Python ExternalTrackManager.getPreProcessedTrackFromGalaxyTN方法代码示例

# 需要导入模块: from quick.application.ExternalTrackManager import ExternalTrackManager [as 别名]
# 或者: from quick.application.ExternalTrackManager.ExternalTrackManager import getPreProcessedTrackFromGalaxyTN [as 别名]
 def _collectTracks(self):
     tracks = [self._track, self._track2]
     if 'trackNameIntensity' in self._kwArgs:
         assert not 'extraTracks' in self._kwArgs
         self._kwArgs['extraTracks'] = self._kwArgs['trackNameIntensity']
         
     if 'extraTracks' in self._kwArgs:
         from gold.track.Track import PlainTrack
         import re
         from config.Config import MULTIPLE_EXTRA_TRACKS_SEPARATOR
         extraTracks = self._kwArgs['extraTracks']
         if type(extraTracks) == str:
             extraTracks = extraTracks.split(MULTIPLE_EXTRA_TRACKS_SEPARATOR)
         for extraT in extraTracks:
             if type(extraT) == str:
                 #extraT = extraT.split('|')
                 #extraT = re.split('\^|\|',extraT)                    
                 extraT = convertTNstrToTNListFormat(extraT)
             if type(extraT) == list:
                 #print 'TEMP1: ', extraT
                 from urllib import unquote
                 extraT = [unquote(part) for part in extraT]
                 from quick.application.ExternalTrackManager import ExternalTrackManager
                 if ExternalTrackManager.isGalaxyTrack(extraT):
                     extraT = ExternalTrackManager.getPreProcessedTrackFromGalaxyTN(self.getGenome(), extraT)
                 extraT = PlainTrack(extraT)
                 tracks.append(extraT)
             
     return tracks

# 需要导入模块: from quick.application.ExternalTrackManager import ExternalTrackManager [as 别名]
# 或者: from quick.application.ExternalTrackManager.ExternalTrackManager import getPreProcessedTrackFromGalaxyTN [as 别名]
    def execute(cls, choices, galaxyFn=None, username=''):
        import time
        start = time.clock()

        # HTML settings
        from gold.result.HtmlCore import HtmlCore
        htmlCore = HtmlCore()
        htmlCore.divBegin(style=cls.HTML_STYLE)

        # Set debug environment
        cls._setDebugModeIfSelected(choices)

        # Print tool information
        cls.htmlClusterTitle(cls.getToolName(), htmlCore)
        cls.htmlClusterSubtext(choices.distanceMeasure, cls.CLUSTER_LIST, choices.linkageCriterion, htmlCore)
        htmlCore.line('Threshold of r<sup>2</sup>: ' + choices.rSquare)

        # Analysis environment
        gSuite = getGSuiteFromGalaxyTN(choices.gSuite)
        analysisBins = GlobalBinSource(gSuite.genome)
        analysisSpec = AnalysisSpec(ExpandTrackAndMatchStat)

        splitName = choices.ldTrack.split(":")
        trackName = ExternalTrackManager.getPreProcessedTrackFromGalaxyTN(gSuite.genome, splitName)
        linkedPointTrack = Track(trackName)

        # Find distance/correlation matrix
        labels = []
        distDict = cls.createDistDict(cls.CLUSTER_LIST)
        size = gSuite.numTracks()
        for i in range(0, size):
            gSuiteTrack1 = gSuite.getTrackFromIndex(i)
            labels.append(gSuiteTrack1.title)
            for j in range(i + 1, size):
                gSuiteTrack2 = gSuite.getTrackFromIndex(j)
                track1 = Track(gSuiteTrack1.trackName)
                track2 = Track(gSuiteTrack2.trackName)
                count = doAnalysis(analysisSpec, analysisBins, [track1, track2, linkedPointTrack]).getGlobalResult()
                cls.updateDistDict(distDict, count)

        # Cluster and print plots
        cls.printDistPlots(distDict, labels, choices.distanceMeasure, choices.linkageCriterion, galaxyFn, htmlCore)

        cls.htmlClusterTime(str(time.clock() - start), htmlCore)
        htmlCore.divEnd()
        print htmlCore

