def distanceTable(frq,method,outfile,met):
keyDict = sorted(np.unique(("/".join(frq.keys())).split("/")));
mapDict = dict()
if method == 'min':
mapDict =minDistance(frq)
elif method == 'prod':
mapDict =prodDistance(frq,met)
pr.printDistanceTableToFile(mapDict,keyDict,outfile)
def addGene(self, name: str, seq: str):
cache = np.zeros(len(self.matrix) + 1)
cur_index = 0
for gene in self.geneList:
dis = minDistance.minDistance(gene[1], seq)[-1][-1]
if dis == 0:
gene[2] += 1
return
cache[cur_index] = dis
cur_index += 1
self.geneList.append([name, seq, 1])
self.matrix = np.insert(self.matrix, len(self.matrix), values=cache[:-1], axis=1)
self.matrix = np.insert(self.matrix, len(self.matrix), values=cache, axis=0)
def computeDistance(frq, method, percentile):
if method == 'min':
return minDistance(frq)
else:
return prodDistance(frq)