def findMutationsForGene(self, geneID, annotation, responseType):
if not annotation in {"all", "coding", "promotor"}:
return responsecreator.createResponse("invalid gene annotation: {:s}".format(annotation), responseType)
if annotation is None or annotation == "":
annotation = "all"
logging.debug("finding {:s} mutations in {:s}".format(annotation, geneID))
if annotation == "all":
result = self._reader.findMutationsInAnnotatedAreaOfGene(
geneID, "coding"
) + self._reader.findMutationsInAnnotatedAreaOfGene(geneID, "promotor")
else:
result = self._reader.findMutationsInAnnotatedAreaOfGene(geneID, annotation)
return responsecreator.createResponse(result, responseType)
def findMutationsInRegion(self, chromosome, fromPos, toPos, responseType):
if chromosome is None:
return responsecreator.createResponse("no chromosome provided", responseType)
if fromPos is None:
return responsecreator.createResponse("no fromPos provided", responseType)
if toPos is None:
return responsecreator.createResponse("no toPos provided", responseType)
fromPos = int(fromPos)
toPos = int(toPos)
if fromPos > toPos:
t = fromPos
fromPos = toPos
toPos = t
logging.debug("finding mutations on chromosome {:s} between {:d} and {:d}".format(chromosome, fromPos, toPos))
result = self._reader.findMutationsInRegion(chromosome, fromPos, toPos)
return responsecreator.createResponse(result, responseType)