Python ExternalTrackManager.extractFnFromGalaxyTN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 extractFnFromGalaxyTN [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.
     '''
     outputFile=open(galaxyFn,"w")
     fnSource = ExternalTrackManager.extractFnFromGalaxyTN(choices[0].split(':'))
     inputFile = open(ExternalTrackManager.extractFnFromGalaxyTN(choices[0].split(':')), 'r')
     
     if choices[2] == 'Filter on exact values':    
         if choices[3]!='Select column..':
             column = int(choices[3][7:])
             filterSet = set([key for key,val in choices[4].items() if val])
             for i in inputFile:
                 if i.split('\t')[column] in filterSet:
                     print>>outputFile, i
             
     else:
         for i in inputFile:
             temptab = i.split('\t')
             for index in range(len(temptab)):
                 locals()['c'+str(index)] = temptab[index]
             if eval(choices[5]):
                 print>>outputFile, i
                 
     inputFile.close()
     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 extractFnFromGalaxyTN [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.
        '''
        resultLines = []

        outputFile=open(galaxyFn,"w")
        fnSource = ExternalTrackManager.extractFnFromGalaxyTN(choices[2].split(':'))
        fnDB = ExternalTrackManager.extractFnFromGalaxyTN(choices[3].split(':'))
        intersectingFactor = 'id' if choices[4] == 'Element id' else 'position'
        
        colsToAdd = []
        colsToAddDict = choices[5]
        for key in colsToAddDict:
            if colsToAddDict[key]:
                colsToAdd.append(key)

        genome = choices[1] if choices[0] == 'Yes' else None
        
        try:
            complementGtrackFileAndWriteToFile(fnSource, fnDB, galaxyFn, intersectingFactor, colsToAdd, genome)
        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 extractFnFromGalaxyTN [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.
        '''
        # get population format
        if choices.format == 'File':
            pop = [];
            popfile = choices.population;
            inFn = ExternalTrackManager.extractFnFromGalaxyTN(popfile.split(":"));
            infile = open(inFn);
            for line in infile:
                pop.append(line.rstrip('\n'));
        else:
            pop = map(str.strip,choices.population.split(","));

        # read in file
        inFn = ExternalTrackManager.extractFnFromGalaxyTN(choices.vcf.split(":"));
        data = open(inFn).read();

        # convert and write to GTrack file
        outfile = open(galaxyFn, 'w');
        outfile.write(addHeader(choices.genome));
        outfile.write(convertToGtrackFile(data, pop, choices.genome));
        outfile.close();

# 需要导入模块: from quick.application.ExternalTrackManager import ExternalTrackManager [as 别名]
# 或者: from quick.application.ExternalTrackManager.ExternalTrackManager import extractFnFromGalaxyTN [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 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.
     '''
     
     try:
         historyInputTN = choices[0].split(':') #from history
         historyGalaxyFn = ExternalTrackManager.extractFnFromGalaxyTN( historyInputTN) #same as galaxyFn in execute of create benchmark..
         randomStatic = RunSpecificPickleFile(historyGalaxyFn) #finds path to static file created for a previous history element, and directs to a pickle file
         myInfo = randomStatic.loadPickledObject()
     except:
         return None
     
     galaxyTN = myInfo[3].split(':')
     myFileName = ExternalTrackManager.extractFnFromGalaxyTN(galaxyTN)
     genome = myInfo[0]
     
     gtrackSource = GtrackGenomeElementSource(myFileName, genome)
     regionList = []
     
     for obj in gtrackSource:
         regionList.append(GenomeRegion(obj.genome, obj.chr, obj.start, obj.end))
     
     extractor = TrackExtractor()
             
     fn = extractor.extract(GenomeInfo.getSequenceTrackName(genome), regionList, galaxyFn, 'fasta')

