def getOptionsBoxPrev(prevChoices):
#return repr(prevChoices),3,True
from proto.hyperbrowser.HtmlCore import HtmlCore
core = HtmlCore()
core.link('Download', 'ftp://something.com/')
from collections import OrderedDict
return [['a','b','c'], [str(core),'2','3'],\
['x','y','z']]
def _buildContent(self):
#iterate through dictionary and for each key create a section (one of [GSuite, Track...])
# each value in the dictionary is a list of GiudeData objects that go into the section defined by the key
htmlCore = HtmlCore()
htmlCore.divBegin('toolGuideInfo')
htmlCore.divBegin(divClass='toolGuideInfoText')
htmlCore.divBegin(divClass='toolGuideInfoTextHeader')
htmlCore.line(TOOL_GUIDE_HELP_HEADER_TEXT)
htmlCore.divEnd()
htmlCore.divBegin(divClass='toolGuideInfoText')
htmlCore.line(TOOL_GUIDE_HELP_HEADER_TEXT_TEXT)
htmlCore.divEnd()
htmlCore.divEnd()
for guideDataKey, guideDataValues in self._guideDataDict.iteritems():
htmlCore.divBegin('toolGuide')
if guideDataKey in TOOL_INPUT_TYPE_TO_TOOL_GUIDE_HELP_HEADER_DICT:
htmlCore.header(TOOL_INPUT_TYPE_TO_TOOL_GUIDE_HELP_HEADER_DICT[
guideDataKey])
for guideDataValue in guideDataValues:
htmlCore.divBegin(divClass='toolGuideData')
htmlCore.divBegin(divClass='toolGuideImgTitle')
if guideDataValue.imgUrl:
htmlCore.image(guideDataValue.imgUrl)
htmlCore.link(text=guideDataValue.toolDisplayName,
url=str(guideDataValue.toolUrl),
args=(' onclick="%s"' % guideDataValue.onclick)
if guideDataValue.onclick else '')
htmlCore.divEnd()
htmlCore.divBegin(divClass='toolGuideDesc')
htmlCore.append(guideDataValue.description)
if guideDataValue.helpPageUrl:
htmlCore.link(text='...read more',
url=str(guideDataValue.helpPageUrl))
htmlCore.divEnd()
htmlCore.divEnd()
htmlCore.divEnd()
htmlCore.divEnd()
#raise Exception(str(htmlCore))#to debug
self._guideContent = str(htmlCore)
def execute(cls, choices, galaxyFn=None, username=''):
file = choices.file
import quick.extra.stefania.Functions_defineDistance_CreateDistanceMatrix_ClusterAnalysis as cdm
if choices.mothers == "":
numMothers = None
else:
numMothers = int(choices.mothers)
# inputFile = open(ExternalTrackManager.extractFnFromGalaxyTN(file.split(':')), 'r')
# with inputFile as f:
# data = [x.strip('\n') for x in f.readlines()]
# f.closed
from proto.hyperbrowser.StaticFile import GalaxyRunSpecificFile
sf = GalaxyRunSpecificFile(["matrix.pickle"],galaxyFn)
sfPng = GalaxyRunSpecificFile(["matrix.png"], galaxyFn)
sfPng1 = GalaxyRunSpecificFile(["Flat1.csv"], galaxyFn)
sfPng2 = GalaxyRunSpecificFile(["Flat2.csv"], galaxyFn)
filename = ExternalTrackManager.extractFnFromGalaxyTN(file.split(':'))
outFn = sf.getDiskPath(ensurePath=True)
outDendrogram = sfPng.getDiskPath(ensurePath=True)
clustersFileOutput1 = sfPng1.getDiskPath(ensurePath=True)
clustersFileOutput2 = sfPng2.getDiskPath(ensurePath=True)
cdm.createDistanceMatrix(filename, outFn, outFileType='pkl', womanIDcolPosition = 0, numRows=numMothers)
cdm.clusteringFunction(outFn, outDendrogram, clustersFileOutput1, clustersFileOutput2, type='hierarchical', method1= 'centroid', method2='complete')
print "Result: ", sf.getLink("pickle-file")
htmlCore = HtmlCore()
htmlCore.begin()
htmlCore.divBegin('plot1')
htmlCore.link('Download plot', sfPng.getURL())
htmlCore.image(sfPng.getURL())
htmlCore.divEnd()
htmlCore.divBegin('plot1')
htmlCore.link('Download file1', sfPng1.getURL())
htmlCore.divEnd()
htmlCore.divBegin('plot1')
htmlCore.link('Download file2', sfPng2.getURL())
htmlCore.divEnd()
htmlCore.end()
print htmlCore
class GtrackSpecParser(object):
def __init__(self, filPath, outFilePath):
self.core = HtmlCore()
self.specStr = open(filPath, 'r').read()
self.outFilePath = outFilePath
self.htmlMal = '<html><body>%s</body></html>'
self.htmlStr = ''
self.divCounter = 0
self.fullContentTab = []
def getContentList(self):
return self.specStr.split('\n----------------')[2].strip().split('\n')
def getContentlineSearcStr(self, line):
anchorIndex = 0
if line.strip().startswith('*'):
anchorIndex = 2
searchStr = line[2:].strip() + '\n----'
