene = 1312 potentialSNPs = dbSNP.getSNP(gene); features = UniprotFeature.getFeatures(gene); mutations = seth.findMutations("p.A123T and Val158Met") for mut in mutations: start, end = mut.getStart(), mut.getEnd() wtRes, mutRes = mut.getWtResidue(), mut.getMutResidue() pos, text = mut.getPosition(), mut.getText() mut.normalizeSNP(potentialSNPs, features, False)