Helper.py

'''
Created on May 22, 2013

@author: david
'''

from datetime import datetime
import argparse, sys, os, subprocess, errno
from collections import defaultdict, OrderedDict
import traceback
import ui
from numpy import arange
from PyQt4 import QtCore
#from matplotlib.backends import qt_compat
#from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas
from matplotlib.pyplot import subplots_adjust, subplots
from shutil import copyfile

class Parameters():
    '''
    Reads and saves the default values from the configuration File 'configurtion.txt'
    '''

    
    def __init__(self,source="configuration.txt"):
        '''
        creates an parameter object which contains all the parameters for RnaEditor
        :param source: either a QWidget or a textFile from where the parameters are read from
        '''
        if type(source)==str:
            self.readDefaultsFromFile(source)
        elif isinstance(source, ui.InputTab.InputTab):
            self.getParametersFromInputTab(source)
        else:
            Helper.error("Parameter source has wrong Type [str or QWidget]")
       
    def getParametersFromInputTab(self,inputTab):
        '''
        get the Parameters and update the default Parameters from the Default class 
        '''
        self.refGenome = str(inputTab.refGenomeTextBox.text())
        self.gtfFile = str(inputTab.gtfFileTextBox.text())
        self.dbsnp = str(inputTab.dbsnpTextBox.text())
        self.hapmap = str(inputTab.hapmapTextBox.text())
        self.omni = str(inputTab.omniTextBox.text())
        self.esp = str(inputTab.espTextBox.text())
        self.aluRegions = str(inputTab.aluRegionsTextBox.text())
        self.output = str(inputTab.outputTextBox.text())
        self.sourceDir = str(inputTab.sourceDirTextBox.text())
        
        self.threads = str(inputTab.threadsSpinBox.value())
        self.maxDiff = str(inputTab.maxDiffSpinBox.value())
        self.seedDiff = str(inputTab.seedSpinBox.value())
        self.standCall = str(inputTab.standCallSpinBox.value())
        self.standEmit = str(inputTab.standEmitSpinBox.value())
        self.edgeDistance = str(inputTab.edgeDistanceSpinBox.value())
        self.intronDistance = str(inputTab.intronDistanceSpinBox.value())
        self.minPts = str(inputTab.minPtsSpinBox.value())
        self.eps = str(inputTab.epsSpinBox.value())
        self.paired = inputTab.pairedCheckBox.isChecked()
        self.overwrite = inputTab.overwriteCheckBox.isChecked()
        self.keepTemp = inputTab.keepTempCheckBox.isChecked()
                  
    def readDefaultsFromFile(self,file):
        try:
            confFile = open(file)
        except IOError:
            Helper.error("Unable to open configuration file")
        for line in confFile:
            if line.startswith("#"):
                continue
            if line == "\n":
                continue
            
            line=line.rstrip()
            id, value = line.split("=")
            id=id.strip()
            value=value.strip()

            if id=="refGenome":
                self.refGenome=value
            elif id=="dbSNP":
                self.dbsnp=value
            elif id=="hapmap":
                self.hapmap=value
            elif id=="omni":
                self.omni=value
            elif id=="esp":
                self.esp=value
            elif id == "aluRegions":
                self.aluRegions=value
            elif id == "gtfFile":
                self.gtfFile=value
            elif id == "output":
                self.output=value
            elif id == "sourceDir":
                self.sourceDir=value
            elif id == "maxDiff":
                self.maxDiff=str(value)
            elif id == "seedDiff":
                self.seedDiff=str(value)
            elif id == "paired":
                #Parameters.paired=float(value)
                if str(value).lower() in ("yes", "y", "true",  "t", "1"): self.paired = True
                if str(value).lower() in ("no",  "n", "false", "f", "0", "0.0", "", "none", "[]", "{}"): self.paired=False
            elif id == "standCall":
                self.standCall=str(value)
            elif id == "standEmit":
                self.standEmit=str(value)    
            elif id == "edgeDistance":
                self.edgeDistance=str(value)
            elif id == "intronDistance":
                self.intronDistance=str(value)
            elif id== "minPts":
                self.minPts=str(value)
            elif id== "eps":
                self.eps=str(value)
            elif id == "threads":
                self.threads=str(value)
            elif id == "keepTemp":
                #Parameters.paired=float(value)
                if str(value).lower() in ("yes", "y", "true",  "t", "1"): self.keepTemp = True
                if str(value).lower() in ("no",  "n", "false", "f", "0", "0.0", "", "none", "[]", "{}"): self.keepTemp=False
            elif id == "overwrite":
                #Parameters.paired=float(value)
                if str(value).lower() in ("yes", "y", "true",  "t", "1"): self.overwrite = True
                if str(value).lower() in ("no",  "n", "false", "f", "0", "0.0", "", "none", "[]", "{}"): self.overwrite=False
                

