def summarizeOneFeature(tmDataList, columnName, intervals=50, outName="a.txt"):
'''takes that column, makes a histogram for each structure'''
outFile = open(outName, 'w')
columnNum = tmDataList[0].titleToColumn(columnName)
treeData = {}
overallMax = 0.
for tm3tree in tmDataList:
data = tm3tree.getListColumn(columnNum)
overallMax = max(overallMax, max(data))
treeData[tm3tree] = data
if intervals == "max":
intervals = overallMax # 1 per
interval = overallMax/intervals # number of intervals desired
#print a header
outFile.write("name\tcount\tmean\tstddev\t")
currentOut = 0.
while currentOut < overallMax:
outFile.write(str(currentOut) + "\t")
currentOut += interval
outFile.write("\n")
for tm3tree in tmDataList:
tm3data = treeData[tm3tree]
avgData = statistics.computeMean(tm3data)
stddevData = statistics.computeStdDev(tm3data, avgData)
histo, outMax = statistics.computeHistogram(tm3data, interval, overallMax)
outFile.write(tm3tree.inputFileName + "\t")
outFile.write(str(len(tm3data)) + "\t")
outFile.write(str(avgData) + "\t")
outFile.write(str(stddevData) + "\t")
for histoCount in histo:
outFile.write(str(histoCount) + "\t")
outFile.write("\n")
outFile.close()
def calcColumnsMeanStddev(columnList, tmDataList):
"""returns a dict of column number to mean and another dict to stddev."""
columnsToMean = {}
columnsToStddev = {}
for column in columnList:
colData = []
for tmData in tmDataList:
colData.extend(tmData.getListColumn(column))
colAvg = statistics.computeMean(colData)
colStddev = statistics.computeStdDev(colData, colAvg)
columnsToMean[column] = colAvg
columnsToStddev[column] = colStddev
return columnsToMean, columnsToStddev
def makeResidueReport(
residueData, outputFilename="residue.bfactor",
maxY=False, maxYBeta=False, runGraphs=False):
#residueNames = residueData.keys()
residueNames = aminoAcid3Codes
residueNames.sort()
fileTemp = open(outputFilename + ".txt", 'w')
fileTemp.write("ResidueName Mean StdDev Low High Count\n")
averages, stddevs = {}, {}
betaAverages, betaStddevs = {}, {}
for residueName in residueNames:
#assemble into one big list
totalList = []
if residueName in residueData:
for data in residueData[residueName].values():
totalList.extend(data)
average = statistics.computeMean(totalList)
averages[residueName] = average
stddev = statistics.computeStdDev(totalList, average)
stddevs[residueName] = stddev
betaList = []
if residueName in residueData:
data = residueData[residueName]
betaList.extend(data[carbonBetaCodes[residueName]])
else:
data = []
if len(betaList) > 0:
betaAvg = statistics.computeMean(betaList)
betaAverages[residueName] = betaAvg
betaStddevs[residueName] = statistics.computeStdDev(betaList, betaAvg)
if len(totalList) > 0:
fileTemp.write(
residueName + " " + str(average) + " " + str(stddev) + " " +
str(min(totalList)) + " " + str(max(totalList)) + " " +
str(len(totalList)) + "\n")
else:
fileTemp.write(
residueName + " " + str(average) + " " + str(stddev) + " " +
str(0.) + " " + str(0.) + " " + str(0.) + "\n")
fileTemp.close()
if gnuplotAvailable and runGraphs:
plotter = Gnuplot.Gnuplot(debug=0)
yLabels = '('
yData, yError, yMin, yMax = [], [], 10, 0
yBetaData, yBetaError, yBetaMin, yBetaMax = [], [], 10, 0