# 需要导入模块: from quick.application.ExternalTrackManager import ExternalTrackManager [as 别名]
# 或者: from quick.application.ExternalTrackManager.ExternalTrackManager import extractFnFromGalaxyTN [as 别名]
 def getOptionsBox6(prevChoices):
     if prevChoices[3]:
         extraDbColumnsDict = OrderedDict()
         fnSource = ExternalTrackManager.extractFnFromGalaxyTN(prevChoices[2].split(':'))
         fnDB = ExternalTrackManager.extractFnFromGalaxyTN(prevChoices[3].split(':'))
         
         gtrackDB = GtrackGenomeElementSource(fnDB)
         gtrackSource = GtrackGenomeElementSource(fnSource)
         
         extraDbColumns = [v for v in gtrackDB.getColumns() if not v in gtrackSource.getColumns()] #list(set(gtrackDBColumnSpec) - set(gtrackSourceColumnSpec))
         for column in extraDbColumns:
             extraDbColumnsDict[column] = False
         return extraDbColumnsDict

# 需要导入模块: from quick.application.ExternalTrackManager import ExternalTrackManager [as 别名]
# 或者: from quick.application.ExternalTrackManager.ExternalTrackManager import extractFnFromGalaxyTN [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 extractFnFromGalaxyTN [as 别名]
    def execute(choices, galaxyFn=None, username=''):
        #'Genome:','Source of seed TF:','Seed TF: ','Flank size: ', 'Source of potentially cooperative TFs:'
        #genome
        genome = choices[0]
        seedSource = choices[1]
        seedTfTnInput = choices[2]
        if seedSource == 'TFBS from history':
            seedFn = ExternalTrackManager.extractFnFromGalaxyTN(seedTfTnInput.split(':'))
        else:
            tfTrackNameMappings = TfInfo.getTfTrackNameMappings(genome)
            seedTfTn = tfTrackNameMappings[seedSource] + [seedTfTnInput]
            #tfTrackName = tfTrackNameMappings[tfSource] + [selectedTF]
            seedFns = getOrigFns(genome, seedTfTn, '')
            assert len(seedFns) == 1
            seedFn = seedFns[0]
            
        flankSize = choices[3]
        flankSize = int(flankSize) if flankSize != '' else 0
        cooperativeTfSource = choices[4]
        #flankSize = int(choices[4])
        #TFsFromGenes.findOverrepresentedTFsFromGeneSet('hg18', 'UCSC tfbs conserved', ['ENSGflankSizeflankSizeflankSizeflankSizeflankSize2flankSize8234','ENSGflankSizeflankSizeflankSizeflankSizeflankSize199674'],flankSize, flankSize, galaxyFn)
        #TFsFromGenes.findOverrepresentedTFsFromGeneSet('hg18', tfSource, choices[5].split(','),flankSize, flankSize, 'Ensembl', galaxyFn)
        
        #TFsFromRegions.findOverrepresentedTFsFromGeneSet(genome, tfSource, ensembleGeneIdList,upFlankSize, downFlankSize, geneSource, galaxyFn)
        
        #TFsFromGenes.findTFsTargetingGenes('hg18', tfSource, choices[5].split(','),flankSize, flankSize, 'Ensembl', galaxyFn)

        TFsFromRegions.findTFsOccurringInRegions(genome, cooperativeTfSource, seedFn, flankSize, flankSize, galaxyFn)

# 需要导入模块: from quick.application.ExternalTrackManager import ExternalTrackManager [as 别名]
# 或者: from quick.application.ExternalTrackManager.ExternalTrackManager import extractFnFromGalaxyTN [as 别名]
 def _getHeaders(prevChoices):
     numCols = TabularToGtrackTool._getFileContentsInfo(prevChoices).numCols
     if prevChoices.columnSelection == 'Select individual columns':
         header = []
         for i in xrange(numCols):
             if hasattr(prevChoices, 'column%s' % i):
                 colHeader = getattr(prevChoices, 'column%s' % i)
                 if colHeader is None or colHeader == '-- ignore --':
                     header.append('')
                 elif colHeader == '-- custom --':
                     header.append(getattr(prevChoices, 'customColumn%s' % i).strip())
                 else:
                     header.append(colHeader)
             else:
                 header.append('')
         return header
     else:
         genome = prevChoices.genome if prevChoices.selectGenome == 'Yes' else None
         inFn = ExternalTrackManager.extractFnFromGalaxyTN(prevChoices.colSpecFile.split(':'))
         try:
             geSource = GtrackGenomeElementSource(inFn, genome=genome)
             geSource.parseFirstDataLine()
             return geSource.getColumns()[:numCols]
         except Exception, e:
             return []