           
class Helper():
    '''
    Helpfunctions
    '''

    
    prefix = "*** "
    praefix = " ***"
    colors = ["red","green","blue","olive","grey"]
    #dummy element is added to the array to avoid 0/1 problem from the Tab array and these arrays
    #otherwise i had to add -1 every time i want to access the following arrays
    runningThreads=["dummy"]

    
    
    @staticmethod
    def getSampleName(fq):
                #get name from input File
        if fq.endswith(".fastq"):
            sampleName = fq[fq.rfind("/")+1:fq.rfind(".fastq")]
        elif fq.endswith(".fq"):
            sampleName = fq[fq.rfind("/")+1:fq.rfind(".fq")]
        elif fq.endswith(".bam"):
            sampleName = fq[fq.rfind("/")+1:fq.rfind(".bam")]
        else:
            return None
        return sampleName
    
    @staticmethod
    def readable_dir(prospective_dir):
        if not os.path.isdir(prospective_dir):
            raise argparse.ArgumentTypeError("readable_dir:{0} is not a valid path".format(prospective_dir))
        if os.access(prospective_dir, os.R_OK):
            return prospective_dir
        else:
            raise argparse.ArgumentTypeError("readable_dir:{0} is not a readable dir".format(prospective_dir))
    

    @staticmethod
    def getTime():
        '''
        return current time
        '''
        curr_time = datetime.now()
        #return "["+curr_time.strftime("%c")+"]"
        return curr_time
    
    
    @staticmethod
    def convertPhred64toPhred33(fastqFile,outFile,logFile,textField):
        """
        converts the inputFile to phred33 Quality and writes it into the ourdir
        :rtype: String to converted FastQ file
        """
        startTime=Helper.getTime()
        Helper.info("[" + startTime.strftime("%c") + "] * * * convert Quality encoding: " + fastqFile[fastqFile.rfind("/")+1:]   + " * * *",logFile,textField)
        
        
        if os.path.exists(outFile):
            Helper.info("* * * [Skipping] Result File already exists * * *",logFile,textField)
            return outFile
        
        outFile = open(outFile,"w")
        fastqFile=open(fastqFile,"r")
        
        lineNumber = 0 
        for line in fastqFile:
            lineNumber+=1
            if lineNumber%4==0:
                a=[]
                for char in line.rstrip():
                    phredQual=ord(char)-64
                    if phredQual<0: #correct unvalid values
                        phredQual=0
                    elif phredQual>40:
                        phredQual=40
                    phredChar=chr(phredQual+33)
                    a.append(phredChar)
                outFile.write("".join(a) + "\n")
            else:
                outFile.write(line)
        outFile.close()
        return outFile.name
    
    @staticmethod
    def isPhred33Encoding(inFastqFile,lines,logFile, runNumber):
        """
        check in the first lines if the quality encoding is phred33
        """
        fastqFile=open(inFastqFile,"r")
        lineNumber=0

        lines=lines*4
        for line in fastqFile:
            lineNumber+=1
            if lineNumber%4==0:
                for char in line.rstrip():
                    if ord(char)>74 and ord(char)<105:
                        #print line.rstrip()
                        fastqFile.close()
                        return False
                    if ord(char)>105:
                        Helper.error("%s has no valid quality encoding. \n\t Please use a valid FastQ file??" % fastqFile.name,logFile, runNumber)
            if lineNumber > lines:
                fastqFile.close()
                return True
            
        Helper.error("%s has less than %i Sxequences. \n These are not enough reads for editing detection!!" % (fastqFile.name,lines),logFile, runNumber)
    