for index, code in enumerate(aminoAcid3Codes):
yLabels += '"' + str(code) + '" ' + str(index)
if index != len(aminoAcid3Codes) - 1:
yLabels += ', '
if code in averages:
yData.append(averages[code])
yError.append(stddevs[code])
yMin = min(yMin, yData[-1]-yError[-1])
yMax = max(yMax, yData[-1]+yError[-1])
yBetaData.append(betaAverages[code])
yBetaError.append(betaStddevs[code])
yBetaMin = min(yBetaMin, yBetaData[-1]-yBetaError[-1])
yBetaMax = max(yBetaMax, yBetaData[-1]+yBetaError[-1])
else: # none of that residue
yData.append(0)
yError.append(0)
yBetaData.append(0)
yBetaError.append(0)
yLabels += ')'
graphData = Gnuplot.Data(range(20), yData, yError)
plotter('set terminal png')
plotter('set output "' + outputFilename + '.png"')
plotter('set data style yerrorbars')
plotter('set boxwidth 0.9 absolute')
plotter('set xtics ' + yLabels)
if maxY is False:
plotter('set yrange [' + str(yMin-0.2) + ':' + str(yMax+0.2) + ']')
else:
plotter('set yrange [0:' + str(maxY) + ']')
plotter('set xrange [-1:20]')
plotter.xlabel('Residue')
plotter.ylabel('Mean Travel In Distance')
plotter.plot(graphData)
#do another graph with just carbon-betas
plotter('set output "' + outputFilename + '.beta.png"')
graphDataBeta = Gnuplot.Data(range(20), yBetaData, yBetaError)
plotter.ylabel('Mean Travel In Distance of Carbon Beta')
if maxYBeta is False:
plotter(
'set yrange [' + str(yBetaMin-0.2) + ':' + str(yBetaMax+0.2) + ']')
else:
plotter('set yrange [0:' + str(maxYBeta) + ']')
plotter.plot(graphDataBeta)
def makeAtomReport(residueData, outputFilename="atom.bfactor", runGraphs=True):
residueNames = residueData.keys()
residueNames.sort()
fileTemp = open(outputFilename + '.txt', 'w')
fileTemp.write("ResidueName AtomName Mean StdDev Low High Count\n")
resAtomAverage = {}
for residueName in residueNames:
resAtomAverage[residueName] = {}
atomNames = residueData[residueName].keys()
atomNames.sort()
for atomName in atomNames:
totalList = residueData[residueName][atomName]
average = statistics.computeMean(totalList)
resAtomAverage[residueName][atomName] = average
stddev = statistics.computeStdDev(totalList, average)
fileTemp.write(
residueName + " " + atomName + " " + str(average) + " " +
str(stddev) + " " + str(min(totalList)) + " " +
str(max(totalList)) + " " + str(len(totalList)) + "\n")
fileTemp.close()
if gnuplotAvailable and runGraphs:
#first make backbone-sidechain report
plotter = Gnuplot.Gnuplot(debug=0)
yLabels = '('
yDataBackbone, yDataSidechain = [], []
yDataCa, yDataCb = [], []
for index, code in enumerate(aminoAcid3Codes):
yLabels += '"' + str(code) + '" ' + str(index)
if index != len(aminoAcid3Codes) - 1:
yLabels += ', '
backValues, sideValues = [], []
caValues, cbValues = [], []
try:
for key, values in residueData[code].iteritems():
if string.strip(key) in backboneAtomCodes:
backValues.extend(values)
else:
sideValues.extend(values)
if string.strip(key) == caCode:
caValues.extend(values)
elif string.strip(key) == cbCode:
cbValues.extend(values)
except KeyError: # sometimes one residue won't be represented
pass # but that is okay
if len(backValues) == 0:
yDataBackbone.append(0)
else:
yDataBackbone.append(sum(backValues)/float(len(backValues)))
if len(sideValues) == 0:
yDataSidechain.append(0)
