本文整理匯總了Python中quick.application.ExternalTrackManager.ExternalTrackManager.preProcess方法的典型用法代碼示例。如果您正苦於以下問題：Python ExternalTrackManager.preProcess方法的具體用法？Python ExternalTrackManager.preProcess怎麽用？Python ExternalTrackManager.preProcess使用的例子？那麽, 這裏精選的方法代碼示例或許可以為您提供幫助。您也可以進一步了解該方法所在類quick.application.ExternalTrackManager.ExternalTrackManager的用法示例。
在下文中一共展示了ExternalTrackManager.preProcess方法的1個代碼示例，這些例子默認根據受歡迎程度排序。您可以為喜歡或者感覺有用的代碼點讚，您的評價將有助於係統推薦出更棒的Python代碼示例。
示例1: findOverrepresentedTFsFromGeneSet
# 需要導入模塊: from quick.application.ExternalTrackManager import ExternalTrackManager [as 別名]
# 或者: from quick.application.ExternalTrackManager.ExternalTrackManager import preProcess [as 別名]
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)