# 需要导入模块: from quick.application.ExternalTrackManager import ExternalTrackManager [as 别名]
# 或者: from quick.application.ExternalTrackManager.ExternalTrackManager import extractFnFromGalaxyTN [as 别名]
    def getOptionsBoxFileContentsInfo(prevChoices):
        if prevChoices.history or prevChoices.input:
            if prevChoices.history:
                inputFile = open(ExternalTrackManager.extractFnFromGalaxyTN(prevChoices.history.split(':')), 'r')
            else:
                inputFile = StringIO(prevChoices.input)
            
            for i in xrange(TabularToGtrackTool._getNumSkipLines(prevChoices)):
                inputFile.readline()
            
            table = []
            splitChar = TabularToGtrackTool._getSplitChar(prevChoices)
            numCols = None
            error = None
            for i,line in enumerate(inputFile):
                row = [x.strip() for x in line.strip().split(splitChar)]
                if numCols == None:
                    numCols = len(row)
                elif numCols != len(row):
                    numCols = max(numCols, len(row))
#                    error = 'Error: the number of columns varies over the rows of the tabular file.'
                    
                table.append(row)
                if i == TabularToGtrackTool.NUM_ROWS_IN_TABLE:
                    break
            
            numCols = max(len(row) for row in table) if len(table) > 0 else 0
            
            if error is None:
                if numCols > TabularToGtrackTool.NUM_COLUMN_FUNCTIONS:
                    error = 'Error: the tabular file has more columns than is allowed by the tool (%s > %s).' % (numCols, TabularToGtrackTool.NUM_COLUMN_FUNCTIONS)
                
            return ('__hidden__', FileContentsInfo(table=table, numCols=numCols, error=error))

# 需要导入模块: from quick.application.ExternalTrackManager import ExternalTrackManager [as 别名]
# 或者: from quick.application.ExternalTrackManager.ExternalTrackManager import extractFnFromGalaxyTN [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.genome if choices.selectGenome == 'Yes' else None
     onlyNonDefault = choices.allHeaders == 'Only non-default headers'
     
     
     try:
         if choices.history:
             inFn = ExternalTrackManager.extractFnFromGalaxyTN(choices.history.split(':'))
             expandHeadersOfGtrackFileAndWriteToFile(inFn, galaxyFn, genome, onlyNonDefault)
         else:
             if choices.whitespace == 'Keep whitespace exact':
                 input = choices.input
             else:
                 input = ''
                 for line in choices.input.split(os.linesep):
                     line = line.strip()
                     if (line.startswith('###') and len(line) > 3 and line[3] != '#') \
                         or not line.startswith('#'):
                         line = line.replace(' ', '\t')
                     else:
                         line = line.replace('\t', ' ')
                     input += line + os.linesep
         
             composer = expandHeadersOfGtrackFileAndReturnComposer('', genome, strToUseInsteadOfFn=input)
             composer.composeToFile(galaxyFn, onlyNonDefault=onlyNonDefault)
     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 extractFnFromGalaxyTN [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.
     '''
     
