def annotateFile(art, file): # example pmid = art.pmid if art.pmid == "" or not int(pmid) in pmidToGenes: logging.debug("No pmid for article %s" % art.articleId) raise StopIteration genes = pmidToGenes[int(art.pmid)].split(",") genes = [int(x) for x in genes] mutations = seth.findMutations(file.content) for gene in genes: potentialSNPs = dbSNP.getSNP(int(gene)) features = UniprotFeature.getFeatures(gene) for mut in mutations: print("mutation found: ", str(mut)) start = mut.getStart() end = mut.getEnd() mut.normalizeSNP(potentialSNPs, features, False) normalized = mut.getNormalized() for snp in normalized: wtRes = mut.getWtResidue() mutRes = mut.getMutResidue() pos = mut.getPosition() text = mut.getText() rsId = snp.getRsID() yield [ start, end, str(gene), wtRes, pos, mutRes, "rs" + str(rsId), text ]
def annotateFile(art, file): # example pmid = art.pmid if art.pmid=="" or not int(pmid) in pmidToGenes: logging.debug("No pmid for article %s" % art.articleId) raise StopIteration genes = pmidToGenes[int(art.pmid)].split(",") genes = [int(x) for x in genes] mutations = seth.findMutations(file.content) for gene in genes: potentialSNPs = dbSNP.getSNP(int(gene)) features = UniprotFeature.getFeatures(gene); for mut in mutations: print "mutation found: ", str(mut) start = mut.getStart() end = mut.getEnd() mut.normalizeSNP(potentialSNPs, features, False) normalized = mut.getNormalized() for snp in normalized: wtRes = mut.getWtResidue() mutRes = mut.getMutResidue() pos = mut.getPosition() text = mut.getText() rsId = snp.getRsID() yield [start, end, str(gene), wtRes, pos, mutRes, "rs"+str(rsId), text]
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])
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]))
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])