else:
yDataSidechain.append(sum(sideValues)/float(len(sideValues)))
if len(caValues) == 0:
yDataCa.append(0)
else:
yDataCa.append(sum(caValues)/float(len(caValues)))
if len(cbValues) == 0:
yDataCb.append(0)
else:
yDataCb.append(sum(cbValues)/float(len(cbValues)))
if len(backValues + sideValues + caValues + cbValues) > 0:
makeAminoAcidHistogram(
plotter, backValues, sideValues, caValues, cbValues,
outputFilename + "." + str(code))
yLabels += ')'
graphDataBackbone = Gnuplot.Data(range(20), yDataBackbone, title="Backbone")
graphDataSidechain = Gnuplot.Data(
range(20), yDataSidechain, title="Sidechain")
graphDataCa = Gnuplot.Data(range(20), yDataCa, title="C-alpha")
graphDataCb = Gnuplot.Data(range(20), yDataCb, title="C-beta")
plotter('set terminal png')
plotter('set output "' + outputFilename + '.png"')
plotter('set data style points')
plotter('set key right top')
plotter('set xtics ' + yLabels)
plotter(
'set yrange [' + str(min(yDataBackbone + yDataSidechain) - 0.5) +
':' + str(max(yDataBackbone+yDataSidechain)+0.5) + ']')
plotter('set xrange [-1:20]')
plotter.xlabel('Residue')
plotter.ylabel('Mean Travel In Distance')
plotter.plot(graphDataBackbone, graphDataSidechain)
plotter('set output "' + outputFilename + '.ab.png"')
if "buried" in outputFilename:
plotter('set yrange [' + str(min(yDataCa + yDataCb) - 0.5) + ':6.]')
else:
plotter(
'set yrange [' + str(min(yDataCa + yDataCb) - 0.5) + ':' +
str(max(yDataCa + yDataCb) + 0.5) + ']')
plotter.plot(graphDataCa, graphDataCb)
def makeCompareResidueReport(
residueBoth, outputFilename="residue.bfactor", maxY=False, maxYBeta=False,
numTests=9):
ranges = [-0.3, 0.6]
residueNames = []
for residueName in residueBoth[0].keys() + residueBoth[1].keys():
if residueName not in residueNames:
residueNames.append(residueName)
residueNames.sort()
#residueNames = aminoAcid3Codes #for now ignore what is in the files
fileTemp = open(outputFilename + ".txt", 'w')
fileTemp.write("ResidueName AtomName Mean StdDev Low High Count\n")
fileTemp2 = open(outputFilename + ".pvals.txt", 'w')
fileTemp2.write("ResidueName DiffMeans MeanA MeanB pValAbove pValBelow\n")
fileTemp3 = open(outputFilename + ".pvals.beta.txt", 'w')
fileTemp3.write("ResidueName DiffMeans MeanA MeanB pValAbove pValBelow\n")
averages, stddevs = ({}, {}), ({}, {})
betaAverages, betaStddevs = ({}, {}), ({}, {})
totalLists, betaLists = ({}, {}), ({}, {})
for residueName in residueNames:
totalList = [], []
betaList = [], []
for indexSet, residueData in enumerate(residueBoth):
try:
for data in residueData[residueName].values():
totalList[indexSet].extend(data)
totalLists[indexSet][residueName] = totalList[indexSet]
average = statistics.computeMean(totalList[indexSet])
averages[indexSet][residueName] = average
#print average, residueName
stddev = statistics.computeStdDev(totalList[indexSet], average)
stddevs[indexSet][residueName] = stddev
data = residueData[residueName]
betaList[indexSet].extend(data[carbonBetaCodes[residueName]])
betaLists[indexSet][residueName] = betaList[indexSet]
if len(betaList[indexSet]) > 0:
betaAvg = statistics.computeMean(betaList[indexSet])
#print betaAvg, residueName
betaAverages[indexSet][residueName] = betaAvg