    @staticmethod
    def proceedCommand(description,cmd,infile,outfile,rnaEdit):
        '''
        run a specific NGS-processing-step on the system
        '''
        logFile=rnaEdit.logFile
        textField=rnaEdit.textField
        overwrite=rnaEdit.params.overwrite
        
        startTime=Helper.getTime()
        Helper.info("[" + startTime.strftime("%c") + "] * * * " + description + " * * *",logFile,textField)
        
        
        #check if infile exists
        if not os.path.isfile(infile):
            Helper.error(infile + " does not exist, Error in previous Step",logFile,textField)
            #Exception(infile + "does not exist, Error in previous Step")
            #exit(1)
        
        #check if outfile already exists
        
        if not os.path.isfile(outfile) or overwrite==True:
            if outfile == "None":
                resultFile=None
            else:
                resultFile=open(outfile,"w+")
            try:    
                
                #print " ".join(cmd),resultFile,logFile
                
                #retcode = subprocess.call(cmd, stdout=resultFile, stderr=logFile)
                rnaEdit.runningCommand = subprocess.Popen(cmd, stdout=resultFile, stderr=logFile)
                retcode = rnaEdit.runningCommand.wait()
                """while retcode==None:
                    #print "check if process is still running"
                    sleep(10)
                    retcode=Helper.runningCommand[runNumber].wait()
                """
                #print retcode
                
                #del Helper.runningCommand[runNumber]
                rnaEdit.runningCommand=False
                if retcode != 0:
                    if retcode == -9:
                        Helper.error(description+ " canceled by User!!!",logFile,textField)
                    else:
                        Helper.error(description+ " failed!!!",logFile,textField)
                    
                    if resultFile!=None:
                        os.remove(resultFile.name)
                    #exit(1)
            except OSError as o:
                if o.errno == errno.ENOTDIR or o.errno == errno.ENOENT:
                    Helper.error(cmd[0] + " Command not found on this system",logFile,textField)
                    if resultFile!=None:
                        os.remove(resultFile.name)
                    #exit(1)
                else:
                    Helper.error(cmd[0] + o.strerror,logFile,textField)
                    if resultFile!=None:
                        os.remove(resultFile.name)
                    #exit(1)
            Helper.printTimeDiff(startTime, logFile, textField, "green")
        else:
            Helper.info("\t [SKIP] File already exist",logFile,textField, "green") 

    @staticmethod
    def getPositionDictFromVcfFile(vcfFile,runNumber):
        """
        return a dictionary whith chromosome as keys and a set of variants as values
        variantDict={chromosome:(variantPos1,variantPos2,....)}
        """
        variantFile=open(vcfFile)
        variantDict=defaultdict(set)
        Helper.info("reading Variants from %s" % vcfFile,runNumber)
        for line in variantFile:
            #skip comments
            if line.startswith("#"): continue
            line=line.split("\t")
            chromosome,position,ref,alt = line[0],line[1],line[3],line[4]
            variantDict[chromosome].add(position)
        return variantDict
    
    @staticmethod
    def removeVariantsAFromVariantsB(variantsDictA,variantsDictB):        
        if type(variantsDictA) is str:
            variantsDictA = Helper.returnVariantDictFromVcfFile(variantsDictA)
        if type(variantsDictB) is str:
            variantsDictB = Helper.returnVariantDictFromVcfFile(variantsDictB)
            
        resultDict = defaultdict(set)
        for variant in variantsDictB.iterkeys():
            if variant not in variantsDictA[chr]:
                resultDict[chr].append(variant)
        return resultDict
       
    @staticmethod
    def returnVariantDictFromVcfFile(vcfFile):
        """
        returns the vcfFile as a two instance dictionary with chromosome as first key and a Tuple of (position,ref,alt) as second key  and  the rest of the vcfLine as a list
        {chr1: {(position1, 'A', 'G'): [dbSNP_id, ' quality', 'filter', 'attributes'], (4, 324, 'dsgdf', 'dsfsd'): [42, 243, 324]}})
        """
        vcfFile=open(vcfFile)
        vcfDict = defaultdict(dict)
        for line in vcfFile:
            #skip comments
            if line.startswith("#"): continue
            line=line.rstrip().split()
            chromosome,position,ref, alt = line[0],line[1], line[3], line[4]
            vcfDict[chromosome][position,ref,alt]=([line[2]]+line[5:])
        return vcfDict

