Python ExternalTrackManager.extractFileSuffixFromGalaxyTN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 extractFileSuffixFromGalaxyTN [as 别名]
    def createRSquareGraph(cls, ldGraphTrackName, r2_threshold):
        """
        Creates a dictionary of all pairs in a linked point track.
        Variants in LD must have rsquare >= the rsquare threshold passed to the function.

        :param ldGraphTrackName: linked point track, as chosen in tool (choices.ldtrack)
        :param r2_threshold: Lower limit of square value
        :return: Dictionary of all ld-pairs with sorted key = (rsid1, rsid2), value = rSquare
        """
        from quick.application.ExternalTrackManager import ExternalTrackManager
        from gold.origdata.GtrackGenomeElementSource import GtrackGenomeElementSource

        fileName = ExternalTrackManager.extractFnFromGalaxyTN(ldGraphTrackName)
        suffix = ExternalTrackManager.extractFileSuffixFromGalaxyTN(ldGraphTrackName)
        gtSource = GtrackGenomeElementSource(fileName, suffix=suffix)

        r2graph = {}

        for ge in gtSource:
            rsid = ge.id
            edges = ge.edges
            weights = ge.weights

            for i in range(0, len(edges)):
                ldRsid = edges[i]
                r2 = weights[i]

                if r2 >= float(r2_threshold):
                    cls.addEdge(r2graph, rsid, ldRsid, r2)

        return r2graph

# 需要导入模块: from quick.application.ExternalTrackManager import ExternalTrackManager [as 别名]
# 或者: from quick.application.ExternalTrackManager.ExternalTrackManager import extractFileSuffixFromGalaxyTN [as 别名]
 def validateAndReturnErrors(choices):
     genome = choices.genome if choices.selectGenome == 'Yes' else None
     
     if genome == '':
         return 'Please select a genome build.'
 
     error = GeneralGuiTool._checkHistoryTrack(choices, 'history', GenomeElementSource, genome)
     if error:
        return error
         
     if choices.conversion is None:
         suffix = ExternalTrackManager.extractFileSuffixFromGalaxyTN(choices.history.split(':'))
         return 'No conversions available for the selected file. Please make ' \
                'sure that the file type is correct. Current file type: %s' % suffix

# 需要导入模块: from quick.application.ExternalTrackManager import ExternalTrackManager [as 别名]
# 或者: from quick.application.ExternalTrackManager.ExternalTrackManager import extractFileSuffixFromGalaxyTN [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.gtr
     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[1] if choices[0] == 'Yes' else None
     suffix = ExternalTrackManager.extractFileSuffixFromGalaxyTN(choices[2].split(':'))
     inFn = ExternalTrackManager.extractFnFromGalaxyTN(choices[2].split(':'))
     
     try:
         standardizeGtrackFileAndWriteToFile(inFn, galaxyFn, genome, suffix=suffix)
     except Exception, e:
         import sys
         print >> sys.stderr, e

# 需要导入模块: from quick.application.ExternalTrackManager import ExternalTrackManager [as 别名]
# 或者: from quick.application.ExternalTrackManager.ExternalTrackManager import extractFileSuffixFromGalaxyTN [as 别名]
 def getRegsAndBinsSpec(choices): 
     '''
     Returns teh regSpec and binSpec for the choices made on the gui.
     '''
     regsMapper = {'Chromosome arms':'__chrArms__','Chromosomes':'__chrs__','Cytobands':'__chrBands__','Genes(Ensembl)':'__genes__','ENCODE Pilot regions':'__encode__'}
     if choices.CompareIn == 'Custom specification':
         regSpec = choices.CustomRegion
         binSpec = choices.BinSize
     elif regsMapper.get(choices.CompareIn):
         regSpec = regsMapper[choices.CompareIn]
         binSpec = choices.Bins
     else:
         histItem = choices.HistoryBins.split(':')
         binSpec = ExternalTrackManager.extractFnFromGalaxyTN(histItem)
         regSpec = ExternalTrackManager.extractFileSuffixFromGalaxyTN(histItem)
     
     return regSpec, binSpec

# 需要导入模块: from quick.application.ExternalTrackManager import ExternalTrackManager [as 别名]
# 或者: from quick.application.ExternalTrackManager.ExternalTrackManager import extractFileSuffixFromGalaxyTN [as 别名]
 def _checkHistoryTrack(prevChoices, historyChoiceIndex, geSourceCls, genome=None, filetype='', validateFirstLine=True):
     fileStr = filetype + ' file' if filetype else 'file'
     
     if type(historyChoiceIndex) == int:
         historyTrackName = prevChoices[historyChoiceIndex]
     else:
         historyTrackName = getattr(prevChoices, historyChoiceIndex)
     
     if historyTrackName is None:
         return 'Please select a ' + fileStr + ' from history.'
     