     # Retrieve the pickled benchmark object from history
     try:
         historyInputTN = choices[0].split(':')
         #same as galaxyFn in execute of create benchmark..
         historyGalaxyFn = ExternalTrackManager.extractFnFromGalaxyTN(historyInputTN) 
         #finds path to static file created for a previous history element, and directs to a pickle file
         randomStatic = RunSpecificPickleFile(historyGalaxyFn) 
         benchmarkSpecification = randomStatic.loadPickledObject()
     except:
         return None
     
     genome = benchmarkSpecification[0]
     benchmarkLevel = benchmarkSpecification[2]
     regionTrackName = benchmarkSpecification[3]
     benchmarkUtil = BenchmarkUtil(galaxyFn, genome)
     
     if benchmarkLevel == 'Base pair probability level':
         return benchmarkUtil.retrieveFeatureTrack(genome, galaxyFn, regionTrackName, benchmarkSpecification[5])
     elif type(regionTrackName) is str: # If string, we're dealing with a single track so just retrieve it
         return benchmarkUtil.retrieveTrack(regionTrackName, galaxyFn)
     elif type(regionTrackName) is list: # If list, we're dealing with a benchmark suite which will have to be zipped
         print benchmarkUtil.retrieveBenchmarkSuiteAsZipFile(regionTrackName)
     else:
         raise Exception('Invalid benchmark')

# 需要导入模块: from quick.application.ExternalTrackManager import ExternalTrackManager [as 别名]
# 或者: from quick.application.ExternalTrackManager.ExternalTrackManager import extractFnFromGalaxyTN [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 extractFnFromGalaxyTN [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.
     '''
     print 'Executing...'
     
     tempinfofile=ExternalTrackManager.extractFnFromGalaxyTN(choices[0].split(":"))
     abbrv=GenomeImporter.getGenomeAbbrv(tempinfofile)
     gi = GenomeInfo(abbrv)
     chrNamesInFasta=gi.sourceChrNames
     
     chromNamesDict={}
     chrDict = InstallGenomeTool._getRenamedChrDictWithSelection(choices)
         
     for i, key in enumerate(chrDict.keys()):
         if chrDict[key]:
             chromNamesDict[chrNamesInFasta[i]]=key
     print 'All chromosomes chosen: ' + str(chromNamesDict)
         
     stdChrDict = InstallGenomeTool._getRenamedChrDictWithSelection(choices, stdChrs=True)
     stdChrs = [x for x in stdChrDict if stdChrDict[x]]
     print 'Standard chromosomes chosen: ' + ", ".join(stdChrs)
     
     GenomeImporter.createGenome(abbrv, gi.fullName, chromNamesDict, stdChrs, username=username)
     
     gi.installedBy = username
     gi.timeOfInstallation = datetime.now()
     gi.store()

# 需要导入模块: from quick.application.ExternalTrackManager import ExternalTrackManager [as 别名]
# 或者: from quick.application.ExternalTrackManager.ExternalTrackManager import extractFnFromGalaxyTN [as 别名]
 def _getTempChromosomeNames(galaxyTn):
     if isinstance(galaxyTn, str):
         galaxyTn = galaxyTn.split(":")
     tempinfofile=ExternalTrackManager.extractFnFromGalaxyTN(galaxyTn)
     abbrv=GenomeImporter.getGenomeAbbrv(tempinfofile)
     
     return os.linesep.join(GenomeInfo(abbrv).sourceChrNames)

# 需要导入模块: from quick.application.ExternalTrackManager import ExternalTrackManager [as 别名]
# 或者: from quick.application.ExternalTrackManager.ExternalTrackManager import extractFnFromGalaxyTN [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.
        '''
        fnSource = ExternalTrackManager.extractFnFromGalaxyTN(choices[2].split(':'))
        
        core = HtmlCore()
        core.begin()
        
        valid = False
        try:
            core.header('Validating GTrack headers')
            core.styleInfoBegin(styleClass='debug')

            print str(core)
            core = HtmlCore()

            gtrackSource = GtrackGenomeElementSource(fnSource, choices[1] if choices[0]=='Yes' else None, printWarnings=True)
            
            core.append('Done')
            core.styleInfoEnd()
            core.header('Validating complete GTrack file')
            core.styleInfoBegin(styleClass='debug')
            
            print str(core)
            core = HtmlCore()
            
            try:
                for ge in gtrackSource:
                    pass
            except Exception, e:
                pass
            else: