import P1 import P2 import P3 import P4 labelSequenceList = P1.ParseSeqFile("P1_sequences.txt") print(labelSequenceList) alignedSequencesDict = P2.AlignByDP(labelSequenceList) print(alignedSequencesDict) distMatrix = P3.ComputeDistMatrix(alignedSequencesDict) print(distMatrix) labelList = [ "Mouse", "Bovine", "Gibbon", "Orangutan", "Gorilla", "Chimp", "Human" ] binaryTreeString = P4.Cluster(distMatrix, labelList) print(binaryTreeString)
import P1 import P2 import P3 import P4 #RunCode start1 = time.time() a = P1.ParseSeqFile('sequencefile.txt') end1 = time.time() print('*******************\nParseSeqFile: \n*******************\n\n', a, '\n\n') labels = [] for tuples in a: labels.append(tuples[0]) start2 = time.time() b = P2.AlignByDP(a) end2 = time.time() print('*******************\nAlignByDP: \n*******************\n\n') print(b, '\n\n') start3 = time.time() c = P3.ComputeDistMatrix(b) end3 = time.time() print('*******************\nComputeDistMatrix: \n*******************\n\n') for line in c: lines = [] for element in line: lines.append('%010.8f' % element) print(lines) start4 = time.time() d = P4.Cluster(c, labels) end4 = time.time()