Python GenomeInfo.getStdGeneRegsTn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 getStdGeneRegsTn [as 别名]
    def findOverrepresentedTFsFromGeneSet(genome, tfSource, ensembleGeneIdList,upFlankSize, downFlankSize, geneSource, galaxyFn):
        #galaxyFn = '/usit/insilico/web/lookalike/galaxy_dist-20090924-dev/database/files/003/dataset_3347.dat'
        #print 'overriding galaxyFN!: ', galaxyFn
        galaxyId = extractIdFromGalaxyFn(galaxyFn)
        uniqueWebPath = getUniqueWebPath(extractIdFromGalaxyFn(galaxyFn))

        assert genome == 'hg18'
        
        tfTrackNameMappings = TfInfo.getTfTrackNameMappings(genome)
        tfTrackName = tfTrackNameMappings[tfSource]
        
        
        #Get gene track
        assert geneSource == 'Ensembl'
        targetGeneRegsTempFn = uniqueWebPath + os.sep + 'geneRegs.bed'
        geneRegsTrackName = GenomeInfo.getStdGeneRegsTn(genome)
        geneRegsFn = getOrigFn(genome, geneRegsTrackName, '.category.bed')
        GalaxyInterface.getGeneTrackFromGeneList(genome, geneRegsTrackName, ensembleGeneIdList, targetGeneRegsTempFn )
        
        assert upFlankSize == downFlankSize == 0 #Should instead extend regions to include flanks
        
        tcGeneRegsTempFn = uniqueWebPath + os.sep + 'tcGeneRegs.targetcontrol.bedgraph'
        #Think this will be okay, subtraction not necessary as targets are put first:
        controlGeneRegsTempFn = geneRegsFn
        #print targetGeneRegsTempFn, controlGeneRegsTempFn, tcGeneRegsTempFn
        GalaxyInterface.combineToTargetControl(targetGeneRegsTempFn, controlGeneRegsTempFn, tcGeneRegsTempFn)
        
        #tcGeneRegsExternalTN = ['external'] +galaxyId +  [tcGeneRegsTempFn]
        tcGeneRegsExternalTN = ExternalTrackManager.createStdTrackName(galaxyId, 'tempTc')
        
        #tcGeneRegsExternalTN = ['external'] +targetGalaxyId +  [tcGeneRegsTempFn]
        #tcGeneRegsExternalTN = ['galaxy', externalId, tcGeneRegsTempFn]
        
        targetGeneRegsExternalTN = ExternalTrackManager.createStdTrackName(galaxyId, 'tempTc', '1')
        controlGeneRegsExternalTN = ExternalTrackManager.createStdTrackName(galaxyId, 'tempTc', '0')
        
        #pre-process
        print 'Pre-processing file: %s, with trackname: %s ' % (tcGeneRegsTempFn, tcGeneRegsExternalTN)
        ExternalTrackManager.preProcess(tcGeneRegsTempFn, tcGeneRegsExternalTN, 'targetcontrol.bedgraph',genome)
        print 'Pre-processing TN: ', targetGeneRegsExternalTN
        ExternalTrackManager.preProcess(targetGeneRegsTempFn, targetGeneRegsExternalTN, 'bed',genome)
        print 'Pre-processing TN: ', controlGeneRegsExternalTN
        ExternalTrackManager.preProcess(controlGeneRegsTempFn, controlGeneRegsExternalTN, 'bed',genome)
        
        #print tcGeneRegsExternalTN
        trackName1, trackName2 = tfTrackName, tcGeneRegsExternalTN
        
        analysisDef = 'Categories differentially located in targets?: Which categories of track1-points fall more inside case than control track2-segments? [rawStatistic:=PointCountInsideSegsStat:]' +\
                  '[tf1:=SegmentToStartPointFormatConverter:] [tf2:=TrivialFormatConverter:]' +\
                  '-> DivergentRowsInCategoryMatrixStat'
        regSpec, binSpec = '*','*'
        
        #print 'skipping preproc!!'
        #ExternalTrackManager.preProcess(tcGeneRegsExternalTN[-1], tcGeneRegsExternalTN, 'targetcontrol.bedgraph', genome)
        #ExternalTrackManager.preProcess(targetGeneRegsTempFn, targetGeneRegsExternalTN, 'bed', genome)
        
