Python ExternalTrackManager.extractNameFromHistoryTN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 extractNameFromHistoryTN [as 别名]
    def execute(choices, galaxyFn=None, username=''):
        '''Is called when execute-button is pushed by web-user.
        Should print output as HTML to standard out, which will be directed to a results page in Galaxy history.
        If getOutputFormat is anything else than HTML, the output should be written to the file with path galaxyFn.
        If needed, StaticFile can be used to get a path where additional files can be put (e.g. generated image files).
        choices is a list of selections made by web-user in each options box.
        '''
        from time import time
        startTime = time()
        from quick.application.ExternalTrackManager import ExternalTrackManager
        from quick.util.StaticFile import GalaxyRunSpecificFile
        import os

        motifFn = ExternalTrackManager.extractFnFromGalaxyTN( choices[0].split(':'))
        observedFasta = ExternalTrackManager.extractFnFromGalaxyTN( choices[1].split(':'))

        randomGalaxyTN = choices[2].split(':')
        randomName = ExternalTrackManager.extractNameFromHistoryTN(randomGalaxyTN)
        randomGalaxyFn = ExternalTrackManager.extractFnFromGalaxyTN( randomGalaxyTN)
        randomStatic = GalaxyRunSpecificFile(['random'],randomGalaxyFn) #finds path to static file created for a previous history element (randomFn), and directs to a folder containing several files..
        #print os.listdir(randomStatic.getDiskPath())
        randomFastaPath = randomStatic.getDiskPath()

        #motifFn, observedFasta, randomFastaPath = '/Users/sandve/egne_dokumenter/_faglig/NullModels/DnaSeqExample/liver.pwm', 'liver.fa', 'randomFastas'
        testStatistic = choices[3]
        if testStatistic == 'Average of max score per sequence':
            scoreFunc = scoreMotifOnFastaAsAvgOfBestScores
        elif testStatistic == 'Sum of scores across all positions of all sequences':
            scoreFunc = scoreMotifOnFastaAsSumOfAllScores
        elif testStatistic == 'Score of Frith et al. (2004)':
            scoreFunc = lr4
        elif testStatistic == 'Product of max per sequence':
            scoreFunc = scoreMotifOnFastaAsProductOfBestScores
        else:
            raise
        
        pvals = mcPvalFromMotifAndFastas(motifFn, observedFasta, randomFastaPath, scoreFunc)
        print 'Pvals for motifs (%s) against observed (%s) vs random (%s - %s) sequences.' % (motifFn, observedFasta, randomName, randomFastaPath)
        for motif,pval in sorted(pvals.items()):
            print motif+'\t'+('%.4f'%pval)
            
        from quick.util.StaticFile import GalaxyRunSpecificFile
        from gold.application.RSetup import r, robjects
        histStaticFile = GalaxyRunSpecificFile(['pvalHist.png'],galaxyFn)
        #histStaticFile.openRFigure()
        histStaticFile.plotRHist(pvals.values(), [x/40.0 for x in range(41)], 'Histogram of p-values', xlim=robjects.FloatVector([0.0, 1.0]))
        #r.hist(robjects.FloatVector(pvals.values()), breaks=robjects.FloatVector([x/40.0 for x in range(41)]), xlim=robjects.FloatVector([0.0, 1.0]), main='Histogram of p-values' )
        #histStaticFile.closeRFigure()
        print histStaticFile.getLink('Histogram')
        print 'Time (s):', time()-startTime

# 需要导入模块: from quick.application.ExternalTrackManager import ExternalTrackManager [as 别名]
# 或者: from quick.application.ExternalTrackManager.ExternalTrackManager import extractNameFromHistoryTN [as 别名]
    def _getResultsLists(histChoices):
        if len([x for x in histChoices.values() if x!=None])==0:
            return [],[]
        #print 'histChoices',histChoices
        #return []

        galaxyTNs = [x.split(':') for x in histChoices.values() if x!=None]
                
        galaxyFns = [ExternalTrackManager.extractFnFromGalaxyTN(tn) for tn in galaxyTNs]
        historyNames= [ExternalTrackManager.extractNameFromHistoryTN(tn) for tn in galaxyTNs]
        staticFiles = [GalaxyRunSpecificFile(['results.pickle'], gfn) for gfn in galaxyFns]
        fileSpecificFile = [GalaxyRunSpecificFile([], gfn) for gfn in galaxyFns]
        print 'Using pickles: ', [x.getDiskPath() for x in staticFiles]
        
        paths = [x.getDiskPath()+'/0' for x in fileSpecificFile]
        pngList = [[v for v in x[2] if v.find('.png')>0] for x in os.walk(paths[0])]
        
        resultsLists = [load(sf.getFile('r')) for sf in staticFiles]
        return resultsLists, historyNames

