def testRandUniformInput(): MACROSTATES = enum("E-DHF-NADPH", "E-NADPH", "E-OPEN", "E-THF", "E-THF-NADPX", "TS"); RESIDUES = enum('A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y'); # only looking at MACROSTATE.TS # only optimizing backrub temperature and steepness ensembleSizes = numpy.array([50]); backrubTemps = numpy.array([0.3, 0.6, 0.9, 1.2, 1.5, 1.8]); boltzmannTemps = numpy.array([0, -1, 1, 5.0]); steepnessRange = numpy.array([0.5, 5]); minWeights = numpy.array([0, 0, 0, 0, 0, 0]); maxWeights = numpy.array([1, 1, 0, 1, 1, 1]); print("Initializing objects\n"); targetFreqs = "C:\\Users\\Candy\\SkyDrive\\Documents\\rotation 2\\ecDHFR_openseq_bacterial_representative_final_align_trim.fasta"; targetFreqsAlt = "C:\\Users\\Candy_000\\SkyDrive\\Documents\\rotation 2\\ecDHFR_openseq_bacterial_representative_final_align_trim.fasta"; data = "C:\\Users\\Candy\\SkyDrive\\Documents\\rotation 2\\DHFR_MSD_M20loop\\DHFR_MSD_M20loop_repeat1.tsv"; dataAlt = "C:\\Users\\Candy_000\\SkyDrive\\Documents\\rotation 2\\DHFR_MSD_M20loop\\DHFR_MSD_M20loop_repeat1.tsv"; optimizer = Optimizer(MACROSTATES); # slightly different paths on my two computers try: optimizer.readTargetFrequencies(targetFreqs); optimizer.readData(data); except: optimizer.readTargetFrequencies(targetFreqsAlt); optimizer.readData(dataAlt); # make energies uniform for model in optimizer.models: optimizer.models[model].macrostateResidueEnergies = numpy.ones_like(optimizer.models[model].macrostateResidueEnergies); search = CuckooSearch(optimizer.models, JensenShannonDistance(optimizer.targetFrequencies), False, 1, 1, 0.25); search.setMaxIterations(1); search.setParamBounds(ensembleSizes, backrubTemps, boltzmannTemps, steepnessRange, minWeights, maxWeights); search.setSearchParameters(False, False, False, False, numpy.array([False, False, False, False, False, False])); optimizer.useAlgorithm(search); outfile = open("uniform energy similarities.txt", 'w'); optimizer.optimize(); outfile.write("JSD: {:.4f}\n".format(optimizer.getBestParameters()['match'])); search.setSimilarityMeasure(CosineSimilarity(optimizer.targetFrequencies)); optimizer.optimize(); outfile.write("Cosine similarity: {:.4f}\n".format(optimizer.getBestParameters()['match'])); search.setSimilarityMeasure(KLDivergence(optimizer.targetFrequencies)); optimizer.optimize(); outfile.write("K-L divergence: {:.4f}\n".format(optimizer.getBestParameters()['match'])); search.setSimilarityMeasure(EntropyWeightsMixedSimilarity(CosineSimilarity(), JensenShannonDistance(), optimizer.targetFrequencies)); optimizer.optimize(); outfile.write("Weighted mixed similarity: {:.4f}\n".format(optimizer.getBestParameters()['match'])); outfile.close(); return None;