    @staticmethod
    def getCommandOutput(command):
        #print command
        #print os.path.dirname(os.path.abspath(__file__))
        #print os.getcwd()
        return subprocess.check_output(command)
    
    @staticmethod
    def countOccurrences(inFile,column=0,logFile=None,textField=0):
        '''
        Counts how often a value appears in the given column
        :param file: 
        :param column: hold the data wich should be counted
        '''
        if type(column)!=int:
            column=int(column)
        if type(inFile) == str:
            try:
                inFile=open(inFile)
            except IOError:
                Helper.warning("Could not open %s to write Variant" % file ,logFile,textField)
        if type(inFile) != file:   
            raise AttributeError("Invalid file type in 'countOccurrences' (need string or file, %s found)" % type(inFile))
        
        keySet=()
        countDict={}
        
        for line in inFile:
            if line.startswith("#"):
                continue
            value=line.split()[column]
            if value in keySet:
                countDict[value]+=1
            else:
                keySet+=(value,)
                countDict[value]=1
        
        return countDict
    
    @staticmethod
    def createBarplot(valueMatrix,fileName,barNamesTuple,legendTuple,width=0.25,title="",yLim=None, barText=True, yText=""):
        '''
        
        :param valueMatrix: [[ValuesBar1][ValuesBar2][ValuesBar3]]
        :param fileName: 
        :param barNamesTuple: Name of Groups (has to be equal to Number of Values per Group (len(ValueArray[0])) )
        :param legendTuple: Name of each bar (equal to len(valueArray))
        :param width:
        :param title:
        '''
        valueLen=len(valueMatrix[0])
        
        
        
        for values in valueMatrix:
            assert valueLen==len(values), "ValueMatrix has to be Symmetric"
         
        assert len(legendTuple) == len(valueMatrix), "legendTuple has to have the same length as ValueArray "
        assert len(barNamesTuple) == len(valueMatrix[0]), "barNamesTuple has to have the same length as ValueArray[0] "
        
        ind = arange(len(valueMatrix[0]))  # the x locations for the groups
        fig, ax = subplots()
        
        subplots_adjust(bottom=0.24)
        ax.set_title(title)
        ax.set_ylabel(yText)
        ax.set_xticks(ind+width)
        ax.set_xticklabels( barNamesTuple, rotation='vertical' )
        ax.set_xlim(min(ind)-0.1,max(ind)+(width*len(valueMatrix))*1.1)
        if yLim!=None:
            ax.set_ylim(0,yLim)
        
        color=['b','g','r','y']*len(valueMatrix)
        
        
        rects=()
        
        def autolabel(rects):# attach some text labels
            for rect in rects:
                height = rect.get_height()
                ax.text(rect.get_x()+rect.get_width()/2., height/2  , '%1.0f'%float(height), ha='center', va='bottom', fontsize=8, rotation='vertical', )
        
        i=0
        for values,c in zip(valueMatrix,color):
            rect=ax.bar((ind+width*i), values, width, color=c, )
            rects+=(rect,)
            
            if barText==True:
                autolabel(rect)
            i+=1
        ax.legend( rects, legendTuple )
        
        fig.savefig(fileName)
        
    @staticmethod
    def printResultHtml(stats,logFile=None,textField=0):
        '''
        print the HTML file wich is shown when rnaEditor is finished
        :param output: output prefix from rnaEdit object
        '''
        
        htmlOutPrefix="html/"+stats.sampleName
        
        #copy rnaEditor logo to htmlOutPrefix
        fileDir = os.path.dirname(os.path.realpath(__file__))
        copyfile(fileDir + '/ui/icons/rnaEditor_512x512.png',stats.outdir+"html/rnaEditor_512x512.png")
        