# 需要导入模块: from quick.application.ExternalTrackManager import ExternalTrackManager [as 别名]
# 或者: from quick.application.ExternalTrackManager.ExternalTrackManager import extractNameFromHistoryTN [as 别名]
    def getRunDescription(trackName1, trackName2, trackNameIntensity, analysisDef, ubSource, revEngBatchLine, \
                          urlForTrackAutoSelection, manualSeed, **kwArgs):
        genome = ubSource.genome
        core = HtmlCore()

        analysis = Analysis(analysisDef, genome, trackName1, trackName2, **kwArgs)
        
        core.header('GENOME')
        core.append(GenomeInfo(genome).mainInfo(printEmpty=False))
        core.divider()
                
        formatChoices = analysis.getFormatConverterChoicesAsText().items()
        tr1FormatChoice, tr2FormatChoice = formatChoices if len(formatChoices) == 2 else (None, None) 
        
        first = True
        for tn,label,formatChoice in zip([trackName1,trackName2,trackNameIntensity], \
                                         ['TRACK 1','TRACK 2','INTENSITY TRACK'], \
                                         [tr1FormatChoice,tr2FormatChoice,None]):
            if tn in [None, []]:
                continue
            
            if not first:
                core.divider()

            core.header(label)
            trackInfo = TrackInfo(genome, tn)
            trackText = ''
            if ExternalTrackManager.isHistoryTrack(tn):
                assert len(tn)>=4, 'Length of external track name < 4: %s' % str(tn)
                core.descriptionLine('Name', ExternalTrackManager.extractNameFromHistoryTN(tn) + ' (from history)' + os.linesep)
            else:
                core.descriptionLine('Name', ':'.join(tn) + os.linesep)
            core.append(trackInfo.mainInfo(printEmpty=False))

            if formatChoice is not None:
                core.descriptionLine('Treated as', formatChoice[1])
            
            first = False
        
        core.divider()
        core.header('ANALYSIS')
        core.paragraph( ''.join(str(analysis).split(':')[1:]) )

        first = True
        for label,choice in analysis.getInterfaceChoicesAsText().items():
            if first:
                core.divider()
                core.header('OPTIONS')
            
            if manualSeed is not None and label == 'Random seed' and choice == 'Random':
                choice = str(manualSeed)
                
            core.descriptionLine(label, choice)
            first = False
            
        h0 = analysis.getH0()
        if h0 is not None:
            core.divider()
            core.header('NULL HYPOTHESIS')
            core.paragraph(h0)
            
        h1 = analysis.getH1()
        if h1 is not None:
            core.divider()
            core.header('ALTERNATIVE HYPOTHESIS')
            core.paragraph(h1)
            
        core.divider()
        core.header('ANALYSIS REGIONS')
        if hasattr(ubSource, 'description'):
            core.paragraph(ubSource.description)
            
        core.divider()
        core.header('SOLUTION')

        statClass = analysis.getStat()
        #One alternative is to put getDescription in MagicStatFactory-hierarchy as class-method, and get real class behind partial-object.
        #if isinstance(statClass, functools.partial):
            #statClass = statClass.func
        #core.paragraph( statClass.getDescription() )

        #Chosen alternative is to Instantiate an object, which will automatically give object of real class..
        #and then use the following two lines, which will get class in Statistic-hierarchy instead of MagicStatFactory-hierarchy ..
        try:
            reg = ubSource.__iter__().next()
        except:
            core.paragraph('Solution not relevant, as there are no specified analysis regions..')
        else:
            track1, track2 = analysis.getTracks()
            if statClass is None:
                core.paragraph('Solution not available, due to currently invalid analysis')
                logMessage('Solution not available, with params: ' + str([trackName1, trackName2, analysisDef]), level=logging.WARN )
            else:
                statObj = statClass(reg,track1, track2)
                statDescr = statObj.getDescription()
                replPat = '<a href=' + os.sep.join([STATIC_REL_PATH,'notes','stats','']) + r'\1>note</a>'
                statDescr = re.sub('<note>(.*)</note>', replPat, statDescr)
        
                core.paragraph( statDescr )

#.........这里部分代码省略.........