def findTFsOccurringInRegions(cls, genome, tfSource, regionsBedFn,
upFlankSize, downFlankSize, galaxyFn):
uniqueWebPath = GalaxyRunSpecificFile([], galaxyFn).getDiskPath()
#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]])
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)
def execute(cls, choices, galaxyFn=None, username=''):
genome = choices.genome
from quick.multitrack.MultiTrackCommon import getGSuiteDataFromGalaxyTN
trackTitles, refTrackNameList, genome = getGSuiteDataFromGalaxyTN(choices.gsuite)
queryTrackName = ExternalTrackManager.extractFnFromGalaxyTN(choices.targetTrack)
if choices.isBasic:
suffix = ExternalTrackManager.extractFileSuffixFromGalaxyTN(choices.targetTrack, False)
regSpec = suffix
binSpec = queryTrackName
else:
regSpec, binSpec = UserBinMixin.getRegsAndBinsSpec(choices)
#targetTrack = choices.targetTrack.split(':')
#targetTrackTitle = targetTrack[-1]
#print targetTrackTitle
#
#binSpec = targetTrackTitle
#Phenotype and disease associations:Assorted experiments:Virus integration, HPV specific, Kraus and Schmitz, including 50kb flanks
from gold.gsuite.GSuiteConstants import TITLE_COL
from gold.gsuite.GSuite import GSuite
from proto.hyperbrowser.StaticFile import GalaxyRunSpecificFile
from gold.gsuite.GSuiteEditor import selectColumnsFromGSuite
staticFile=[]
results = []
for refTrack in refTrackNameList:
analysisDef = '-> ProportionCountStat' #ProportionCountStat #CountStat
res = GalaxyInterface.runManual([refTrack], analysisDef, regSpec, binSpec, genome, username=username, galaxyFn=galaxyFn, printRunDescription=False, printResults=False, printProgress=False)
segCoverageProp = [res[seg]['Result'] for seg in res.getAllRegionKeys()]
results.append(segCoverageProp)
regFileNamer = GalaxyRunSpecificFile(refTrack, galaxyFn)
staticFile.append([regFileNamer.getLink('Download bed-file'), regFileNamer.getLoadToHistoryLink('Download bed-file to History')])
refGSuite = getGSuiteFromGalaxyTN(choices.gsuite)
if TITLE_COL == choices.selectColumns:
selected = trackTitles
else:
selected = refGSuite.getAttributeValueList(choices.selectColumns)
yAxisNameOverMouse=[]
metadataAll =[]
for x in range(0, len(selected)):
if selected[x] == None:
yAxisNameOverMouse.append(str(trackTitles[x]) + ' --- ' + 'None')
else:
if TITLE_COL == choices.selectColumns:
yAxisNameOverMouse.append(selected[x].replace('\'', '').replace('"', ''))
else:
metadata = str(selected[x].replace('\'', '').replace('"', ''))
yAxisNameOverMouse.append(str(trackTitles[x]) + ' --- ' + metadata)
metadataAll.append(metadata)
colorListForYAxisNameOverMouse = []
if len(metadataAll) > 0:
import quick.webtools.restricted.visualization.visualizationGraphs as vg
cList = vg.colorList().fullColorList()
uniqueCList = list(set(metadataAll))
for m in metadataAll:
colorListForYAxisNameOverMouse.append(cList[uniqueCList.index(m)])
#startEnd - order in res
startEndInterval = []
startEnd = []
i=0
extraX=[]
rowLabel = []
for ch in res.getAllRegionKeys():
rowLabel.append(str(ch.chr) + ":" + str(ch.start) + "-" + str(ch.end) + str(' (Pos)' if ch.strand else ' (Neg)'))
if not i==0 and not i==len(res.getAllRegionKeys())-1:
start = ch.start
if start-end > 0:
startEnd.append(start-end)
else:
startEnd.append('null')
extraX.append("""{ color: 'orange', width: 5, value: '""" + str(i-0.5) + """' }""")
startEndInterval.append(ch.end - ch.start)
else:
startEndInterval.append(ch.end - ch.start)
end = ch.end
i+=1
extraXAxis='plotLines: [ '
extraXAxis = extraXAxis + ",".join(extraX)
extraXAxis = extraXAxis + """ ], """
#rowLabel = res.getAllRegionKeys()
#rowLabel = [str(x) for x in rowLabel]
import quick.webtools.restricted.visualization.visualizationPlots as vp