        outDict={"title":"Result Page for "+ stats.sampleName,
                 "sampleName":stats.sampleName,
                 "icon":stats.outdir+"html/rnaEditor_512x512.png",
              "baseCounts":htmlOutPrefix+"_baseCounts.png",
              "editingPositions":htmlOutPrefix+"_EditingPositions.png",
              "3UTR":htmlOutPrefix+".editedGenes(3UTR).png",
              "5UTR":htmlOutPrefix+".editedGenes(5UTR).png",
              "Exon":htmlOutPrefix+".editedGenes(Exon).png",
              "Intron":htmlOutPrefix+".editedGenes(Intron).png",
              "Total":htmlOutPrefix+".editedGenes(Total).png",
              "currentTime":Helper.getTime().strftime("%d.%m.%Y %H:%M"),
              "totalAluNumber": str(stats.totalAluNumber),
              "totalNonAluNumber" : str(stats.totalNonAluNumber),
              "totalNumber": str(stats.totalNumber),
              "percentageEditing": str(stats.percentageEditing)+"%",
              "baseCoutHtmlTable": str(stats.baseCountHTMLTable),
              "editingPositionHTMLTable": str(stats.editingPositionHTMLTable),
              "utr3HtmlTable":  str(stats.utr3HtmlTable),
              "utr5HtmlTable": str(stats.utr5HtmlTable),
              "exonHtmlTable": str(stats.exonHtmlTable),
              "intronHtmlTable": str(stats.intronHtmlTable),
              "totalHtmlTable": str(stats.totalHtmlTable)
              }
        

        outfile=open(stats.output+".html","w+")
        
        outfile.write("""<!DOCTYPE html PUBLIC '-//W3C//DTD XHTML 1.0 Strict//EN'
    'http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd'>
<html xmlns='http://www.w3.org/1999/xhtml' xml:lang='en' lang='en'>
<head>
    <title>sampleName Results</title>
    <meta http-equiv='content-type' content='text/html;charset=utf-8' />
    <meta name='RnaEditor' content='Results from RnaEditor' />
<style type='text/css'>
    body {background-color: #F6F6F6;}
    html, body {height: 100%;margin:0px;padding: 0px;font-family: sans-serif;}
    h1,h2,h3,h4,h5,h6{margin-top: 1em;margin-bottom: 0.6em;}
    h2{    font-size: 100%;font-weight: bold;}
    h3{margin-left:1em;font-size: 90%;    font-weight: bold;}
    .contentBlock{margin-top: 1em;border-width: 1px 1px 3px 1px;border-style: solid;border-color: #A7D7F9; max-width: 950px}
    #left{width: 11em;position: absolute;}
    #toc{margin-top: 40px;margin-left: 5px;}
    #toc ul{padding-left: 10px;list-style-type:none;list-style-image:none;font-size: 90%;line-height: 1.9;}
    #page, #header{z-index: 0;position: relative;padding: 0.1em 1.5em;margin-left: 11em;margin-right: 1em;border-width: 1px 1px 1px 1px;border-style: solid;border-color: #A7D7F9;}
    #page{border-width: 0px 1px 1px 1px;background: #fff;}
    #header{background-position: left bottom;background-color: #fff;}
    img {}
    table {font-size: 80%;background-color: #DDD;width:70%;max-width: 850px;margin-left:auto;margin-right:auto; text-align: center;}
    th {text-align: center;background-color: #0000FF;color: #FFF;padding: 0.4em;}      
    td {text-align: center;background-color: #FFF;color: #000;padding: 0.4em;}
    .geneTable{width: 500px;}

    figure {padding: 5px;border: 1px solid #cccccc;border-radius: 5px;max-width: 900px}
    figure img {border-radius: 3px 3px 0 0;height: 70%;width: 90%;max-width: 850px;max-height: 550px;}
    figure figcaption {font-size: 70%; padding: 2px 4px 2px 4px;background-color: #636363;color: #cccccc;font-style: italic;border-radius: 0 0 3px 3px;text-align:center}
</style>
</head>""")
        
        htmlString="""
<body>
    <div id='left'>
        <div id='logo' class='logo'>
            <img src='%(icon)s' height=140 width=140>
        </div>
    