     if validateFirstLine:
         from quick.application.ExternalTrackManager import ExternalTrackManager
         galaxyTN = historyTrackName.split(':')
         suffix = ExternalTrackManager.extractFileSuffixFromGalaxyTN(galaxyTN)
         fn = ExternalTrackManager.extractFnFromGalaxyTN(galaxyTN)
         
         try:
             geSourceCls(fn , genome, suffix=suffix).parseFirstDataLine()
 
         except Exception, e:
             return fileStr.capitalize() + ' invalid: ' + str(e)

# 需要导入模块: from quick.application.ExternalTrackManager import ExternalTrackManager [as 别名]
# 或者: from quick.application.ExternalTrackManager.ExternalTrackManager import extractFileSuffixFromGalaxyTN [as 别名]
    def createPositionDict(cls, ldGraphTrackName):
        """
        Creates position dictionary from linked point track. To be used for empiric exploration of positions,
        based on LD correlation (rsquare values)
        :param ldGraphTrackName: linked point track, as chosen in tool (choices.ldtrack)
        :return: Dictionary of all nodes in track with key = rsid, value = position

        """
        from quick.application.ExternalTrackManager import ExternalTrackManager
        from gold.origdata.GtrackGenomeElementSource import GtrackGenomeElementSource

        fileName = ExternalTrackManager.extractFnFromGalaxyTN(ldGraphTrackName)
        suffix = ExternalTrackManager.extractFileSuffixFromGalaxyTN(ldGraphTrackName)
        gtSource = GtrackGenomeElementSource(fileName, suffix=suffix)

        positionDict = {}

        for ge in gtSource:
            rsid = ge.id
            position = ge.start
            cls.addPosition(positionDict, rsid, position)

        return positionDict

# 需要导入模块: from quick.application.ExternalTrackManager import ExternalTrackManager [as 别名]
# 或者: from quick.application.ExternalTrackManager.ExternalTrackManager import extractFileSuffixFromGalaxyTN [as 别名]
    def validateUserBins(choices):
        '''
        See getOptionsBox1().
        '''
        from quick.util.GenomeInfo import GenomeInfo
        genome = choices.Genome
        
        regsMapper = {'Chromosome arms':'__chrArms__','Chromosomes':'__chrs__','Cytobands':'__chrBands__','Genes(Ensembl)':'__genes__','ENCODE Pilot regions':'__encode__'}
        if choices.CompareIn == 'Custom specification':

            regSpec = choices.CustomRegion
            binSpec = choices.BinSize
            if re.match('[0-9]+[mk]?', binSpec).end() != len(binSpec):
                return 'Invalid Syntax for Bin size(only numbers and the characters "mk" allowed)'
            
        elif regsMapper.get(choices.CompareIn):
            regSpec = regsMapper[choices.CompareIn]
            binSpec = choices.Bins
        else:
            histItem = choices.HistoryBins.split(':')
            binSpec = ExternalTrackManager.extractFnFromGalaxyTN(histItem)
            regSpec = ExternalTrackManager.extractFileSuffixFromGalaxyTN(histItem)
        
        return regSpec, binSpec

# 需要导入模块: from quick.application.ExternalTrackManager import ExternalTrackManager [as 别名]
# 或者: from quick.application.ExternalTrackManager.ExternalTrackManager import extractFileSuffixFromGalaxyTN [as 别名]
 def _getGESource(choices):
     genome = choices.genome if choices.selectGenome == 'Yes' else None
     galaxyTN = choices.history.split(':')
     suffix = ExternalTrackManager.extractFileSuffixFromGalaxyTN(galaxyTN)
     fn = ExternalTrackManager.extractFnFromGalaxyTN(galaxyTN)
     return GenomeElementSource(fn, genome=genome, printWarnings=False, suffix=suffix)