def makeAminoAcidHistogram(
plotter, backValues, sideValues, caValues, cbValues, outNameAmino,
interval=0.5):
'''makes one histogram for one amino acid for the backbone/sidechain values'''
outTextFileName = outNameAmino + ".res.txt"
maxBoth = max(backValues+sideValues+caValues+cbValues)
#print outNameAmino,
#print len(backValues), len(sideValues), len(caValues), len(cbValues), maxBoth
histoBack, maxBothRet = statistics.computeHistogram(
backValues, interval, maxBoth)
histoSide, maxBothRet = statistics.computeHistogram(
sideValues, interval, maxBoth)
histoCa, maxBothRet = statistics.computeHistogram(
caValues, interval, maxBoth)
histoCb, maxBothRet = statistics.computeHistogram(cbValues, interval, maxBoth)
xVals = []
for cutoff in range(2+int(maxBoth/interval)):
xVals.append(cutoff*interval)
graphDataBack = Gnuplot.Data(xVals, histoBack, title="Backbone")
graphDataSide = Gnuplot.Data(xVals, histoSide, title="Sidechain")
graphDataCa = Gnuplot.Data(xVals, histoCa, title="C-alpha")
graphDataCb = Gnuplot.Data(xVals, histoCb, title="C-beta")
if outTextFileName:
outTextFile = open(outTextFileName, 'w')
outTextFile.write("xVal\tback\tside\tca\tcb\tbackN\tsideN\tcaN\tcbN\n")
for index in range(max(len(xVals), len(histoBack))):
outTextFile.write(str(xVals[index]) + "\t")
outTextFile.write(str(histoBack[index]) + "\t")
outTextFile.write(str(histoSide[index]) + "\t")
outTextFile.write(str(histoCa[index]) + "\t")
outTextFile.write(str(histoCb[index]) + "\t")
if sum(histoBack) > 0.:
outTextFile.write(str(float(histoBack[index])/sum(histoBack)) + "\t")
else:
outTextFile.write("0.\t")
if sum(histoSide) > 0.:
outTextFile.write(str(float(histoSide[index])/sum(histoSide)) + "\t")
else:
outTextFile.write("0.\t")
if sum(histoCa) > 0.:
outTextFile.write(str(float(histoCa[index])/sum(histoCa)) + "\t")
else:
outTextFile.write("0.\t")
if sum(histoCb) > 0.:
outTextFile.write(str(float(histoCb[index])/sum(histoCb)) + "\n")
else:
outTextFile.write("0.\n")
outTextFile.close()
plotter('set terminal png')
plotter('set output "' + outNameAmino + '.png"')
#plotter('set data style boxes')
plotter('set data style linespoints')
plotter('set key right top')
plotter('set xrange [' + str(min(xVals)-1) + ':' + str(max(xVals)+1) + ']')
plotter(
'set yrange [' + str(0.) + ':' + str(1.05*max(histoBack+histoSide)) + ']')
plotter.xlabel('Travel In Distance')
plotter.ylabel('Atom Count')
plotter.plot(graphDataBack, graphDataSide, graphDataCa, graphDataCb)
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 processData(dataList, nameList, listPaths, outputFileName="processed.foundholes."):
# first do the one big summary output file
bestLists = []
compCols = [8, 9, 10, 11, 12, 13, 14]
comps = ["min", "max", "max", "min", "max", "max", "min"]
compThreshs = [5.0, 0.4, 0.8, 2.5, 0.5, 0.8, 2.5]
for index, colIdx in enumerate(compCols):
bestList = []
for data in dataList:
if comps[index] == "min":
bestVal, bestIndex = getMinColumn(data, colIdx) # index 8 is the prmsd
else:
bestVal, bestIndex = getMaxColumn(data, colIdx) # index 8 is the prmsd
bestList.append(bestVal)
bestLists.append(bestList)
# fileOut = open(outputFileName + colNamesBonus[colIdx-4] + ".best.log", 'w')
# for index, name in enumerate(nameList):
# fileOut.write(name + " " + str(bestList[index]) + "\n")
# fileOut.close()
fileOut = open(outputFileName + "overall.best.log", "w")
fileOut.write("name pRMSD coverage span wRMSD less1 lessRad radiicomp\n")
for index, name in enumerate(nameList):
fileOut.write(name + " ")
for index2 in range(len(compCols)):
fileOut.write(str(bestLists[index2][index]) + " ")
fileOut.write("\n")
fileOut.close()
for colIdx, sortColNumber in enumerate(compCols):
bestRankStrings, sortedEvals, backwardsEvals = [], [], []
for index, data in enumerate(dataList):
bestRankString, sortedEval, backEval = processDataOne(data, nameList[index], sortColNumber, comps[colIdx])