            <!-- Table of Content-->
        <div id='toc' class='toc'>
        <div id='toctitle'><h2>Content</h2></div>
        <ul>
            <li class='toclevel-1 tocsection-1'><a href='#basicStats'><span class='tocnumber'>1</span> <span class='toctext'>Basic Statistic</span></a></li>
            <li class='toclevel-1 tocsection-2'><a href='#NucleotideChanges'><span class='tocnumber'>2</span> <span class='toctext'>Nucleotide Changes</span></a></li>
            <li class='toclevel-1 tocsection-3'><a href='#EditingPerPosition'><span class='tocnumber'>3</span> <span class='toctext'>Editing Sites per Position</span></a></li>
            <ul>
                <li class='toclevel-2 tocsection-3.1'><a href='#3utr'><span class='tocnumber'>3.1</span> <span class='toctext'>3'UTR</span></a></li>
                <li class='toclevel-2 tocsection-3.2'><a href='#5utr'><span class='tocnumber'>3.2</span> <span class='toctext'>5'UTR</span></a></li>
                <li class='toclevel-2 tocsection-3.3'><a href='#exon'><span class='tocnumber'>3.3</span> <span class='toctext'>Exons</span></a></li>
                <li class='toclevel-2 tocsection-3.4'><a href='#intron'><span class='tocnumber'>3.4</span> <span class='toctext'>Introns</span></a></li>
                <li class='toclevel-2 tocsection-3.4'><a href='#total'><span class='tocnumber'>3.5</span> <span class='toctext'>Total</span></a></li>
            </ul>
            <li class='toclevel-1 tocsection-4'><a href='#EditedGenes'><span class='tocnumber'>4</span> <span class='toctext'>Highly Edited Genes</span></a></li>
            <li class='toclevel-1 tocsection-5'><a href='#EditedIslands'><span class='tocnumber'>5</span> <span class='toctext'>Editing Islands</span></a></li>
        </ul>
        </div>
    </div>    
    
    <div id='header'>
        <h1 >Results for %(sampleName)s</h1>
        <p style="text-align: right;">%(currentTime)s</p>
    </div>
    
    
    <div id='page' class='page'>

        <!-- Content -->
        <div id='content' class='content'>
            <div class='contentBlock'>
            <h2><span class='mw-headline' id='basicStats'>Basic Statistic</span></h2>
                <p>
                    <table>
                        <tbody>
                            <tr>
                                <th>Measure</th>
                                <th>Value</th>        
                            </tr>
                            <tr>
                                <td>Total Number of editing sites:</td>
                                <td>%(totalNumber)s</td>
                            </tr>
                            <tr>
                                <td>in Alu Regions:</td>
                                <td>%(totalAluNumber)s</td>
                            </tr>
                            <tr>
                                <td>in non-Alu Regions:</td>
                                <td>%(totalNonAluNumber)s</td>
                            </tr>
                            <tr>
                                <td>Percentage of edited Genes:</td>
                                <td>%(percentageEditing)s</td>
                            </tr>
                        </tbody>
                    </table>
                </p>
            </div>
            <div class='contentBlock'>
            <h2><span class='mw-headline' id='NucleotideChanges'>Nucleotide Changes</span></h2>
                <p>Nucleotide changes after all the filters have been applied. 
                   A high amount of A->G and T->C missmatches is indicative for a high editing rate.</p>
                <figure>
                    <img src='%(baseCounts)s'  alt='Base Counts' >
                    <figcaption>Number of mismatsch types</figcaption>
                </figure>
                %(baseCoutHtmlTable)s
            </div>
            <div class='contentBlock'>
            <h2><span class='mw-headline' id='EditingPerPosition'>Editing Sites per Position</span></h2>
                <p>Positions where editing takes place.</p>
                <figure>
                    <img src='%(editingPositions)s'  alt='Editing Positions' >
                    <figcaption>Number of editing sites in different gene regions</figcaption>
                </figure>
                %(editingPositionHTMLTable)s
            </div>
            <div class='contentBlock'>
            <h2><span class='mw-headline' id='EditedGenes'>Highly Edited Genes</span></h2>
                    <p>This paragraph shows highly edited genes for each segment of the genes.</p>
                    <h3 id='3utr'>3' UTR</h3>
                        <figure>
                            <img src='%(3UTR)s' alt='highly edited genes in 3'UTR'>
                            <figcaption>Highly edited Genes in 3'UTR Regions</figcaption>
                        </figure>
                        %(utr3HtmlTable)s
                    <h3 id='5utr'>5' UTR</h3>
                        <figure>
                            <img src='%(5UTR)s' alt='highly edited genes in 5'UTR'>
                            <figcaption>Highly edited Genes in 5'UTR Regions</figcaption>
                        </figure>
                        %(utr5HtmlTable)s
                    <h3 id='exon'>Exons</h3>
                        <figure>
                            <img src='%(Exon)s' alt='highly edited genes in exons'>
                            <figcaption>Highly edited Genes in Exon Regions</figcaption>
                        </figure>
                        %(exonHtmlTable)s
                    <h3 id='intron'>Introns</h3>
                        <figure>
                            <img src='%(Intron)s' alt='highly edited genes in introns'>
                            <figcaption>Highly edited Genes in Intron Regions</figcaption>
                        </figure>
                        %(intronHtmlTable)s
                    <h3 id='total'>Total</h3>
                        <figure>
                            <img src='%(Total)s' alt='highly edited genes (total)'>
                            <figcaption>Highly edited Genes in 5'UTR Regions</figcaption>
                        </figure>
                        %(totalHtmlTable)s
            </div>   
            <div class='contentBlock'>
            <h2><span class='mw-headline' id='EditedIslands'>Editing Islands</span></h2>
                <p> Detected Editing Islands</p>
            </div>
                
            
        </div>
    </div>
</body>
</html>
        
"""%outDict
        outfile.write(htmlString)
        
    @staticmethod
    def getPercentage(list):
        '''
        returns the percentage as a list
        :param list:
        '''
        array=[]
        summe=float(sum(list))
        for value in list:
            array.append(round((float(value)/summe)*100.0,2))
        #print array    
        return array   

    @staticmethod
    def getMMBaseCounts(vcfFile):
        '''
        Count the number of base mismatches and return the Dictionary with the numbers
        :param vcf File:
        '''
        if type(vcfFile) == str:
            if os.path.getsize(vcfFile) == 0: #getsize raises OSError if file is not existing
                raise IOError("%s File is empty" % vcfFile)
            vcfFile = open(vcfFile,"r")
        elif type(vcfFile) != file:
            raise TypeError("Invalid type in 'parseVcfFile' (need string or file, %s found)" % type(vcfFile)) 
        
        mmBaseCounts=OrderedDict([("A->C",0),("A->G",0),("A->T",0),("C->A",0),("C->G",0),("C->T",0),("G->A",0),("G->C",0),("G->T",0),("T->A",0),("T->C",0),("T->G",0)])
        
        for line in vcfFile:
            if line.startswith('#'): continue
            line=line.split()
            if line[3]=="A" and line[4]=="C": mmBaseCounts["A->C"]+=1
            elif line[3]=="A" and line[4]=="G": mmBaseCounts["A->G"]+=1
            elif line[3]=="A" and line[4]=="T": mmBaseCounts["A->T"]+=1
            elif line[3]=="C" and line[4]=="A": mmBaseCounts["C->A"]+=1
            elif line[3]=="C" and line[4]=="G": mmBaseCounts["C->G"]+=1
            elif line[3]=="C" and line[4]=="T": mmBaseCounts["C->T"]+=1
            elif line[3]=="G" and line[4]=="A": mmBaseCounts["G->A"]+=1
            elif line[3]=="G" and line[4]=="C": mmBaseCounts["G->C"]+=1
            elif line[3]=="G" and line[4]=="T": mmBaseCounts["G->T"]+=1
            elif line[3]=="T" and line[4]=="A": mmBaseCounts["T->A"]+=1
            elif line[3]=="T" and line[4]=="C": mmBaseCounts["T->C"]+=1
            elif line[3]=="T" and line[4]=="G": mmBaseCounts["T->G"]+=1
            
        return mmBaseCounts
        
    @staticmethod
    def printTimeDiff(startTime,logFile=None,textField=0,color="green"):
        duration = Helper.getTime() - startTime
        if textField!=0:
            #currentAssay = Helper.runningAssays[textField] 
            if color in Helper.colors:
                textField.append(QtCore.QString("<font color=\""+color+"\">%1</font>").arg("[DONE] Duration [" + str(duration) + "]"  + Helper.praefix + "\n"))
            else:
                textField.append(Helper.prefix + "[DONE] Duration [" + str(duration) + "]"  + Helper.praefix + "\n")
        if logFile!=None:
            logFile.write("\t" + Helper.prefix + "[DONE] Duration [" + str(duration) + "]"  + Helper.praefix + "\n")
        
        sys.stderr.write("\t" + Helper.prefix + "[DONE] Duration [" + str(duration) + "]"  + Helper.praefix + "\n")