elif len(line.strip()) and line.strip().startswith('-'):
anchorIndex = line.find('-') + 4
searchStr = line.strip()[2:].strip() + '\n ----'
elif line.strip() != '':
anchorIndex = 8
searchStr = line.strip().replace(' ', ' ') + '\n ----'
else:
searchStr = None
return searchStr, anchorIndex
#x. Comments
def findAll(self, substring, string):
starts = [
match.start()
for match in re.finditer(re.escape(substring), string)
]
return [
x for i, x in enumerate(starts)
if i == 0 or i > 0 and x - starts[i - 1] != len(substring)
]
def checkHeader(self, header, contentStr, devNotes=True):
headerIndex = contentStr.find(header)
falseHeaderIndex = contentStr.find('"' + header)
if headerIndex != -1 and not (falseHeaderIndex != -1
and headerIndex == falseHeaderIndex + 1):
devChunckList = contentStr.split(header)
resultStr = devChunckList[0]
for value in devChunckList[1:]:
resultStr += '''<a onclick ="javascript:ShowHide('HiddenDiv%s')" href="javascript:;" >%s</a>''' % (
str(self.divCounter), header)
dashLine = '-' * len(header)
if devNotes:
dotList = value.split(dashLine)
resultStr += '<div class="mid" id="HiddenDiv%s" style="DISPLAY: none" >%s%s%s%s</div>' % (
str(self.divCounter), dotList[0], dashLine, dotList[1],
dashLine) + dashLine.join(dotList[2:])
else:
lastDashLine = self.findAll('----', value)[-1]
if value[lastDashLine - 2:lastDashLine] == ' ':
lastDashLine -= 2
mainContent = ''.join(value[1:lastDashLine])
newHeader = ''.join(value[lastDashLine:])
resultStr += '<div class="mid" id="HiddenDiv%s" style="DISPLAY: none" >%s</div>\n ' % (
str(self.divCounter),
mainContent) + dashLine + '\n\n' + newHeader
self.divCounter += 1
return resultStr
else:
return contentStr
def checkRestrictions(self, contentStr):
if contentStr.find('- Restrictions') > 0:
devChunckList = contentStr.split('- Restrictions')
resultStr = devChunckList[0]
for value in devChunckList[1:]:
resultStr += '''- <a onclick ="javascript:ShowHide('HiddenDiv%s')" href="javascript:;" >Restrictions</a>\n''' % str(
self.divCounter)
restrictTab, extraTab = [], []
valueTab = value.split('\n')
for index, resVal in enumerate(valueTab):
if resVal.strip() == '' or (len(resVal) > 2
and resVal[2].isspace()):
restrictTab.append(resVal)
else:
extraTab = valueTab[index:]
break
for val in restrictTab:
if val.strip() == '':
restrictTab = restrictTab[1:]
else:
break
for val in reversed(restrictTab):
if val.strip() == '':
restrictTab = restrictTab[:-1]
else:
break
resultStr += '<div class="mid" id="HiddenDiv%s" style="DISPLAY: none" >\n%s</div>' % (
str(self.divCounter),
'\n'.join(restrictTab)) + '\n\n' + '\n'.join(extraTab)
self.divCounter += 1
return resultStr
else:
return contentStr
def parseSpecFile(self):
contentList = self.getContentList()
self.core.begin()
self.core.script(
"function ShowHide(divId)\n{\nif(document.getElementById(divId).style.display == 'none')\n{\ndocument.getElementById(divId).style.display='block';\n}\nelse\n{\ndocument.getElementById(divId).style.display = 'none';\n}\n}\n"
)
self.core.append('<pre class="largefont">' +
self.specStr.split(contentList[0])[0])
for i in contentList:
searchStr, entry = self.getContentlineSearcStr(i)
self.core.append(i[:entry])
self.core.link(i[entry:], '#' + searchStr.split('\n')[0])
self.core.append('\n')
self.core.append('\n\n\n')
for index, value in enumerate(contentList):
print value
startPoint, entry = self.getContentlineSearcStr(value)
endPoint, entry = self.getContentlineSearcStr(
contentList[index +
1]) if index + 1 < len(contentList) else (None, 0)
self.core.anchor('', startPoint.split('\n')[0])
content = self.specStr[self.specStr.find(
startPoint):] if not endPoint else self.specStr[
self.specStr.find(startPoint):self.specStr.find(endPoint)]
# content = self.checkHeader('Parser notes:', content, True)
content = self.checkRestrictions(content)
self.core.append(content)
self.core.append('</pre>')
self.core.end()
utfil = open(self.outFilePath, 'w')
utfil.write(str(self.core))
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