htmlCore = HtmlCore()
htmlCore.begin()
htmlCore.divBegin(divId='results-page')
htmlCore.divBegin(divClass='results-section')
htmlCore.divBegin('plotDiv')
htmlCore.line(vp.addJSlibs())
htmlCore.line(vp.useThemePlot())
htmlCore.line(vp.addJSlibsExport())
htmlCore.line(vp.axaddJSlibsOverMouseAxisisPopup())
#vp.addGuideline(htmlCore)
htmlCore.line(vp._addGuidelineV1())
htmlCore.line(vp.addJSlibsHeatmap())
from config.Config import DATA_FILES_PATH
from proto.StaticFile import StaticFile, GalaxyRunSpecificFile
#sf = GalaxyRunSpecificFile(['result.txt'], galaxyFn)
#outFile = sf.getDiskPath(ensurePath=True)
htmlCore.divBegin()
writeFile = open(
cls.makeHistElement(galaxyExt='tabular',
title='result'), 'w')
# htmlCore.link('Get all results', sf.getURL())
htmlCore.divEnd()
i = 0
writeFile.write('Track' + '\t' + '\t'.join(rowLabel)+ '\n')
for rList in results:
writeFile.write(str(yAxisNameOverMouse[i]) + '\t' + '\t'.join([str(r) for r in rList]) + '\n')
i+=1
fileOutput = GalaxyRunSpecificFile(['heatmap.png'],
galaxyFn)
ensurePathExists(fileOutput.getDiskPath())
fileOutputPdf = GalaxyRunSpecificFile(['heatmap.pdf'],
galaxyFn)
ensurePathExists(fileOutputPdf.getDiskPath())
cls.generateStaticRPlot(results, colorListForYAxisNameOverMouse, rowLabel, yAxisNameOverMouse,
colorMaps[choices.colorMapSelectList],
fileOutput.getDiskPath(), fileOutputPdf.getDiskPath())
htmlCore.divBegin(divId='heatmap', style="padding: 10px 0 px 10 px 0px;margin: 10px 0 px 10 px 0px")
htmlCore.link('Download heatmap image', fileOutputPdf.getURL())
htmlCore.divEnd()
if len(results) * len(results[1]) >= 10000:
htmlCore.image(fileOutput.getURL())
else:
min = 1000000000
max = -1000000000
for rList in results:
for r in rList:
if min > r:
min = r
if max < r:
max = r
if max-min != 0:
resultNormalised = []
for rList in results:
resultNormalisedPart = []
for r in rList:
resultNormalisedPart.append((r-min)/(max-min))
resultNormalised.append(resultNormalisedPart)
addText = '(normalised to [0, 1])'
else:
resultNormalised = results
addText = ''
hm, heatmapPlotNumber, heatmapPlot = vp.drawHeatMap(
resultNormalised,
colorMaps[choices.colorMapSelectList],
label='this.series.xAxis.categories[this.point.x] + ' + "'<br >'" + ' + yAxisNameOverMouse[this.point.y] + ' + "'<br>Overlap proportion" + str(addText) + ": <b>'" + ' + this.point.value + ' + "'</b>'",
yAxisTitle= 'Reference tracks',
categories=rowLabel,
tickInterval=1,
plotNumber=3,
interaction=True,
otherPlotNumber=1,
titleText='Overlap with reference tracks for each local region',
otherPlotData=[startEnd, startEndInterval],
overMouseAxisX=True,
overMouseAxisY=True,
yAxisNameOverMouse=yAxisNameOverMouse,
overMouseLabelY=" + 'Track: '" + ' + this.value + ' + "' '" + ' + yAxisNameOverMouse[this.value] + ',
overMouseLabelX = ' + this.value.substring(0, 20) +',
extrOp = staticFile
)
htmlCore.line(hm)
htmlCore.line(vp.drawChartInteractionWithHeatmap(
[startEndInterval, startEnd],
tickInterval=1,
type='line',
categories=[rowLabel, rowLabel],
seriesType=['line', 'column'],
minWidth=300,
height=500,
lineWidth=3,
titleText=['Lengths of segments (local regions)','Gaps between consecutive segments'],
label=['<b>Length: </b>{point.y}<br/>', '<b>Gap length: </b>{point.y}<br/>'],
subtitleText=['',''],
yAxisTitle=['Lengths','Gap lengths'],
seriesName=['Lengths','Gap lengths'],
xAxisRotation=90,
legend=False,
extraXAxis=extraXAxis,
heatmapPlot=heatmapPlot,
heatmapPlotNumber=heatmapPlotNumber,
overMouseAxisX=True,
overMouseLabelX = ' + this.value.substring(0, 20) +'
))
htmlCore.divEnd()
htmlCore.divEnd()
htmlCore.divEnd()
htmlCore.end()
htmlCore.hideToggle(styleClass='debug')
print htmlCore