Python GenomeInfo.getPropertyTrackName方法代码示例

# 需要导入模块: from quick.util.GenomeInfo import GenomeInfo [as 别名]
# 或者: from quick.util.GenomeInfo.GenomeInfo import getPropertyTrackName [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 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.
     '''
     genome = choices[0]
     nmer = choices[1].lower()
     regSpec = choices[2]
     binSpec = '*'
     trackName = GenomeInfo.getPropertyTrackName(genome, 'nmer') + [str(len(nmer))+'-mers',nmer]
     assert galaxyFn is not None
     GalaxyInterface.extractTrackManyBins(genome, trackName, regSpec, binSpec, True, 'point bed', False, False, galaxyFn)

# 需要导入模块: from quick.util.GenomeInfo import GenomeInfo [as 别名]
# 或者: from quick.util.GenomeInfo.GenomeInfo import getPropertyTrackName [as 别名]
    def yielder(self, curTn):
        if self._avoidLiterature and curTn == GenomeInfo.getPropertyTrackName(self._genome, 'literature'):
            return
        
        for subtype in ProcTrackOptions.getSubtypes(self._genome, curTn, self._fullAccess):
            #if self._avoidLiterature and subtype == 'Literature':
            
            if subtype[0] in ['.','_']:
                continue

            newTn = curTn + [subtype]

            doBreak = False
            for subTn in self.yielder(newTn):
                yield subTn

        if ProcTrackOptions.isValidTrack(self._genome, curTn, self._fullAccess):
            yield curTn

# 需要导入模块: from quick.util.GenomeInfo import GenomeInfo [as 别名]
# 或者: from quick.util.GenomeInfo.GenomeInfo import getPropertyTrackName [as 别名]
    def execute(cls, 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 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.
        '''
        genome = choices[0]
        nmer = choices[1].lower()
        regSpec = choices[2]
        analysisRegions = parseRegSpec(regSpec, genome)
        
        binSize = cls._calcBinSize(nmer, analysisRegions)
        binSpec = '*' if binSize is None else str( binSize ) 
        numBins = len( AutoBinner(analysisRegions, binSize) )
        
        from quick.application.GalaxyInterface import GalaxyInterface
        from quick.util.GenomeInfo import GenomeInfo
        trackName1 = GenomeInfo.getPropertyTrackName(genome, 'nmer') + [str(len(nmer))+'-mers',nmer]
        trackName2 = ['']
        analysisDef = 'Counts: The number of track1-points -> CountPointStat'
        #regSpec = '*'
        #print 'Using binSize: ',binSpec
        #print 'TN1: ',trackName1
        from gold.result.HtmlCore import HtmlCore
        print str(HtmlCore().styleInfoBegin(styleClass='debug'))
        GalaxyInterface.run(trackName1, trackName2, analysisDef, regSpec, binSpec, genome, galaxyFn)
        print str(HtmlCore().styleInfoEnd())

        plotFileNamer = GalaxyRunSpecificFile(['0','CountPointStat_Result_gwplot.pdf'], galaxyFn)
        textualDataFileNamer = GalaxyRunSpecificFile(['0','CountPointStat_Result.bedgraph'], galaxyFn)
        
        core = HtmlCore()
        core.paragraph('Inspect nmer frequency variation as a %s or as underlying %s.</p>' % ( plotFileNamer.getLink('plot'), textualDataFileNamer.getLink('textual data') ))
        core.divider()
        core.paragraph('The occurrence frequency of your specified nmer ("%s") has been computed along the genome, within your specified analysis region ("%s").' % (nmer, regSpec))
        core.paragraph('The analysis region was divided into %i bins, based on calculations trying to find appropriate bin size (get enough data per bin and restrict maximum number of bins).' % numBins)
        
        trackName1modified = trackName1[0:-2] + trackName1[-1:]
        preSelectedAnalysisUrl = createHyperBrowserURL(genome, trackName1modified,[''], analysis='Counts',method='auto',region=regSpec, binsize=binSpec)
        core.divider()
        core.paragraph('If you do not find the inferred bin size to be appropriate, you can set this manually in a ' + str(HtmlCore().link('new analysis', preSelectedAnalysisUrl)) + '.')
        print str(core)

# 需要导入模块: from quick.util.GenomeInfo import GenomeInfo [as 别名]
# 或者: from quick.util.GenomeInfo.GenomeInfo import getPropertyTrackName [as 别名]
 def _isLiteratureTrack(genome, trackName):
     return ':'.join(trackName).startswith( ':'.join(GenomeInfo.getPropertyTrackName(genome, 'literature')) )

# 需要导入模块: from quick.util.GenomeInfo import GenomeInfo [as 别名]
# 或者: from quick.util.GenomeInfo.GenomeInfo import getPropertyTrackName [as 别名]
 def __init__(self, userBinSource, genome, **kwArgs):
     track = PlainTrack(GenomeInfo.getPropertyTrackName(genome, 'gaps'))
     StatJob.__init__(self, userBinSource, track, None, AssemblyGapCoverageStat, **kwArgs)