def getSubtracksAsGSuite(genome, parentTrack, username=''):
from gold.description.TrackInfo import TrackInfo
from quick.application.GalaxyInterface import GalaxyInterface
from quick.application.ProcTrackNameSource import ProcTrackNameSource
fullAccess = GalaxyInterface.userHasFullAccess(username)
procTrackNameSource = ProcTrackNameSource(genome,
fullAccess=fullAccess,
includeParentTrack=False)
gSuite = GSuite()
for trackName in procTrackNameSource.yielder(parentTrack):
trackType = TrackInfo(genome, trackName).trackFormatName.lower()
trackType = cleanUpTrackType(trackType)
uri = HbGSuiteTrack.generateURI(trackName=trackName)
title = prettyPrintTrackName(trackName)
if title.startswith("'") and title.endswith("'") and len(title) > 1:
title = title[1:-1]
gSuite.addTrack(
GSuiteTrack(uri, title=title, trackType=trackType, genome=genome))
return gSuite
def execute(cls, choices, galaxyFn=None, username=''):
'''
Is called when execute-button is pushed by web-user. Should print
output as HTML to standard out, which will be directed to a results page
in Galaxy history. If getOutputFormat is anything else than HTML, the
output should be written to the file with path galaxyFn. If needed,
StaticFile can be used to get a path where additional files can be put
(e.g. generated image files). choices is a list of selections made by
web-user in each options box.
'''
from quick.application.GalaxyInterface import GalaxyInterface
from proto.hyperbrowser.HtmlCore import HtmlCore
print GalaxyInterface.getHtmlBeginForRuns(galaxyFn)
print GalaxyInterface.getHtmlForToggles(withRunDescription=False)
print str(HtmlCore().styleInfoBegin(styleClass='debug'))
from quick.application.ExternalTrackManager import ExternalTrackManager
datasetId = ExternalTrackManager.extractIdFromGalaxyFn(ExternalTrackManager.extractFnFromGalaxyTN(choices[0]))[1]
#print datasetId
#print choices
##batchid = index for kjoering i batch. Ikke-batch-kjoering: 0
#batchid = 0
##mapId = Definer hva slags type innhold i Google map-bokser (naar du trykker). Innholdet er definert (hardkodet) i GoogleMapsInterface.py: getHtmlText() og getClusterHtmlText()
##Eks: encode_tf_vs_tf
if choices[1] != 'make new map id':
mapId = choices[1]
else:
mapId = choices[2]
from quick.application.ExternalTrackManager import ExternalTrackManager
histHtml = open(ExternalTrackManager.extractFnFromGalaxyTN(choices[0].split(':'))).read()
#rowTrackName = histHtml.split('<h3>TRACK 1</h3>')[-1].split('</b>')[1].split('\n')[0].strip()#.split(':')
#colTrackName = histHtml.split('<h3>TRACK 2</h3>')[-1].split('</b>')[1].split('\n')[0].strip()#.split(':')
from quick.application.GalaxyInterface import GalaxyInterface
batchLine = histHtml.split('<h3>CORRESPONDING BATCH COMMAND LINE</h3>')[-1].split('<p>')[1].split('/p')[0].strip()
genome = histHtml.split('<h3>GENOME</h3>')[-1].split('name:</b>')[1].split('<')[0].strip()
fullAccess = GalaxyInterface.userHasFullAccess(username)
from quick.batch.BatchRunner import BatchRunner
batchContents = BatchRunner.parseBatchLine(batchLine, genome, fullAccess)
rowTrackName = ':'.join(batchContents.cleanedTrackName1)
colTrackName = ':'.join(batchContents.cleanedTrackName2)
from quick.extra.CreateGoogleMapType import createMapType
createMapType(mapId, genome, rowTrackName, colTrackName, 'None', 'None', 'None')
from config.Config import HB_SOURCE_CODE_BASE_DIR
GMapInterfaceFn = HB_SOURCE_CODE_BASE_DIR+'/quick/extra/GoogleMapsInterface.py'
GMapInterfaceContent = open(GMapInterfaceFn).read()
replaceStr = "'%s', 'encode_gwas_vs_dhs'" % mapId
GMapInterfaceContent = GMapInterfaceContent.replace("'encode_gwas_vs_dhs'", replaceStr)
open(GMapInterfaceFn,'w').write(GMapInterfaceContent)
#title = navn paa Regulomet slik brukeren ser det, Eks: "ENCODE test, TFs vs TFs"
title = choices[3]
##name = navn paa katalog for google map: Eks: encode_test_tf_vs_tf
name = choices[4]
from quick.extra.CreateGoogleMap import GoogleMapCreator
from quick.extra.GoogleMapsInterface import Map
onMedSeqProd = False
#batchid
creator = GoogleMapCreator(name, datasetId, mapId, genome=genome)
creator.tile(onMedSeqProd)
creator.copyResultFiles()
creator.createResultShelves()
creator.createIndexFile(title, genome)
creator.fixPermissions()
print str(HtmlCore().styleInfoEnd())
map = Map(name)
row = []
row.append( str(HtmlCore().link(map.getPrettyName(), map.getUrl())) )
row.append( str(HtmlCore().link('Run description', map.getRunDescriptionUrl())) )
row.append( str(HtmlCore().link('Counts', map.getCountUrl())) )
row.append( str(HtmlCore().link('Effect size', map.getEffectSizeUrl())) )
row.append( str(HtmlCore().link('P-values', map.getPvalUrl())) )
core = HtmlCore()