# 需要导入模块: from quick.application.ExternalTrackManager import ExternalTrackManager [as 别名]
# 或者: from quick.application.ExternalTrackManager.ExternalTrackManager import getPreProcessedTrackFromGalaxyTN [as 别名]
 def execute(cls, choices, galaxyFn=None, username=''):
     from gold.origdata.TrackGenomeElementSource import TrackViewListGenomeElementSource
     from gold.origdata.GtrackComposer import StdGtrackComposer
     genome = choices[0]
     if choices[1] == 'Track':
         trackName = choices[2].split(':')
     else:
         trackName = ExternalTrackManager.getPreProcessedTrackFromGalaxyTN(genome, choices[2].split(':'))
         
     outFn = galaxyFn
     if choices[4] == 'Write to Standardised file':
         outFn = createOrigPath(genome, choices[-1].split(':'), 'collapsed_result.bedgraph')
         ensurePathExists(outFn[:outFn.rfind('/')+1])
            
     threshold = choices[3]
     analysisDef = 'dummy [threshold=%s] -> ForEachSegmentDistToNearestInSameTrackStat' % threshold #'Python'
     res = GalaxyInterface.runManual([trackName], analysisDef, '*', '*', genome, username=username, \
                                     printResults=False, printHtmlWarningMsgs=False)
             
     tvGeSource = TrackViewListGenomeElementSource(genome, [x['Result'] for x in res.values()], trackName)    
     StdGtrackComposer(tvGeSource).composeToFile(outFn)

# 需要导入模块: from quick.application.ExternalTrackManager import ExternalTrackManager [as 别名]
# 或者: from quick.application.ExternalTrackManager.ExternalTrackManager import getPreProcessedTrackFromGalaxyTN [as 别名]
 def execute(cls, choices, galaxyFn=None, username=''):
     from quick.application.ExternalTrackManager import ExternalTrackManager
     
     genome = choices[0]
     preProcTN1 = ExternalTrackManager.getPreProcessedTrackFromGalaxyTN(genome, choices[2].split(':')) if choices[1] == 'History' else choices[2].split(':')
     chrSizeDict =  dict([ ( chrom, GenomeInfo.getChrLen(genome, chrom)) for chrom in GenomeInfo.getChrList(genome)])
     
     
     trackType = choices[3].split(':')[1]
     fnSource = ExternalTrackManager.extractFnFromGalaxyTN(choices[3].split(':'))
     
     if trackType in ['marked.bed', 'category.bed', 'bed']:
         geSource = GenomeElementSorter(BedGenomeElementSource(fnSource, genome=genome)).__iter__()
         
     elif trackType == 'gtrack':
         geSource = GenomeElementSorter(GtrackGenomeElementSource(fnSource, genome=genome)).__iter__()
         #headLinesStr = geSource.getHeaderLines().replace('##','\n##')
     else:
         raise InvalidFormatError('The Binning must be of the following formats: gtrack, marked.bed, category.bed ,bed ...')
         
         
     cls.PrintResultToHistItem( galaxyFn, geSource, preProcTN1, genome, username)

# 需要导入模块: from quick.application.ExternalTrackManager import ExternalTrackManager [as 别名]
# 或者: from quick.application.ExternalTrackManager.ExternalTrackManager import getPreProcessedTrackFromGalaxyTN [as 别名]
    def execute(cls, choices, galaxyFn=None, username=''):
        from quick.application.GalaxyInterface import GalaxyInterface

        fileformat = choices[9];
        outputFile = open(galaxyFn, "w")
        
        if fileformat == "html":
            print GalaxyInterface.getHtmlBeginForRuns(galaxyFn)
            print GalaxyInterface.getHtmlForToggles(withRunDescription=False)
            t = calendar.timegm(time.gmtime())
            htmlfile = GalaxyRunSpecificFile(["css", str(t)], galaxyFn);


        genome = choices[0]
        track1 = choices[1].split(":")
        track2 = choices[2].split(":")
        tn1 = ExternalTrackManager.getPreProcessedTrackFromGalaxyTN(genome, track1)
        tn2 = ExternalTrackManager.getPreProcessedTrackFromGalaxyTN(genome, track2)

        compare = choices[3] != "Count individual SNP-differences in window"
        if choices[4] == "Classical MDS":
            mds = 0;
        elif choices[4] == "SMACOF":
            mds = 1;
        else:
            mds = 2;
        windowSize = int(choices[5])
        windowStep = int(choices[6])
        
        mcTreshold = int(choices[7])
        mcRuns = int(choices[8])

        outputFile.write("#seqid\tstart\tscore\tp\n")
        if fileformat == "html":
            text = "#seqid\tstart\tscore\tp\n";