bestRankStrings.append(bestRankString)
sortedEvals.append(sortedEval)
backwardsEvals.append(backEval)
fileOut = open(outputFileName + colNamesBonus[sortColNumber - 4] + ".best.rankings.log", "w")
for bestRankStr in bestRankStrings:
fileOut.write(bestRankStr + "\n")
fileOut.close()
for index, colName in enumerate(colNames):
fileOut = open(
outputFileName + "rankings." + colName + "." + colNamesBonus[sortColNumber - 4] + ".log", "w"
)
for line in sortedEvals:
fileOut.write(line[index] + "\n")
fileOut.close()
fileOut = open(
outputFileName + "rankings.reverse." + colName + "." + colNamesBonus[sortColNumber - 4] + ".log", "w"
)
for line in backwardsEvals:
fileOut.write(line[index] + "\n")
fileOut.close()
drilledData = [False, False, False, False, [], [], [], [], [], [], [], [], [], []]
for drilledPath in listPaths:
drilledData[4].append(float(len(drilledPath)))
drilledData[5].append(float(paths.pathLength(drilledPath)))
drilledData[6].append(float(paths.pathMinRadius(drilledPath)))
drilledData[7].append(float(paths.pathMaxInsideRadius(drilledPath)))
for column in range(4, 14):
columnName = colNamesBonus[column - 4]
for colIdx, sortColNumber in enumerate(compCols):
# print columnName, colNamesBonus[sortColNumber - 4]
columnData = []
selectColumnData = []
bestColumnData = []
for data in dataList:
if comps[colIdx] == "min":
bestVal, bestIndex = getMinColumn(data, sortColNumber)
selectColumnData.extend(getFromColumnIfMin(data, column, sortColNumber, compThreshs[colIdx]))
bestColumnData.extend(getFromColumnIfMin(data, column, sortColNumber, bestVal))
else:
bestVal, bestIndex = getMaxColumn(data, sortColNumber)
selectColumnData.extend(getFromColumnIfMax(data, column, sortColNumber, compThreshs[colIdx]))
bestColumnData.extend(getFromColumnIfMax(data, column, sortColNumber, bestVal))
columnData.extend(getOneColumn(data, column))
if len(drilledData[column]) > 0:
maxHere = max(max(columnData), max(drilledData[column])) + 1.0
else:
maxHere = max(columnData) + 1.0
interval = maxHere / 40.0
histogram = statistics.computeHistogram(columnData, interval, maxData=maxHere)
# selectHistogram = statistics.computeHistogram(
# selectColumnData, interval, maxData=histogram[1])
bestHistogram = statistics.computeHistogram(bestColumnData, interval, maxData=histogram[1])
if len(drilledData[column]) > 0:
realHistogram = statistics.computeHistogram(drilledData[column], interval, maxData=histogram[1])
else:
realHistogram = False
# need to scale select part of data to be same height as histogram
maxHeight = max(histogram[0])
# maxSelectHeight = max(selectHistogram[0])
maxBestHeight = max(bestHistogram[0])
if realHistogram:
maxRealHeight = max(realHistogram[0])
realScaledHistogram = [[], realHistogram[1]]
for histPoint in realHistogram[0]:
realScaledHistogram[0].append(histPoint * maxHeight / maxRealHeight)
# selectScaledHistogram = [[], selectHistogram[1]]
bestScaledHistogram = [[], bestHistogram[1]]
# for histPoint in selectHistogram[0]:
# selectScaledHistogram[0].append(histPoint*maxHeight/maxSelectHeight)
for histPoint in bestHistogram[0]:
bestScaledHistogram[0].append(histPoint * maxHeight / maxBestHeight)
# print histogram, len(histogram[0])
# print selectHistogram, len(selectHistogram[0])
# make gnuplot version if possible
if gnuplotAvailable:
# plotter = Gnuplot.Gnuplot(debug=0)
xVals = []
for cutoff in range(2 + int(histogram[1] / interval)):
xVals.append(cutoff * interval)
graphData = Gnuplot.Data(xVals, histogram[0], title="All")
# if comps[colIdx] == 'min':
# graphSelectData = Gnuplot.Data(
# xVals, selectScaledHistogram[0],
# title="<" + str(compThreshs[colIdx]) + " " +
# str(colNamesBonus[sortColNumber-4]) + " Scaled by " +
# str(maxHeight/maxSelectHeight))
# else:
# graphSelectData = Gnuplot.Data(
# xVals, selectScaledHistogram[0], title=">" +
# str(compThreshs[colIdx]) + " " +
# str(colNamesBonus[sortColNumber-4]) + " Scaled by " +
# str(maxHeight/maxSelectHeight))
graphBestData = Gnuplot.Data(