def smalltestPrevOptimalVals(): MACROSTATES = enum("E-DHF-NADPH", "E-NADPH", "E-OPEN", "E-THF", "E-THF-NADPX", "TS"); RESIDUES = enum('A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y'); # only looking at MACROSTATE.TS # only optimizing backrub temperature and steepness ensembleSizes = numpy.array([50]); backrubTemps = numpy.array([1.8]); boltzmannTemps = numpy.array([0.0]); steepnessRange = numpy.array([3.0]); minWeights = numpy.array([0.80, 0.55, 0, 0.90, 0.35, 1.00]); maxWeights = numpy.array([0.80, 0.55, 0, 0.90, 0.35, 1.00]); print("Initializing objects\n"); targetFreqs = "C:\\Users\\Candy\\SkyDrive\\Documents\\rotation 2\\ecDHFR_openseq_bacterial_representative_final_align_trim.fasta"; targetFreqsAlt = "C:\\Users\\Candy_000\\SkyDrive\\Documents\\rotation 2\\ecDHFR_openseq_bacterial_representative_final_align_trim.fasta"; data = "C:\\Users\\Candy\\SkyDrive\\Documents\\rotation 2\\DHFR_MSD_M20loop\\DHFR_MSD_M20loop_repeat6.tsv"; dataAlt = "C:\\Users\\Candy_000\\SkyDrive\\Documents\\rotation 2\\DHFR_MSD_M20loop\\DHFR_MSD_M20loop_repeat5.tsv"; optimizer = Optimizer(MACROSTATES); # slightly different paths on my two computers try: optimizer.readTargetFrequencies(targetFreqs); optimizer.readData(data); except: optimizer.readTargetFrequencies(targetFreqsAlt); optimizer.readData(dataAlt); print("Files read in"); search = CuckooSearch(optimizer.models, JensenShannonDistance(optimizer.targetFrequencies), False, 1, 1, 0.25); search.setMaxIterations(1); search.setParamBounds(ensembleSizes, backrubTemps, boltzmannTemps, steepnessRange, minWeights, maxWeights); search.setSearchParameters(False, False, False, False, numpy.array([False, False, False, False, False, False])); optimizer.useAlgorithm(search); #print("Cos similiarity"); #optimizer.optimize(); #optimizer.writeFrequenciesToFASTA(optimizer.getBestFrequencies(), "testOutCos.fasta"); #print(optimizer.getBestParameters()['match']); print("\nJS Dist"); #search.setSimilarityMeasure(JensenShannonDistance(optimizer.targetFrequencies)); optimizer.optimize(); now = datetime.now(); optimizer.writeFrequenciesToFASTA(optimizer.getBestFrequencies(), "prev opt vals " + now.strftime('%Y%m%d%H%M') + ".fasta"); optimizer.writeBestParamsToText("prev opt vals " + now.strftime('%Y%m%d%H%M')) print(optimizer.getBestParameters()['match']); return None;
def testChi2(iterations = 64): print("Hello!\n"); MACROSTATES = enum("E-DHF-NADPH", "E-NADPH", "E-OPEN", "E-THF", "E-THF-NADPX", "TS"); RESIDUES = enum('A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y'); # only looking at MACROSTATE.TS # only optimizing backrub temperature and steepness ensembleSizes = numpy.array([20, 50]); backrubTemps = numpy.array([0.3, 0.6, 0.9, 1.2, 1.5, 1.8]); boltzmannTemps = numpy.array([0, -1, 1, 5.0]); steepnessRange = numpy.array([0.5, 5]); minWeights = numpy.array([0, 0, 0, 0, 0, 0]); maxWeights = numpy.array([1, 1, 0, 1, 1, 1]); print("Initializing objects\n"); data = "/netapp/home/tianjiao.zhang/data/DHFR_MSD_M20loop_repeat1.tsv"; #data = "C:\\Users\\Candy\\SkyDrive\\Documents\\rotation 2\\DHFR_MSD_M20loop\\DHFR_MSD_M20loop_repeat" + str(i + 1) + ".tsv"; #targetFreqs = "C:\\Users\\Candy\\SkyDrive\\Documents\\rotation 2\\ecDHFR_openseq_bacterial_representative_final_align_trim.fasta"; targetFreqs = "/netapp/home/tianjiao.zhang/data/ecDHFR_openseq_bacterial_representative_final_align_trim.fasta"; optimizer = Optimizer(MACROSTATES); # slightly different paths on my two computers try: optimizer.readTargetFrequencies(targetFreqs); optimizer.readData(data); except: optimizer.readTargetFrequencies(targetFreqsAlt); optimizer.readData(dataAlt); print("Files read in"); search = CuckooSearch(optimizer.models, Chi2Kernel(optimizer.targetFrequencies), False, 64, 1, 0.25); search.setMaxIterations(iterations); search.setParamBounds(ensembleSizes, backrubTemps, boltzmannTemps, steepnessRange, minWeights, maxWeights); search.setSearchParameters(False, True, True, True, numpy.array([True, True, False, True, True, True])); optimizer.useAlgorithm(search); print("\nChi2 kernel"); #search.setSimilarityMeasure(JensenShannonDistance(optimizer.targetFrequencies)); optimizer.optimize(); now = datetime.now(); optimizer.writeFrequenciesToFASTA(optimizer.getBestFrequencies(), "Chi2 test " + now.strftime('%Y%m%d%H%M%S') + ".fasta"); optimizer.writeBestParamsToText("Chi2 test " + now.strftime('%Y%m%d%H%M%S')); print(optimizer.getBestParameters()['match']); return None;
def DHFRcomparemeasures(similarity:int): MACROSTATES = enum("E-DHF-NADPH", "E-NADPH", "E-OPEN", "E-THF", "E-THF-NADPX", "TS"); RESIDUES = enum('A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y'); ensembleSizes = numpy.array([20, 50]); backrubTemps = numpy.array([0.3, 0.6, 0.9, 1.2, 1.5, 1.8]); boltzmannTemps = numpy.array([0, -1, 1, 5.0]); steepnessRange = numpy.array([0.5, 5]); minWeights = numpy.array([0, 0, 0, 0, 0, 0]); maxWeights = numpy.array([1, 1, 0, 1, 1, 1]); data = "/netapp/home/tianjiao.zhang/data/DHFR_MSD_M20loop_repeat1.tsv"; targetFreqs = "/netapp/home/tianjiao.zhang/data/ecDHFR_openseq_bacterial_representative_final_align_trim.fasta"; optimizer = Optimizer(MACROSTATES); optimizer.readTargetFrequencies(targetFreqs); optimizer.readData(data); measure = ""; if similarity == 0: search = CuckooSearch(optimizer.models, JensenShannonDistance(optimizer.targetFrequencies), False, 64, 1, 0.25); measure = " JSD"; elif similarity == 1: search = CuckooSearch(optimizer.models, CosineSimilarity(optimizer.targetFrequencies), False, 64, 1, 0.25); measure = " Cos"; elif similarity == 2: search = CuckooSearch(optimizer.models, KLDivergence(optimizer.targetFrequencies), False, 64, 1, 0.25); measure = " KLD"; elif similarity == 3: search = CuckooSearch(optimizer.models, EntropyWeightsMixedSimilarity(CosineSimilarity(), JensenShannonDistance(), optimizer.targetFrequencies), False, 64, 1, 0.25); measure = " Mix" elif similarity == 4: search = CuckooSearch(optimizer.models, EntropyWeightedSimilarity(JensenShannonDistance(), optimizer.targetFrequencies), False, 64, 1, 0.25); measure = "Weighted JSD"; else: search = CuckooSearch(optimizer.models, Chi2Kernel(optimizer.targetFrequencies), False, 64, 1, 0.25); measure = "Chi2 kernel"; search.setMaxIterations(2048); search.setParamBounds(ensembleSizes, backrubTemps, boltzmannTemps, steepnessRange, minWeights, maxWeights); search.setSearchParameters(True, True, True, True, numpy.array([True, True, False, True, True, True])); optimizer.useAlgorithm(search); optimizer.optimize(); name = "DHFR compare measures " + measure + " " + datetime.now().strftime('%Y%m%d%H%M'); optimizer.writeFrequenciesToFASTA(optimizer.getBestFrequencies(), name + ".fasta", 3); optimizer.writeBestParamsToText(name + ".txt");