betaStddevs[indexSet][residueName] = statistics.computeStdDev(
betaList[indexSet], betaAvg)
fileTemp.write(
residueName + " " + str(average) + " " + str(stddev) + " " +
str(min(totalList)) + " " + str(max(totalList)) + " " +
str(len(totalList)) + "\n")
except (ZeroDivisionError, KeyError):
pass # probably don't really need this residue anyway
fileTemp.close()
for index, code in enumerate(aminoAcid3Codes): # now do the pvalue tests
meanA = averages[0][code]
meanB = averages[1][code]
listA = totalLists[0][code]
listB = totalLists[1][code]
pvals = statistics.pvalueDiffMeans(listA, listB, meanA-meanB, numTests)
#fileTemp2.write("ResidueName DiffMeans MeanA MeanB pValAbove pValBelow\n")
fileTemp2.write(code + " " + str(meanA-meanB) + " " + str(meanA) + " ")
fileTemp2.write(str(meanB) + " " + str(pvals[0]) + " " + str(pvals[1]))
fileTemp2.write("\n")
meanA = betaAverages[0][code]
meanB = betaAverages[1][code]
listA = betaLists[0][code]
listB = betaLists[1][code]
pvals = statistics.pvalueDiffMeans(listA, listB, meanA-meanB, numTests)
fileTemp3.write(code + " " + str(meanA-meanB) + " " + str(meanA) + " ")
fileTemp3.write(str(meanB) + " " + str(pvals[0]) + " " + str(pvals[1]))
fileTemp3.write("\n")
fileTemp2.close()
fileTemp3.close()
if gnuplotAvailable:
plotter = Gnuplot.Gnuplot(debug=0)
yLabels = '('
yData, yError, yMin, yMax = [], [], 10, 0
yBetaData, yBetaError, yBetaMin, yBetaMax = [], [], 10, 0
for index, code in enumerate(aminoAcid3Codes):
yLabels += '"' + str(code) + '" ' + str(index)
if index != len(aminoAcid3Codes) - 1:
yLabels += ', '
yData.append(averages[0][code] - averages[1][code])
#yError.append(stddevs[0][code])
#yMin = min(yMin, yData[-1] - yError[-1])
#yMax = max(yMax, yData[-1] + yError[-1])
yMin = min(yMin, yData[-1])
yMax = max(yMax, yData[-1])
#print betaAverages[0][code]
#print betaAverages[1][code]
betaAvgDiff = 0.
try:
betaAvg0 = betaAverages[0][code]
betaAvg1 = betaAverages[1][code]
betaAvgDiff = betaAvg0 - betaAvg1
except KeyError:
print code
betaAvgDiff = 0.
yBetaData.append(betaAvgDiff)
#yBetaError.append(betaStddevs[0][code])
yBetaMin = min(yBetaMin, yBetaData[-1])
yBetaMax = max(yBetaMax, yBetaData[-1])
yLabels += ')'
graphData = Gnuplot.Data(range(20), yData)
plotter('set terminal png')
plotter('set output "' + outputFilename + '.png"')
plotter('set data style points')
plotter('set boxwidth 0.9 absolute')
plotter('set xtics ' + yLabels)
if ranges:
plotter('set yrange [' + str(ranges[0]) + ':' + str(ranges[1]) + ']')
elif maxY is False:
plotter('set yrange [' + str(yMin-0.2) + ':' + str(yMax+0.2) + ']')
else:
plotter('set yrange [0:' + str(maxY) + ']')
plotter('set xrange [-1:20]')
plotter.xlabel('Residue')
plotter.ylabel('Mean Travel In Distance')
plotter.plot(graphData)
#do another graph with just carbon-betas
plotter('set output "' + outputFilename + '.beta.png"')
graphDataBeta = Gnuplot.Data(range(20), yBetaData)
plotter.ylabel('Mean Travel In Distance of Carbon Beta')
if ranges:
plotter('set yrange [' + str(ranges[0]) + ':' + str(ranges[1]) + ']')
elif maxYBeta is False:
plotter(
'set yrange [' + str(yBetaMin-0.2) + ':' + str(yBetaMax+0.2) + ']')
else:
plotter('set yrange [0:' + str(maxYBeta) + ']')
plotter.plot(graphDataBeta)