def topGenes(self,sumDict, fileName,number=20,value=4):
if number > len(sumDict):
if len(sumDict)<1:
Helper.warning("no edited genes found", self.logFile, self.textField)
return
Helper.warning("The number of top genes you wanted is bigger than the number of edited genes", self.logFile, self.textField)
number=len(sumDict)
if value > 4:
Helper.error("sumDict only hold four values", self.logFile, self.textField)
counts=collections.OrderedDict(sorted(sumDict.items(), key=lambda t: t[1][value],reverse=True)[:number])
barNameTuple=()
valueMatrix=[[]]
for array in counts.values():
valueMatrix[0].append(array[value])
for gene in counts.keys():
barNameTuple+=(gene.names[0],)
if value==0:
barName="3'-UTR"
elif value==1:
barName="5'-UTR"
elif value==2:
barName="Exonic"
elif value==3:
barName="Intronic"
elif value==4:
barName="Total"
yLim=max(max(i) for i in valueMatrix)+1
Helper.createBarplot(valueMatrix, fileName, barNameTuple, [barName], width=0.35, title="Highly Edited Genes",yLim=yLim,barText=False,yText="Editing Counts")
def topGenes(sumDict, fileName, number=20, value=5, logFile=None, textField=0):
if number > len(sumDict):
if len(sumDict) < 1:
Helper.warning("no edited genes found", logFile, textField)
return
Helper.warning(
"The given gene number is bigger than the number of total edited genes",
logFile, textField)
number = len(sumDict)
if value not in (1, 2, 3, 4, 5):
Helper.error("sumDict hast to be between 1 an 5", logFile, textField)
counts = OrderedDict(
sorted(sumDict.items(), key=lambda t: t[1][value],
reverse=True)[:number])
barNameTuple = ()
valueMatrix = [[]]
for array in counts.values():
valueMatrix[0].append(array[value])
for gene in counts.keys():
barNameTuple += (counts[gene][0], )
if value == 1:
barName = "3'-UTR"
elif value == 2:
barName = "5'-UTR"
elif value == 3:
barName = "Exonic"
elif value == 4:
barName = "Intronic"
elif value == 5:
barName = "Total"
yLim = max(max(i) for i in valueMatrix) + 1
Helper.createBarplot(valueMatrix,
fileName,
barNameTuple, [barName],
width=0.35,
title="Highly Edited Genes",
yLim=yLim,
barText=False,
yText="Editing Counts")
file = open(fileName.replace("png", "txt"), "w")
file.write("\t".join(["Gene_Symbol", "Number_of_editing_sites"]) + "\n")
htmlStr = "<table class='geneTable'><tr><th>GeneName</th><th>Number of editing sites</th></tr>"
for gene in counts:
htmlStr += "<tr><td>%s</td><td>%s</td></tr>" % (counts[gene][0],
counts[gene][value])
geneName = counts[gene][0]
numbers = str(counts[gene][value])
file.write("\t".join([geneName, numbers]) + "\n")
htmlStr += "</table>"
return htmlStr
def topGenes(sumDict, fileName,number=20,value=5, logFile=None,textField=0):
if number > len(sumDict):
if len(sumDict)<1:
Helper.warning("no edited genes found", logFile, textField)
return
Helper.warning("The given gene number is bigger than the number of total edited genes", logFile, textField)
number=len(sumDict)
if value not in (1,2,3,4,5):
Helper.error("sumDict hast to be between 1 an 5", logFile, textField)
counts=OrderedDict(sorted(sumDict.items(), key=lambda t: t[1][value],reverse=True)[:number])
barNameTuple=()
valueMatrix=[[]]
for array in counts.values():
valueMatrix[0].append(array[value])
for gene in counts.keys():
barNameTuple+=(counts[gene][0],)
if value==1:
barName="3'-UTR"
elif value ==2:
barName="5'-UTR"
elif value==3:
barName="Exonic"
elif value==4:
barName="Intronic"
elif value==5:
barName="Total"
yLim=max(max(i) for i in valueMatrix)+1
Helper.createBarplot(valueMatrix, fileName, barNameTuple, [barName], width=0.35, title="Highly Edited Genes",yLim=yLim,barText=False,yText="Editing Counts")
