def findTFsOccurringInRegions(cls, genome, tfSource, regionsBedFn, upFlankSize, downFlankSize, galaxyFn):
uniqueWebPath = getUniqueWebPath(extractIdFromGalaxyFn(galaxyFn))
#assert genome == 'hg18' #other genomes not supported. TF id links do not specify genome for pre-selection of analysis
tfTrackNameMappings = TfInfo.getTfTrackNameMappings(genome)
assert tfTrackNameMappings != {}, 'No TF info for genome: %s' % genome
tfTrackName = tfTrackNameMappings[tfSource]
if (upFlankSize == downFlankSize == 0):
flankedRegionsFn = regionsBedFn
else:
flankedRegionsFn= uniqueWebPath + os.sep + 'flankedRegs.bed'
GalaxyInterface.expandBedSegments(regionsBedFn, flankedRegionsFn, genome, upFlankSize, downFlankSize)
regSpec, binSpec = 'bed', flankedRegionsFn
res = cls._runCategoryPointCount(genome, regSpec, binSpec, tfTrackName)
tfNames = res.getResDictKeys()
#print 'RES: ', res.getGlobalResult()[tfNames[0]], type(res.getGlobalResult()[tfNames[0]])
import third_party.safeshelve as safeshelve
pwm2tfids = safeshelve.open(os.sep.join([HB_SOURCE_CODE_BASE_DIR,'data','pwm2TFids.shelf']), 'r')
tf2class = safeshelve.open(os.sep.join([HB_SOURCE_CODE_BASE_DIR,'data','TfId2Class.shelf']), 'r')
pwmName2id= safeshelve.open(os.sep.join([HB_SOURCE_CODE_BASE_DIR,'data','pwmName2id.shelf']), 'r')
#print tfNames[0],tfNames[1], ' VS ', pwm2tfids.keys()[0], len(pwm2tfids)
#tfs = list(reversed(sorted([(res.getGlobalResult()[tf], tf, '%s (%i hits (class %s))'%(tf, res.getGlobalResult()[tf]), '/'.join([tf2class[x] for x in pwm2tfids[tf]]) ) for tf in tfNames]))) #num hits, tfName, tfTextInclHits
tfs = list(reversed(sorted([(res.getGlobalResult()[tf], tf, '%s (%i hits )'%(tf, res.getGlobalResult()[tf]) + \
(' (class: %s)'%'/'.join(set([str(tf2class.get(x)) for x in pwm2tfids[pwmName2id[tf]] if x in tf2class]))\
if (tf in pwmName2id and pwmName2id[tf] in pwm2tfids and any([x in tf2class for x in pwm2tfids[pwmName2id[tf]]]))\
else '') ) \
for tf in tfNames])) ) #num hits, tfName, tfTextInclHits
tfsPlural = 's' if len(tfs)!=1 else ''
print '<p>There are %i TF%s targeting your regions of interest, using "%s" as source of TF occurrences.</p>' % (len(tfs), tfsPlural, tfSource)
expansionStr = ' flanked' if not (upFlankSize == downFlankSize == 0) else ''
idHtmlFileNamer = GalaxyRunSpecificFile(['allTfIds.html'],galaxyFn)
idHtmlFileNamer.writeTextToFile('<br>'.join(['<a href=/hbdev/hyper?track1=%s&track2=>%s</a>'%( quote(':'.join(tfTrackName+[tf[1]])), tf[2]) for tf in tfs]))
print '<p>', idHtmlFileNamer.getLink('Inspect html file'), ' of all TF IDs occurring 1 or more times within your%s regions of interest, with each TF ID linking to analysis with this TF pre-selected.</p>' % (expansionStr)
idFileNamer = GalaxyRunSpecificFile(['allTfIds.txt'],galaxyFn)
idFileNamer.writeTextToFile(os.linesep.join([tf[2] for tf in tfs]) + os.linesep)
print '<p>', idFileNamer.getLink('Inspect text file'), ' listing all TF IDs occurring 1 or more times within your%s regions of interest.</p>' % (expansionStr)
extractedTfbsFileNamer = GalaxyRunSpecificFile(['tfbsInGeneRegions.bed'],galaxyFn)
GalaxyInterface.extractTrackManyBins(genome, tfTrackName, regSpec, binSpec, True, 'bed', False, False, extractedTfbsFileNamer.getDiskPath(), True)
print '<p>', extractedTfbsFileNamer.getLoadToHistoryLink('Inspect bed-file'), 'of all TF binding sites occurring within your%s regions of interest.</p>' % (expansionStr)
for dummy,tf,dummy2 in tfs:
extractedTfbsFileNamer = GalaxyRunSpecificFile([tf+'_tfbsInGeneRegions.bed'],galaxyFn)
GalaxyInterface.extractTrackManyBins(genome, tfTrackName+[tf], regSpec, binSpec, True, 'bed', False, False, extractedTfbsFileNamer.getDiskPath())
print '<p>', extractedTfbsFileNamer.getLoadToHistoryLink('Binding sites of the TF %s' %tf, 'bed'), 'occurring within your%s regions of interest (bed-file).</p>' % (expansionStr)
