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)
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 = GalaxyRunSpecificFile([], galaxyFn).getDiskPath()
assert genome in [
'mm9', 'hg18', 'hg19'
] #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'
flankedGeneRegsTempStaticFile = GalaxyRunSpecificFile(
['flankedGeneRegs.bed'], galaxyFn)
flankedGeneRegsTempFn = flankedGeneRegsTempStaticFile.getDiskPath()
geneRegsTrackName = GenomeInfo.getStdGeneRegsTn(genome)
#geneRegsFn = getOrigFn(genome, geneRegsTrackName, '.category.bed')
GalaxyInterface.getGeneTrackFromGeneList(genome, geneRegsTrackName,
ensembleGeneIdList,
unflankedGeneRegsTempFn)
GalaxyInterface.expandBedSegments(unflankedGeneRegsTempFn,
flankedGeneRegsTempFn,
genome,
upFlankSize,
downFlankSize,
suffix='category.bed')
#flankedGeneRegsExternalTN = ['external'] +galaxyId + [flankedGeneRegsTempFn]
regSpec, binSpec = 'category.bed', 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)
if not (upFlankSize == downFlankSize == 0):
print '(using ', flankedGeneRegsTempStaticFile.getLink(
'these genomic regions'), ' for genes)'
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)
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 = GalaxyRunSpecificFile([], galaxyFn).getDiskPath()
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)
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)
