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)
normalized = mut.getNormalized()
for snp in normalized:
rsId = snp.getRsID()
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)
normalized = mut.getNormalized()
for snp in normalized:
rsId = snp.getRsID()
print ",".join([start, end, wtRes, mutRes, pos, "rs"+str(rsId), text])