xVals,
bestScaledHistogram[0],
title="Best "
+ str(colNamesBonus[sortColNumber - 4])
+ " Scaled by "
+ str(maxHeight / maxBestHeight),
)
if realHistogram:
graphRealData = Gnuplot.Data(
xVals, realScaledHistogram[0], title="Drilled Holes Scaled by " + str(maxHeight / maxRealHeight)
)
graphDataCum = Gnuplot.Data(xVals, statistics.computeCumulativeHistogram(histogram[0]))
plotter("set terminal png")
plotter('set output "' + outputFileName + columnName + "." + colNamesBonus[sortColNumber - 4] + '.png"')
plotter("set data style linespoints")
plotter("set xrange [" + str(min(xVals) - 0.01) + ":" + str(max(xVals) + 0.01) + "]")
plotter.xlabel(columnName)
plotter.ylabel("Count")
plotter("set multiplot")
plotter("set key right top")
if realHistogram:
# plotter.plot(
# graphData, graphSelectData, graphBestData, graphRealData)
plotter.plot(graphData, graphBestData, graphRealData)
else:
# plotter.plot(graphData, graphSelectData, graphBestData)
plotter.plot(graphData, graphBestData)
plotter("unset multiplot")
def makeHistogramReport(
residueData, outputFilename="histogram.bfactor", interval=0.1,
yMaxHisto=0.16):
fileTemp = open(outputFilename + ".txt", 'w')
fileTemp.write("LowEndInterval Count\n")
totalList = []
betaList = []
for oneResName, oneResData in residueData.iteritems():
#assemble into one big list
if oneResName in aminoAcid3Codes:
for data in oneResData.values():
totalList.extend(data)
betaList.extend(oneResData[carbonBetaCodes[oneResName]])
resList = {}
betaResList = {}
for oneResKey in aminoAcid3Codes:
resList[oneResKey] = []
betaResList[oneResKey] = []
if oneResKey in residueData:
for data in residueData[oneResKey].values():
resList[oneResKey].extend(data)
betaResList[oneResKey].extend(
residueData[oneResKey][carbonBetaCodes[oneResKey]])
#now do histogram stuff
histogram, maxData = statistics.computeNormalizedHistogram(
totalList, interval, 8.)
betaHistogram, betaMax = statistics.computeNormalizedHistogram(
betaList, interval, 8.)
for index, data in enumerate(histogram):
fileTemp.write(str(index*interval) + " " + str(data) + "\n")
fileTemp.close()
#make gnuplot version if possible
if gnuplotAvailable:
plotter = Gnuplot.Gnuplot(debug=0)
xVals = []
for cutoff in range(2+int(maxData/interval)):
xVals.append(cutoff*interval)
graphData = Gnuplot.Data(xVals, histogram)
graphDataCum = Gnuplot.Data(
xVals, statistics.computeCumulativeHistogram(histogram))
graphDataBeta = Gnuplot.Data(xVals, betaHistogram)
graphDataBetaCum = Gnuplot.Data(
xVals, statistics.computeCumulativeHistogram(betaHistogram))
plotter('set terminal png')
plotter('set output "' + outputFilename + '.png"')
plotter('set data style linespoints')
plotter('set xrange [' + str(min(xVals)-1) + ':' + str(max(xVals)+1) + ']')
plotter('set yrange [' + str(0.) + ':' + str(yMaxHisto) + ']')
plotter.xlabel('Travel In Distance')
plotter.ylabel('Atom Count')
plotter.plot(graphData)
plotter('set output "' + outputFilename + '.beta.png"')
plotter.ylabel('Carbon Beta Atom Count')
plotter.plot(graphDataBeta)
plotter('set output "' + outputFilename + '.cumulative.png"')
plotter('set yrange []') # automatic
plotter.ylabel('Cumulative Atom Count')
plotter.plot(graphDataCum)
plotter.ylabel('Cumulative Beta Atom Count')
plotter('set output "' + outputFilename + '.cumulative.beta.png"')
plotter.plot(graphDataBetaCum)
plotter.ylabel('Atom Count')
#now do one for each residue
plotter('set key right top')
plotter('set data style lines')
ylabels = ('Atom Count', 'Carbon Beta Atom Count')
outputNames = (outputFilename, outputFilename + '.beta')
histogramData = (resList, betaResList)
for index in range(len(histogramData)):
thisResList = histogramData[index]
outputName = outputNames[index]
ylabel = ylabels[index]
plotter.ylabel(ylabel)
histograms = {}
maxOverRes = 0.