def onlyMacro(): MACROSTATES = enum("E-DHF-NADPH", "E-NADPH", "E-OPEN", "E-THF", "E-THF-NADPX", "TS"); RESIDUES = enum('A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y'); i = 0; # only looking at MACROSTATE.TS # only optimizing backrub temperature and steepness ensembleSizes = numpy.array([20, 50]); backrubTemps = numpy.array([0.3, 0.6, 0.9, 1.2, 1.5, 1.8]); boltzmannTemps = numpy.array([0, -1, 1, 5.0]); steepnessRange = numpy.array([0.5, 5]); minWeights = numpy.array([0, 0, 0, 0, 0, 0]); maxWeights = numpy.array([1, 1, 0, 1, 1, 1]); data = "/netapp/home/tianjiao.zhang/data/DHFR_MSD_M20loop_repeat" + str(i + 1) + ".tsv"; #data = "C:\\Users\\Candy\\SkyDrive\\Documents\\rotation 2\\DHFR_MSD_M20loop\\DHFR_MSD_M20loop_repeat" + str(i + 1) + ".tsv"; #targetFreqs = "C:\\Users\\Candy\\SkyDrive\\Documents\\rotation 2\\ecDHFR_openseq_bacterial_representative_final_align_trim.fasta"; targetFreqs = "/netapp/home/tianjiao.zhang/data/ecDHFR_openseq_bacterial_representative_final_align_trim.fasta"; optimizer = Optimizer(MACROSTATES); optimizer.readTargetFrequencies(targetFreqs); optimizer.readData(data); search = CuckooSearch(optimizer.models, JensenShannonDistance(optimizer.targetFrequencies), False, 64, 1, 0.25); measure = " JSD"; search.setMaxIterations(2048); search.setParamBounds(ensembleSizes, backrubTemps, boltzmannTemps, steepnessRange, minWeights, maxWeights); search.setSearchParameters(True, True, True, True, numpy.array([True, True, False, True, True, True])); optimizer.useAlgorithm(search); optimizer.optimize(); name = "Macrostates " + str(i + 1) + measure + datetime.now().strftime('%Y%m%d%H%M'); optimizer.writeFrequenciesToFASTA(optimizer.getBestFrequencies(), name + ".fasta", 3); optimizer.writeBestParamsToText(name + ".txt"); return None;
ensembleSizes = numpy.array([20, 50]) backrubTemps = numpy.array([0.3, 0.6, 0.9, 1.2, 1.5, 1.8]) boltzmannTemps = numpy.array([0, -1, 1, 5.0]) steepnessRange = numpy.array([0.5, 5]) minWeights = numpy.array([0, 0, 0, 0, 0, 0]) maxWeights = numpy.array([1, 1, 0, 1, 1, 1]) data = "/netapp/home/tianjiao.zhang/data/DHFR_MSD_M20loop_repeat1.tsv" targetFreqs = "/netapp/home/tianjiao.zhang/data/ecDHFR_openseq_bacterial_representative_final_align_trim.fasta" optimizer = Optimizer(MACROSTATES) # slightly different paths on my two computers try: optimizer.readTargetFrequencies(targetFreqs) optimizer.readData(data) except: optimizer.readTargetFrequencies(targetFreqsAlt) optimizer.readData(dataAlt) search = CuckooSearch(optimizer.models, JensenShannonDistance(optimizer.targetFrequencies), False, 128, 1, 0.25) search.setMaxIterations(16) search.setParamBounds(ensembleSizes, backrubTemps, boltzmannTemps, steepnessRange, minWeights, maxWeights) search.setSearchParameters(False, True, True, True, numpy.array([True, True, False, True, True, True])) optimizer.useAlgorithm(search) optimizer.optimize() print("16 iterations | runtime {:s} | match {:.6f}".format(