        GalaxyInterface.runManual([trackName1, trackName2], analysisDef, regSpec, binSpec, genome, printResults=True, printHtmlWarningMsgs=False)

# 需要导入模块: from quick.util.GenomeInfo import GenomeInfo [as 别名]
# 或者: from quick.util.GenomeInfo.GenomeInfo import getStdGeneRegsTn [as 别名]
 def validateAndReturnErrors(choices):
     '''
     Should validate the selected input parameters. If the parameters are not valid,
     an error text explaining the problem should be returned. The GUI then shows this text
     to the user (if not empty) and greys out the execute button (also if the text isempty).
     If all parameters are valid, the method should return None, which enables the execute button.
     '''
     genome, tn, tf = ExtractIntersectingGenesTool._getBasicTrackFormat(choices)
     geneRegsTrackName = GenomeInfo.getStdGeneRegsTn(genome)
     
     if not ExtractIntersectingGenesTool._isValidTrack(choices):
         return ""
         return "The selected track (%s) is not valid." % ':'.join(tn)        
     
     if tf.split()[-1] not in ['points', 'segments']:
         return "The track format of the selected track must be either points or segments. Currently: %s" % tf
     
     if not ProcTrackOptions.isValidTrack(genome, geneRegsTrackName, True):
         return "The track used for gene ids (%s) is not valid. This is an internal error." % ':'.join(geneRegsTrackName)        

# 需要导入模块: from quick.util.GenomeInfo import GenomeInfo [as 别名]
# 或者: from quick.util.GenomeInfo.GenomeInfo import getStdGeneRegsTn [as 别名]
 def __init__(self, genome, geneSource, queryTrack, galaxyFn):
     assert geneSource == 'Ensembl'
     geneRegsTrackName = GenomeInfo.getStdGeneRegsTn(genome)
     geneRegsTrackFn = getOrigFn(genome, geneRegsTrackName, '.category.bed')
     TrackIntersection.__init__(self, genome, geneRegsTrackFn, queryTrack, galaxyFn)
     pass

# 需要导入模块: from quick.util.GenomeInfo import GenomeInfo [as 别名]
# 或者: from quick.util.GenomeInfo.GenomeInfo import getStdGeneRegsTn [as 别名]
    def findTFsTargetingGenes(cls, genome, tfSource, ensembleGeneIdList,upFlankSize, downFlankSize, geneSource, galaxyFn):
        #galaxyFn = '/usit/insilico/web/lookalike/galaxy_dist-20090924-dev/database/files/003/dataset_3347.dat'
        #print 'overriding galaxyFN!: ', galaxyFn
        uniqueWebPath = getUniqueWebPath(extractIdFromGalaxyFn(galaxyFn))

        assert genome in ['mm9','hg18'] #other genomes not supported. TF id links do not specify genome for pre-selection of analysis
        
        #if tfSource == 'UCSC tfbs conserved':
        #    tfTrackName = ['Gene regulation','TFBS','UCSC prediction track']
        #else:
        #    raise
        tfTrackNameMappings = TfInfo.getTfTrackNameMappings(genome)
        tfTrackName = tfTrackNameMappings[tfSource]
                
        #Get gene track
        #targetGeneRegsTempFn = uniqueWebPath + os.sep + 'geneRegs.bed'
        #geneRegsTrackName = GenomeInfo.getStdGeneRegsTn(genome)
        #geneRegsFn = getOrigFn(genome, geneRegsTrackName, '.category.bed')
        #GalaxyInterface.getGeneTrackFromGeneList(genome, geneRegsTrackName, ensembleGeneIdList, targetGeneRegsTempFn )
        
        if not (upFlankSize == downFlankSize == 0):            
            unflankedGeneRegsTempFn = uniqueWebPath + os.sep + '_geneRegs.bed'
            flankedGeneRegsTempFn  = uniqueWebPath + os.sep + 'flankedGeneRegs.bed'
            geneRegsTrackName = GenomeInfo.getStdGeneRegsTn(genome)
            #geneRegsFn = getOrigFn(genome, geneRegsTrackName, '.category.bed')
            GalaxyInterface.getGeneTrackFromGeneList(genome, geneRegsTrackName, ensembleGeneIdList, unflankedGeneRegsTempFn )
            GalaxyInterface.expandBedSegments(unflankedGeneRegsTempFn, flankedGeneRegsTempFn, genome, upFlankSize, downFlankSize)
            #flankedGeneRegsExternalTN = ['external'] +galaxyId +  [flankedGeneRegsTempFn]
            regSpec, binSpec = 'file', flankedGeneRegsTempFn
        else:
            regSpec, binSpec = '__genes__', ','.join(ensembleGeneIdList)

        res = cls._runCategoryPointCount(genome, regSpec, binSpec, tfTrackName)