for resName in aminoAcid3Codes:
histogramRes, maxData = statistics.computeHistogram(
thisResList[resName], interval, maxData)
histograms[resName] = histogramRes
maxOverRes = max(maxOverRes, max(histogramRes))
plotter('set yrange [0:' + str(maxOverRes+1000) + ']')
resGraphDatas = [], []
lowGraphDatas = [], []
highGraphDatas = [], []
for resName in aminoAcid3Codes:
plotter('set output "' + outputName + "." + resName + '.png"')
plotter('set yrange [0:' + str(maxOverRes + 1000) + ']')
histogramRes = histograms[resName]
resGraphDatas[0].append(
Gnuplot.Data(xVals, histogramRes, title=resName))
plotter.plot(resGraphDatas[0][-1])
plotter(
'set output "' + outputName + "." + resName + '.cumulative.png"')
plotter('set yrange [0:1]')
cumData = Gnuplot.Data(
xVals, statistics.computeCumulativeHistogram(histogramRes),
title=resName)
plotter.plot(cumData)
resGraphDatas[1].append(cumData)
if resName in highCodes:
highGraphDatas[0].append(resGraphDatas[0][-1])
highGraphDatas[1].append(cumData)
elif resName in lowCodes:
lowGraphDatas[0].append(resGraphDatas[0][-1])
lowGraphDatas[1].append(cumData)
#very stupid hack... plot() is dumb
outNames = (
'set output "' + outputName + ".residues" + '.png"',
'set output "' + outputName + ".residues" + '.cumulative.png"')
lowNames = (
'set output "' + outputName + ".residues.low" + '.png"',
'set output "' + outputName + ".residues.low" + '.cumulative.png"')
highNames = (
'set output "' + outputName + ".residues.high" + '.png"',
'set output "' + outputName + ".residues.high" + '.cumulative.png"')
ranges = (
'set yrange [0:' + str(maxOverRes+1000) + ']', 'set yrange [0:1]')
for count, resGraphData in enumerate(resGraphDatas):
plotter(outNames[count])
plotter('set key right bottom')
plotter(ranges[count])
plotter.plot(
resGraphData[0], resGraphData[1], resGraphData[2],
resGraphData[3], resGraphData[4], resGraphData[5],
resGraphData[6], resGraphData[7], resGraphData[8],
resGraphData[9], resGraphData[10], resGraphData[11],
resGraphData[12], resGraphData[13], resGraphData[14],
resGraphData[15], resGraphData[16], resGraphData[17],
resGraphData[18], resGraphData[19])
lowGraphData = lowGraphDatas[count]
plotter(lowNames[count])
plotter.plot(
lowGraphData[0], lowGraphData[1], lowGraphData[2],
lowGraphData[3], lowGraphData[4], lowGraphData[5],
lowGraphData[6], lowGraphData[7], lowGraphData[8],
lowGraphData[9], lowGraphData[10])
highGraphData = highGraphDatas[count]
plotter(highNames[count])
plotter.plot(
highGraphData[0], highGraphData[1], highGraphData[2],
highGraphData[3], highGraphData[4], highGraphData[5],
highGraphData[6], highGraphData[7], highGraphData[8])
#limits on x dim
outNames2 = (
'set output "' + outputName + ".residues16" + '.png"',
'set output "' + outputName + ".residues" + '.cumulative16.png"')
for count, resGraphData in enumerate(resGraphDatas):
plotter(outNames2[count])
plotter('set key right bottom')
plotter('set xrange [1:6]')
plotter(ranges[count])
plotter.plot(
resGraphData[0], resGraphData[1], resGraphData[2],
resGraphData[3], resGraphData[4], resGraphData[5],
resGraphData[6], resGraphData[7], resGraphData[8],
resGraphData[9], resGraphData[10], resGraphData[11],
resGraphData[12], resGraphData[13], resGraphData[14],
resGraphData[15], resGraphData[16], resGraphData[17],
resGraphData[18], resGraphData[19])