	print "chrs:"+str(GenomeInfo.getChrList(genome))
        reg = "*"
        bins = "*"
        analysisDef = "Dummy: dummy name ([wStep=%g] [wSize=%s] [func=%s] [mds=%s] [mcT=%s] [mcR=%s])-> CategoryClusterSeparationStat" % (windowStep, windowSize, compare, mds, mcTreshold, mcRuns)
        userBinSource = GalaxyInterface._getUserBinSource(reg, bins, genome)
        result = GalaxyInterface.runManual([tn1, tn2], analysisDef, reg, bins, genome, galaxyFn=galaxyFn)
        for key in result.getAllRegionKeys():
            chrom = str(key).split(":")[0];
            r = result[key];
            if 'Result' not in r.keys():
                print "skipping chr:", chrom, r;
                continue;
            r = r['Result'];
            scores = r[0];
            stddev = r[1];
            for i in range(len(scores)):
                if scores[i] != 0:
                    pos = i*windowStep;
                    if fileformat == "tabular":
                        outputFile.write("%s\t%s\t%s\t%s\n" % (str(chrom), pos, str(scores[i]), str(stddev[i])))
                    else:
                        text += "%s\t%s\t%s\t%s\n" % (str(chrom), pos, str(scores[i]), str(stddev[i]));
        if fileformat == "html":
            htmlfile.writeTextToFile(text);
            print htmlfile.getLink("Result file");
            print GalaxyInterface.getHtmlEndForRuns()
        
        outputFile.close();

# 需要导入模块: from quick.application.ExternalTrackManager import ExternalTrackManager [as 别名]
# 或者: from quick.application.ExternalTrackManager.ExternalTrackManager import getPreProcessedTrackFromGalaxyTN [as 别名]
    def execute(cls, choices, galaxyFn=None, username=""):

        from quick.application.GalaxyInterface import GalaxyInterface

        fileformat = choices[6]
        outputFile = open(galaxyFn, "w")

        if fileformat == "html":
            print GalaxyInterface.getHtmlBeginForRuns(galaxyFn)
            print GalaxyInterface.getHtmlForToggles(withRunDescription=False)
            t = calendar.timegm(time.gmtime())
            htmlfile = GalaxyRunSpecificFile(["fet", str(t)], galaxyFn)

        genome = choices[0]
        track1 = choices[1].split(":")
        track2 = choices[2].split(":")
        tn1 = ExternalTrackManager.getPreProcessedTrackFromGalaxyTN(genome, track1)
        tn2 = ExternalTrackManager.getPreProcessedTrackFromGalaxyTN(genome, track2)

        windowSize = int(choices[3])
        windowStep = int(choices[4])
        percentile = float(choices[5])

        # results = {}

        # TODO: why this?
        # tr = Track(tn1)
        # tr.addFormatReq(TrackFormatReq(dense=False, allowOverlaps=True))

        outputFile.write("#seqid\tstart\tscore\tstddev\n")

        if fileformat == "html":
            text = "#seqid\tstart\tscore\tstddev\n"
        print "chrs:", str(GenomeInfo.getChrList(genome))
        reg = "*"
        bins = "*"
        analysisDef = "Dummy: dummy name ([wStep=%g] [wSize=%g] [percentile=%g])-> FisherExactScoreStat" % (
            windowStep,
            windowSize,
            percentile,
        )
        userBinSource = GalaxyInterface._getUserBinSource(reg, bins, genome)
        result = GalaxyInterface.runManual([tn1, tn2], analysisDef, reg, bins, genome, galaxyFn=galaxyFn)
        for key in result.getAllRegionKeys():
            chrom = str(key).split(":")[0]
            r = result[key]
            if "Result" not in r.keys():
                print "skipping chr:", chrom, r
                continue
            r = r["Result"]
            scores = r[0]
            stddev = r[1]
            for i in range(len(scores)):
                if scores[i] != 0:
                    pos = i * windowStep
                    # if choices[5] == "html":
                    # print "%s\t%s\t%s\t%s\n" % (str(chrom), pos, str(scores[i]), str(stddev[i]))
                    if fileformat == "tabular":
                        outputFile.write("%s\t%s\t%s\t%s\n" % (str(chrom), pos, str(scores[i]), str(stddev[i])))
                    else:
                        text += "%s\t%s\t%s\t%s\n" % (str(chrom), pos, str(scores[i]), str(stddev[i]))

        if fileformat == "html":
            htmlfile.writeTextToFile(text)
            print htmlfile.getLink("Result file")
            print GalaxyInterface.getHtmlEndForRuns()

        outputFile.close()