def simpleRepeatTest(): print("Hello!\n"); MACROSTATES = enum("E-DHF-NADPH", "E-NADPH", "E-OPEN", "E-THF", "E-THF-NADPX", "TS"); RESIDUES = enum('A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y'); ensembleSizes = numpy.array([50]); backrubTemps = numpy.array([0.3, 0.6, 0.9, 1.2, 1.5, 1.8]); boltzmannTemps = numpy.array([0, -1, 1, 5.0]); steepnessRange = numpy.array([0.5, 5]); minWeights = numpy.array([0, 0, 0, 0, 0, 1]); maxWeights = numpy.array([0, 0, 0, 0, 0, 1]); print("Initializing objects\n"); targetFreqs = "C:\\Users\\Candy\\SkyDrive\\Documents\\rotation 2\\ecDHFR_openseq_bacterial_representative_final_align_trim.fasta"; targetFreqsAlt = "C:\\Users\\Candy_000\\SkyDrive\\Documents\\rotation 2\\ecDHFR_openseq_bacterial_representative_final_align_trim.fasta"; data = "C:\\Users\\Candy\\SkyDrive\\Documents\\rotation 2\\DHFR_MSD_M20loop\\DHFR_MSD_M20loop_repeat1.tsv"; dataAlt = "C:\\Users\\Candy_000\\SkyDrive\\Documents\\rotation 2\\DHFR_MSD_M20loop\\DHFR_MSD_M20loop_repeat1.tsv"; dataMicro = "C:\\Users\\Candy\\SkyDrive\\Documents\\rotation 2\\20160120_M20_enumeration_scores\\20160120_M20_enumeration_scores.tsv"; dataMicroAlt = "C:\\Users\\Candy_000\\SkyDrive\\Documents\\rotation 2\\20160120_M20_enumeration_scores\\20160120_M20_enumeration_scores.tsv"; optimizer = Optimizer(MACROSTATES); # slightly different paths on my two computers try: optimizer.readTargetFrequencies(targetFreqs); optimizer.readData(data); except: optimizer.readTargetFrequencies(targetFreqsAlt); optimizer.readData(dataAlt); print("Files read in"); search = CuckooSearch(optimizer.models, JensenShannonDistance(optimizer.targetFrequencies), False, 1, 1, 0.25); search.setMaxIterations(1); search.setParamBounds(ensembleSizes, backrubTemps, boltzmannTemps, steepnessRange, minWeights, maxWeights); #search.setSearchParameters(False, True, True, True, numpy.array([True, True, False, True, True, True])); search.setAllSearchToFalse(); search.suppressOutputs = True; optimizer.useAlgorithm(search); print("\nJS Dist"); for i in range(64): optimizer.optimize(); params = optimizer.getBestParameters(); m = search.population[0]; #print(search.similarityMeasure.getSimilarityMeasure(m.getFrequencies())); # TODO: getModelByParams doesn't always return the same object. m1 = Model.constructFromExisting(optimizer.getModelByParams(m.backrubTemp, m.ensembleSize, m.boltzmannTemp), m.ensembleSize, m.backrubTemp, m.boltzmannTemp, m.getWeights(), m.steepness); #print(search.similarityMeasure.getSimilarityMeasure(m1.getFrequencies())); if not m.equalTo(m1): print("\t{:s}".format(Optimizer.calcParamsID(m.backrubTemp, m.ensembleSize, m.boltzmannTemp))); print("\t{:s}".format(Optimizer.calcParamsID(m1.backrubTemp, m1.ensembleSize, m1.boltzmannTemp))); #m2 = Model.constructFromExisting(m, m.ensembleSize, m.backrubTemp, m.boltzmannTemp, m.getWeights(), m.steepness); #print(search.similarityMeasure.getSimilarityMeasure(m2.getFrequencies())); #print(m.equalTo(m2)); #print(m2.backrubTemp); #print(m2.boltzmannTemp); #print(m2.ensembleSize); #print(m2.steepness); #print(m2.weights); #print(search.similarityMeasure.getSimilarityMeasure(m2.getFrequencies())); #print(numpy.sum(numpy.sum(numpy.abs( m.getFrequencies() - m2.getFrequencies())))); return None;