        #trackName1 = tfTrackName
        #
        #analysisDef = 'Category point count: Number of elements each category of track1 (with overlaps)'+\
        #          '[tf1:=SegmentToStartPointFormatConverter:]'+\
        #          '-> FreqByCatStat'
        ##assert len(ensembleGeneIdList)==1
        ##geneId = ensembleGeneIdList[0]
        #
        #print '<div class="debug">'        
        #userBinSource, fullRunArgs = GalaxyInterface._prepareRun(trackName1, None, analysisDef, regSpec, binSpec, genome)
        #res = AnalysisDefJob(analysisDef, trackName1, None, userBinSource, **fullRunArgs).run()
        #
        #print res        
        ##GalaxyInterface._viewResults([res], galaxyFn)
        #print '</div>'
        tfs = res.getResDictKeys()
        
        genesPlural = 's' if len(ensembleGeneIdList)>1 else ''
        tfsPlural = 's' if len(tfs)!=1 else ''
        print '<p>There are %i TF%s targeting your gene%s of interest (%s), using "%s" as source of TF occurrences.</p>' % (len(tfs), tfsPlural, genesPlural, ','.join(ensembleGeneIdList), tfSource)
        
        expansionStr = ' flanked' if not (upFlankSize == downFlankSize == 0) else ''                

        idHtmlFileNamer = GalaxyRunSpecificFile(['allTfIds.html'],galaxyFn)
        idHtmlFileNamer.writeTextToFile('<br>'.join(['<a href=%s/hyper?dbkey=%s&track1=%s&track2=>%s</a>'%(URL_PREFIX, genome, quote(':'.join(tfTrackName+[tf])), tf) for tf in tfs]))
        #idHtmlFileNamer.writeTextToFile('<br>'.join(['<a href=/hbdev/hyper?track1=%s&track2=>%s</a>'%( ':'.join(tfTrackName+[tf]), tf) for tf in tfs]))
        print '<p>', idHtmlFileNamer.getLink('Inspect html file'), ' of all TF IDs occurring 1 or more times within your%s gene region%s of interest, with each TF ID linking to analysis with this TF pre-selected.</p>' % (expansionStr, genesPlural)

        idFileNamer = GalaxyRunSpecificFile(['allTfIds.txt'],galaxyFn)
        idFileNamer.writeTextToFile(os.linesep.join(tfs) + os.linesep)
        print '<p>', idFileNamer.getLink('Inspect text file'), ' listing all TF IDs occurring 1 or more times within your%s gene region%s of interest.</p>' % (expansionStr, genesPlural)
    
        extractedTfbsFileNamer = GalaxyRunSpecificFile(['tfbsInGeneRegions.bed'],galaxyFn)
        GalaxyInterface.extractTrackManyBins(genome, tfTrackName, regSpec, binSpec, True, 'bed', False, False, extractedTfbsFileNamer.getDiskPath())
        print '<p>', extractedTfbsFileNamer.getLink('Inspect bed-file'), 'of all TF binding sites occurring within your%s gene region%s of interest.</p>' % (expansionStr, genesPlural)
        
        #idFile = idFileNamer.getFile()
        #idFile.write(', '.join([str(bin.val) for bin in targetBins if res[bin][resDictKey]>0]) + os.sep)
        #idFile.close()
        
        #print idFileNamer.getLink('Text file'), ' of TF IDs'
        
        #GalaxyInterface.run(tfTrackName, tcGeneRegsExternalTN, analysisDef, regSpec, binSpec, genome, galaxyFn)
        #GalaxyInterface.run(':'.join(tfTrackName), ':'.join(tcGeneRegsExternalTN), analysisDef, regSpec, binSpec, genome, galaxyFn)