file= open(fileName.replace("png","txt"),"w")
file.write("\t".join(["Gene_Symbol","Number_of_editing_sites"])+"\n")
htmlStr="<table class='geneTable'><tr><th>GeneName</th><th>Number of editing sites</th></tr>"
for gene in counts:
htmlStr+="<tr><td>%s</td><td>%s</td></tr>"%(counts[gene][0],counts[gene][value])
geneName=counts[gene][0]
numbers=str(counts[gene][value])
file.write("\t".join([geneName,numbers]) +"\n")
htmlStr+="</table>"
return htmlStr
def createDiagramms(output, geneNumber=20, logFile=None, textField=0):
"""
writes all the diagrams wich are then shown in the resultTab
All the values are stored in an instance of the Class Stats
:param output: output variable of Params.output
"""
Helper.info("Creating Diagrams for %s" % output, logFile, textField)
stats = Stats(output)
stats.output = output
stats.outdir = output[0:output.rfind("/") + 1]
stats.sampleName = output[output.rfind("/") + 1:]
if not os.path.exists(stats.outdir + "html/"):
os.makedirs(stats.outdir + "html/")
# print outdir, sampleName
#################################################
#### Basecount Plot ####
#################################################
counts1 = Helper.getMMBaseCounts(output + ".alu.vcf")
counts2 = Helper.getMMBaseCounts(
output + ".noBlat.vcf"
) # use the var file after all the filters have been applied for nonAlu regions
stats.totalAluNumber = counts1["A->G"] + counts1["T->C"]
stats.totalNonAluNumber = counts2["A->G"] + counts2["T->C"]
stats.totalNumber = stats.totalAluNumber + stats.totalNonAluNumber
# write the baseCounts to a file to open with Excel later
stats.baseCountHTMLTable = "<table><tr><th>Missmatch Type</th><th>Alu</th><th>Non Alu</th></tr>"
file = open(stats.outdir + "html/" + stats.sampleName + "_baseCounts.txt",
"w")
file.write("\t".join(["MM", "alu", "nonAlu"]) + "\n")
for keyAlu, keyNonAlu in zip(counts1.keys(), counts2.keys()):
file.write("\t".join(
[str(keyAlu),
str(counts1[keyAlu]),
str(counts2[keyAlu])]) + "\n")
stats.baseCountHTMLTable += "<tr><td>%s</td><td>%s</td><td>%s</td></tr>" % (
keyAlu, str(counts1[keyAlu]), str(counts2[keyAlu]))
file.close()
stats.baseCountHTMLTable += "</table>"
fileName = stats.outdir + "html/" + stats.sampleName + "_baseCounts.png"
valueMatrix = [counts1.values(), counts2.values()]
Helper.createBarplot(
valueMatrix,
fileName,
counts1.keys(),
("Alu", "non-Alu"),
width=0.4,
title="Variants per Base",
barText=False,
yText="Number",
)
#################################################
#### Editing per Position Plot ####
#################################################
fileName = stats.outdir + "html/" + stats.sampleName + "_EditingPositions.png"
fileNamePercentage = stats.outdir + "html/" + stats.sampleName + "_EditingPositions(Percentage).png"
counts1 = Helper.countOccurrences(output + ".editingSites.alu.gvf", 2,
logFile, textField)
counts2 = Helper.countOccurrences(output + ".editingSites.nonAlu.gvf", 2,
logFile, textField)
file = open(
stats.outdir + "html/" + stats.sampleName + "_editingSites.txt", "w")
file.write("\t".join(["Position", "alu", "nonAlu"]) + "\n")
for key in counts1.keys():
if key in counts2.keys():
file.write("\t".join(
[str(key), str(counts1[key]),
str(counts2[key])]) + "\n")
else:
file.write("\t".join([str(key), str(counts1[key]), "--"]) + "\n")
for key in counts2.keys():
if key not in counts1.keys():
file.write("\t".join([str(key), "--", str(counts2[key])]) + "\n")
file.close()
# set values to 0 if they dont exist in the opposite file
orderList = [
"3'UTR", "5'UTR", "coding-exon", "noncoding-exon", "intron",
"intergenic"
]
aluPositions, nonAluPositions = [], []
for key in orderList:
aluPositions.append(counts1[key]) if key in counts1.keys(
) else aluPositions.append(0.000000001)
nonAluPositions.append(counts2[key]) if key in counts2.keys(
) else nonAluPositions.append(0.00000001)
"""if key in counts1.keys():
aluPositions.append(counts1[key])
else:
aluPositions.append(0)
for key in orderList:
nonAluPositions.append(counts2[key])
"""
sumAlu, sumNonAlu = sum(aluPositions), sum(nonAluPositions)
# aluPositions=[counts1["3'UTR"],counts1["5'UTR"],counts1["coding-exon"],counts1["noncoding-exon"],counts1["intron"],counts1["intergenic"]]
# nonAluPositions=[counts2["3'UTR"],counts2["5'UTR"],counts2["coding-exon"],counts2["noncoding-exon"],counts2["intron"],counts2["intergenic"]]
barNames = [
"3'UTR", "5'UTR", "coding-exon", "noncoding-exon", "intron",
"intergenic"
]
valueMatrix = [aluPositions, nonAluPositions]
Helper.createBarplot(valueMatrix,
fileName,
barNames, ("Alu", "non-Alu"),
width=0.4,
title="Editing Sites per Position",
barText=False,
yText="Total Counts")
valueMatrixPercentage = [
Helper.getPercentage(aluPositions),
Helper.getPercentage(nonAluPositions)
]
Helper.createBarplot(valueMatrixPercentage,
fileNamePercentage,
barNames, ("Alu", "non-Alu"),
width=0.4,
title="Editing Sites per Position",
yLim=100,
yText="Precentage")
# make String for the HTML Table and write to a table for Ecxel
file = open(
stats.outdir + "html/" + stats.sampleName + "_editingSites.txt", "w")
file.write("\t".join(["Position", "alu", "nonAlu"]) + "\n")
stats.editingPositionHTMLTable = "<table><tr><th>Editing Position</th><th>Total Alu</th><th>Alu Percentage</th><th>Total Non Alu</th><th>Non Alu Percentage</th></tr>"
for key in orderList:
alu = counts1[key] if key in counts1.keys() else 0
nonAlu = counts2[key] if key in counts2.keys() else 0
aluNumber = str(counts1[key]) if key in counts1.keys() else "0"
nonAluNumber = str(counts2[key]) if key in counts2.keys() else "0"
aluPercentage = str(round(float(alu) / sumAlu, 3) * 100) + " %"
nonAluPercentage = str(
round(float(nonAlu) / sumNonAlu, 3) * 100) + " %"
file.write("\t".join([str(key), aluNumber, nonAluNumber]) + "\n")
stats.editingPositionHTMLTable += "<tr><td>%s</td><td>%s</td><td>%s</td><td>%s</td><td>%s</td></tr>" % (
key, aluNumber, aluPercentage, nonAluNumber, nonAluPercentage)
file.close()
stats.editingPositionHTMLTable += "</table>"
#################################################
#### Edited Genes Plot ####
#################################################
sumDict, totalGenes = parseSummaryFile(output + ".editingSites.summary",
logFile, textField)
stats.percentageEditing = round(
float(len(sumDict)) / float(totalGenes) * 100.0, 2)
if "intergenic" in sumDict.keys():
del sumDict["intergenic"]
fileName = stats.outdir + "html/" + stats.sampleName + ".editedGenes(3UTR).png"
stats.utr3HtmlTable = topGenesDict = topGenes(sumDict, fileName,
geneNumber, 1)
fileName = stats.outdir + "html/" + stats.sampleName + ".editedGenes(5UTR).png"
stats.utr5HtmlTable = topGenes(sumDict, fileName, geneNumber, 2)
fileName = stats.outdir + "html/" + stats.sampleName + ".editedGenes(Exon).png"
stats.exonHtmlTable = topGenes(sumDict, fileName, geneNumber, 3)
fileName = stats.outdir + "html/" + stats.sampleName + ".editedGenes(Intron).png"
stats.intronHtmlTable = topGenes(sumDict, fileName, geneNumber, 4)
if "intergenic" in sumDict.keys():
del sumDict[
"-"] # delete intergenics, because we only we only want to show highly edited Genes!!!
fileName = stats.outdir + "html/" + stats.sampleName + ".editedGenes(Total).png"
stats.totalHtmlTable = topGenes(sumDict, fileName, geneNumber, 5)
Helper.printResultHtml(stats, logFile, textField)
def createDiagramms(output, geneNumber=20,logFile=None,textField=0):
'''
writes all the diagrams wich are then shown in the resultTab
All the values are stored in an instance of the Class Stats
:param output: output variable of Params.output
'''
Helper.info("Creating Diagrams for %s" % output, logFile, textField)
stats = Stats(output)
stats.output = output
stats.outdir = output[0:output.rfind("/")+1]
stats.sampleName=output[output.rfind("/")+1:]
if not os.path.exists(stats.outdir+"html/"):
os.makedirs(stats.outdir+"html/")
#print outdir, sampleName
#################################################
#### Basecount Plot ####
#################################################
counts1=Helper.getMMBaseCounts(output+".alu.vcf")
counts2=Helper.getMMBaseCounts(output+".noBlat.vcf") #use the var file after all the filters have been applied for nonAlu regions
stats.totalAluNumber = counts1["A->G"] + counts1["T->C"]
stats.totalNonAluNumber = counts2["A->G"] + counts2["T->C"]
stats.totalNumber = stats.totalAluNumber + stats.totalNonAluNumber
#write the baseCounts to a file to open with Excel later
stats.baseCountHTMLTable="<table><tr><th>Missmatch Type</th><th>Alu</th><th>Non Alu</th></tr>"
file=open(stats.outdir+"html/"+stats.sampleName+"_baseCounts.txt","w")
file.write("\t".join(["MM","alu","nonAlu"])+"\n")
for keyAlu,keyNonAlu in zip(counts1.keys(),counts2.keys()):
file.write("\t".join([str(keyAlu),str(counts1[keyAlu]),str(counts2[keyAlu])])+"\n")
stats.baseCountHTMLTable+="<tr><td>%s</td><td>%s</td><td>%s</td></tr>"%(keyAlu,str(counts1[keyAlu]),str(counts2[keyAlu]))
file.close()
stats.baseCountHTMLTable+="</table>"
fileName=stats.outdir+"html/"+stats.sampleName+"_baseCounts.png"
valueMatrix=[counts1.values(),counts2.values()]
Helper.createBarplot(valueMatrix, fileName, counts1.keys(), ("Alu","non-Alu"),width=0.4,title="Variants per Base", barText=False, yText="Number",)
#################################################
#### Editing per Position Plot ####
#################################################
fileName=stats.outdir+"html/"+stats.sampleName+"_EditingPositions.png"
fileNamePercentage=stats.outdir+"html/"+stats.sampleName+"_EditingPositions(Percentage).png"
counts1=Helper.countOccurrences(output+".editingSites.alu.gvf", 2, logFile, textField)
counts2=Helper.countOccurrences(output+".editingSites.nonAlu.gvf", 2, logFile, textField)
file=open(stats.outdir+"html/"+stats.sampleName+"_editingSites.txt","w")
file.write("\t".join(["Position","alu","nonAlu"])+"\n")
for key in counts1.keys():
if key in counts2.keys():
file.write("\t".join([str(key),str(counts1[key]),str(counts2[key])])+"\n")
else:
file.write("\t".join([str(key), str(counts1[key]), "--"]) + "\n")
for key in counts2.keys():
if key not in counts1.keys():
file.write("\t".join([str(key), "--", str(counts2[key])]) + "\n")
file.close()
#set values to 0 if they dont exist in the opposite file
orderList = ["3'UTR","5'UTR","coding-exon","noncoding-exon","intron","intergenic"]
aluPositions,nonAluPositions = [],[]
for key in orderList:
aluPositions.append(counts1[key]) if key in counts1.keys() else aluPositions.append(0.000000001)
nonAluPositions.append(counts2[key]) if key in counts2.keys() else nonAluPositions.append(0.00000001)
"""if key in counts1.keys():
aluPositions.append(counts1[key])
else:
aluPositions.append(0)
for key in orderList:
nonAluPositions.append(counts2[key])
"""
sumAlu,sumNonAlu = sum(aluPositions),sum(nonAluPositions)
#aluPositions=[counts1["3'UTR"],counts1["5'UTR"],counts1["coding-exon"],counts1["noncoding-exon"],counts1["intron"],counts1["intergenic"]]
#nonAluPositions=[counts2["3'UTR"],counts2["5'UTR"],counts2["coding-exon"],counts2["noncoding-exon"],counts2["intron"],counts2["intergenic"]]
barNames=["3'UTR","5'UTR","coding-exon","noncoding-exon","intron","intergenic"]
valueMatrix=[aluPositions,nonAluPositions]
Helper.createBarplot(valueMatrix, fileName, barNames, ("Alu","non-Alu"),width=0.4,title="Editing Sites per Position", barText=False, yText="Total Counts")
valueMatrixPercentage=[Helper.getPercentage(aluPositions),Helper.getPercentage(nonAluPositions)]
Helper.createBarplot(valueMatrixPercentage, fileNamePercentage, barNames, ("Alu","non-Alu"),width=0.4,title="Editing Sites per Position",yLim=100,yText="Precentage")
#make String for the HTML Table and write to a table for Ecxel
file=open(stats.outdir+"html/"+stats.sampleName+"_editingSites.txt","w")
file.write("\t".join(["Position","alu","nonAlu"])+"\n")
stats.editingPositionHTMLTable="<table><tr><th>Editing Position</th><th>Total Alu</th><th>Alu Percentage</th><th>Total Non Alu</th><th>Non Alu Percentage</th></tr>"
for key in orderList:
alu = counts1[key] if key in counts1.keys() else 0
nonAlu = counts2[key] if key in counts2.keys() else 0
aluNumber=str(counts1[key]) if key in counts1.keys() else "0"
nonAluNumber=str(counts2[key]) if key in counts2.keys() else "0"
aluPercentage= str(round(float(alu)/sumAlu,3)*100)+" %"
nonAluPercentage= str(round(float(nonAlu)/sumNonAlu,3)*100)+" %"
file.write("\t".join([str(key),aluNumber,nonAluNumber])+"\n")
stats.editingPositionHTMLTable+="<tr><td>%s</td><td>%s</td><td>%s</td><td>%s</td><td>%s</td></tr>"%(key,aluNumber, aluPercentage,nonAluNumber, nonAluPercentage)
file.close()
stats.editingPositionHTMLTable+="</table>"
#################################################
#### Edited Genes Plot ####
#################################################
sumDict,totalGenes=parseSummaryFile(output+".editingSites.summary", logFile, textField)
stats.percentageEditing = round(float(len(sumDict))/float(totalGenes)*100.0, 2)
if "intergenic" in sumDict.keys():
del sumDict["intergenic"]
fileName=stats.outdir+"html/"+stats.sampleName+".editedGenes(3UTR).png"
stats.utr3HtmlTable = topGenesDict = topGenes(sumDict,fileName, geneNumber, 1)
fileName=stats.outdir+"html/"+stats.sampleName+".editedGenes(5UTR).png"
stats.utr5HtmlTable = topGenes(sumDict,fileName, geneNumber, 2)
fileName=stats.outdir+"html/"+stats.sampleName+".editedGenes(Exon).png"
stats.exonHtmlTable = topGenes(sumDict,fileName, geneNumber, 3)
fileName=stats.outdir+"html/"+stats.sampleName+".editedGenes(Intron).png"
stats.intronHtmlTable = topGenes(sumDict,fileName, geneNumber, 4)
if "intergenic" in sumDict.keys():
del sumDict["-"] #delete intergenics, because we only we only want to show highly edited Genes!!!
fileName=stats.outdir+"html/"+stats.sampleName+".editedGenes(Total).png"
stats.totalHtmlTable = topGenes(sumDict,fileName, geneNumber, 5)
Helper.printResultHtml(stats, logFile, textField)