    @staticmethod
    def newline(quantity=1,
                 logFile=None,
                 textField=0):
        if textField!=0:
            # currentAssay = Helper.runningAssays[runNumber]
            textField.append("\n"*quantity)
        if logFile != None:
            logFile.write("\n"*quantity)
            logFile.flush()
        sys.stderr.write("\n"*quantity)
    @staticmethod
    def info (message,logFile=None,textField=0,color="olive"):
        if textField!=0:
            if color in Helper.colors:
                textField.append(QtCore.QString("<font color=\""+color+"\">%1</font>").arg(Helper.prefix + "STATUS:    "  + message + Helper.praefix))
            else:
                textField.append(Helper.prefix + "INFO:    "  + message + Helper.praefix)
        if logFile!=None:
            logFile.write(Helper.prefix + "INFO:    "  + message + Helper.praefix + "\n")
            logFile.flush()
        sys.stderr.write(Helper.prefix + "INFO:    "  + message + Helper.praefix + "\n")
    @staticmethod
    def warning (message,logFile=None,textField=0):
        if textField!=0:
            textField.append("\n\n" + Helper.prefix + "WARNING:    " + message + Helper.praefix + "\n\n")
        if logFile!=None:
            logFile.write(Helper.prefix + "WARNING:    "  + message + Helper.praefix + "\n")
            logFile.flush()
        sys.stderr.write("\n\n" + Helper.prefix + "WARNING:    " + message + Helper.praefix + "\n\n")
    @staticmethod
    def error (message,logFile=None,textField=0,color="red"):
        if textField!=0:
            if color in Helper.colors:
                textField.append(QtCore.QString("<font color=\""+color+"\">%1</font>").arg(Helper.prefix + "STATUS:    "  + message + Helper.praefix))
            else:
                textField.append(Helper.prefix + "ERROR:    "  + message + Helper.praefix)
        if logFile!=None:
            logFile.write(Helper.prefix + "ERROR:    "  + message + Helper.praefix + "\n")
            logFile.flush()
        print(traceback.format_exc())
        #sys.stderr.write("\n\n" + Helper.prefix + "ERROR:    " + message + Helper.praefix + "\n\n")
        raise Exception("\n\n" + Helper.prefix + "ERROR:    " + message + Helper.praefix + "\n\n")
    @staticmethod
    def debug (message,logFile=None,textField=0):
        if textField!=0:
            textField.append(Helper.prefix + "DEBUG:    "  + message + Helper.praefix)
        if logFile!=None:
            logFile.write(Helper.prefix + "DEBUG:    "  + message + Helper.praefix + "\n")
            logFile.flush()
        sys.stderr.write(Helper.prefix + message + Helper.praefix + "\n")
    @staticmethod
    def status(message,logFile=None,textField=0,color=None,bold=False):
        if textField!=0:
            #currentAssay = Helper.runningAssays[runNumber] 
            if color in Helper.colors:
                if bold==True:
                    textField.append(QtCore.QString("<font color=\""+color+"\"><b>%1</b></font>").arg(Helper.prefix + "STATUS:    "  + message + Helper.praefix))
                else:
                    textField.append(QtCore.QString("<font color=\""+color+"\">%1</font>").arg(Helper.prefix + "STATUS:    "  + message + Helper.praefix))
            else:
                textField.append(Helper.prefix + "STATUS:    "  + message + Helper.praefix)
        if logFile!=None:
            logFile.write(Helper.prefix + "STATUS:    "  + message + Helper.praefix + "\n")
            logFile.flush()
        sys.stdout.write("\r" + Helper.prefix + "STATUS:    "  + message + Helper.praefix + "\n")
        sys.stdout.flush()