def repeatTest(): print("Hello!\n"); MACROSTATES = enum("E-DHF-NADPH", "E-NADPH", "E-OPEN", "E-THF", "E-THF-NADPX", "TS"); RESIDUES = enum('A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y'); ensembleSizes = numpy.array([50]); backrubTemps = numpy.array([0.3, 0.6, 0.9, 1.2, 1.5, 1.8]); boltzmannTemps = numpy.array([0, -1, 1, 5.0]); steepnessRange = numpy.array([0.5, 5]); minWeights = numpy.array([0, 0, 0, 0, 0, 0]); maxWeights = numpy.array([1, 1, 0, 1, 1, 1]); print("Initializing objects\n"); targetFreqs = "C:\\Users\\Candy\\SkyDrive\\Documents\\rotation 2\\ecDHFR_openseq_bacterial_representative_final_align_trim.fasta"; targetFreqsAlt = "C:\\Users\\Candy_000\\SkyDrive\\Documents\\rotation 2\\ecDHFR_openseq_bacterial_representative_final_align_trim.fasta"; data = "C:\\Users\\Candy\\SkyDrive\\Documents\\rotation 2\\DHFR_MSD_M20loop\\DHFR_MSD_M20loop_repeat1.tsv"; dataAlt = "C:\\Users\\Candy_000\\SkyDrive\\Documents\\rotation 2\\DHFR_MSD_M20loop\\DHFR_MSD_M20loop_repeat1.tsv"; dataMicro = "C:\\Users\\Candy\\SkyDrive\\Documents\\rotation 2\\20160120_M20_enumeration_scores\\20160120_M20_enumeration_scores.tsv"; dataMicroAlt = "C:\\Users\\Candy_000\\SkyDrive\\Documents\\rotation 2\\20160120_M20_enumeration_scores\\20160120_M20_enumeration_scores.tsv"; optimizer = Optimizer(MACROSTATES); # slightly different paths on my two computers try: optimizer.readTargetFrequencies(targetFreqs); optimizer.readData(data); except: optimizer.readTargetFrequencies(targetFreqsAlt); optimizer.readData(dataAlt); print("Files read in"); for i in range(32): search = CuckooSearch(optimizer.models, JensenShannonDistance(optimizer.targetFrequencies), False, 8, 1, 0.25); search.setMaxIterations(16); search.suppressOutputs = True; search.setParamBounds(ensembleSizes, backrubTemps, boltzmannTemps, steepnessRange, minWeights, maxWeights); search.setSearchParameters(False, True, True, True, numpy.array([True, True, False, True, True, True])); optimizer.useAlgorithm(search); print("\nJS Dist"); #search.setSimilarityMeasure(JensenShannonDistance(optimizer.targetFrequencies)); optimizer.optimize(); params = optimizer.getBestParameters(); print(params['match']); print(optimizer.verifyFoundParams(params['ensembleSize'], params['backrubTemp'], params['boltzmannTemp'], params['steepness'], params['weights'])); search = CuckooSearch(optimizer.models, CosineSimilarity(optimizer.targetFrequencies), False, 8, 1, 0.25); search.setMaxIterations(16); search.suppressOutputs = True; search.setParamBounds(ensembleSizes, backrubTemps, boltzmannTemps, steepnessRange, minWeights, maxWeights); search.setSearchParameters(False, True, True, True, numpy.array([True, True, False, True, True, True])); optimizer.useAlgorithm(search); print("\nCosine") optimizer.optimize(); params = optimizer.getBestParameters(); print(params['match']); print(optimizer.verifyFoundParams(params['ensembleSize'], params['backrubTemp'], params['boltzmannTemp'], params['steepness'], params['weights'])); return None;