core.tableHeader(None)
core.tableLine(row)
core.tableFooter()
print core
print GalaxyInterface.getHtmlEndForRuns()
def _removeIllegalLines(lines, username):
if GalaxyInterface.userHasFullAccess(username):
return lines
else:
return [x for x in lines if (len(x) > 0 and x[0] != '$') or \
x.startswith('$cluster')] # Hack to allow batch clustering
def execute(choices, galaxyFn=None, username=''):
#setupDebugModeAndLogging()
from time import time
startTime = time()
print HtmlCore().begin()
print '<pre>'
genome = choices[0]
#assert genome=='hg19'
flankSize = choices[3]
if choices[1] == 'Prepared catalogues':
if choices[2] == 'GiulioNewGwas':
gwasTnBase = 'Private:GK:NewGwasBase'.split(':')
elif choices[2] == 'GiulioAllGwas':
gwasTnBase = 'Private:GK:AllGiulioGwasSnpsAsOf9feb13'.split(
':')
elif choices[2] == 'GiulioMay13Gwas':
gwasTnBase = 'Private:GK:Gwas:GiulioMay13'.split(':')
elif choices[2] == 'SmallTest':
gwasTnBase = 'Private:GK:Gwas'.split(':')
else:
raise
gwasTnBase += [flankSize]
elif choices[1] == 'Custom track':
gwasTnBase = choices[2].split(':')
assert flankSize == 'SNPs'
else:
assert False, choices[1]
referenceTrackSource = choices[4]
normalization = choices[5]
assert normalization == 'CoverageDepth'
analysisType = choices[6]
if analysisType == 'Enrichment':
ResultClass = EnrichmentGwasResults
elif analysisType == 'Testing':
ResultClass = HypothesisTestingGwasResults
nullmodelMapping = dict(
zip([
'Sample disease regions uniformly',
'Sample disease regions with preserved inter-region spacings',
'Sample disease regions with preserved distance to nearest exon'
], [
'PermutedSegsAndSampledIntersegsTrack_',
'PermutedSegsAndIntersegsTrack_',
'SegsSampledByDistanceToReferenceTrack_,trackNameIntensity=Genes and gene subsets^Exons^Ensembl exons'
]))
nullmodel = nullmodelMapping[choices[9]]
assert nullmodel in [
'PermutedSegsAndSampledIntersegsTrack_',
'PermutedSegsAndIntersegsTrack_',
'SegsSampledByDistanceToReferenceTrack_,trackNameIntensity=Genes and gene subsets^Exons^Ensembl exons'
]
else:
raise
kernelType = choices[7]
kernelParam = choices[8]
if choices[10] == 'Include links to full underlying results':
includeDetailedResults = True
elif choices[10] == 'Only produce main result values':
includeDetailedResults = False
else:
raise InvalidRunSpecException('Did not understand option: %s' %
choices[12])
mcDepth = choices[11]
if choices[12] == 'yes':
includeLocalResults = True
elif choices[12] == 'no':
includeLocalResults = False
else:
raise InvalidRunSpecException('Did not understand option: %s' %
choices[12])
if choices[15] == 'yes':
useCache = True
elif choices[15] == 'no':
useCache = False
else:
raise InvalidRunSpecException('Did not understand option: %s' %
choices[15])
if choices[16] == 'yes':
printProgress = True
elif choices[16] == 'no':
printProgress = False
else:
raise InvalidRunSpecException('Did not understand option: %s' %
choices[16])
from quick.application.GalaxyInterface import GalaxyInterface
#print GalaxyInterface.getHtmlForToggles()
#print GalaxyInterface.getHtmlBeginForRuns()
#from quick.webtools.GwasAPI import getEnrichmentValues
print 'Progress: '
#print 'base: ',gwasTnBase
#print 'leaves: ',GalaxyInterface.getSubTrackNames(genome, gwasTnBase,deep=False, username=username)
disRes = MultiGwasResults()
from gold.application.HyperBrowserCLI import getSubTrackLeafTerms
from quick.application.ProcTrackOptions import ProcTrackOptions
#for gwasTrackLeaf in GalaxyInterface.getSubTrackNames(genome, gwasTnBase,deep=False, username=username):
allDiseases = getSubTrackLeafTerms(genome,
gwasTnBase,
username=username)
if len(allDiseases) == 0:
assert ProcTrackOptions.isValidTrack(
genome, gwasTnBase, GalaxyInterface.userHasFullAccess(
username)), 'Genome: %s, TN: %s, Access: %s' % (
genome, gwasTnBase,
GalaxyInterface.userHasFullAccess(username))
allDiseases = gwasTnBase[-1:]
gwasTnBase = gwasTnBase[:-1]
for disease in allDiseases:
#print 'Leaf:',gwasTrackLeaf[0]
#if not gwasTrackLeaf[0] in ['11 - Height.txt']:
#if not disease in ['1 - Alzheimer.txt','10 - Graves.txt']:#['Malaria','UC']:
# print 'IGNORING: ', gwasTrackLeaf[0]
# continue
#if gwasTrackLeaf in [[],None] or gwasTrackLeaf[0]=='-- All subtypes --':
#continue
#gwasTn = ':'.join(gwasTnBase + [gwasTrackLeaf[0]])
gwasTn = ':'.join(gwasTnBase + [disease])
#print 'Running API: ', "$getEnrichmentValues(%s, '%s', '%s')" % ([gwasTn], referenceTrackSource, normalization)
#enrichmentsDict = getEnrichmentValues([gwasTn], referenceTrackSource, normalization)#, ['114 - Brain_Mid_Frontal_Lobe.txt','134 - Rectal_Smooth_Muscle.txt'])
#assert len(enrichmentsDict.values())==1
#enrichments = enrichmentsDict.values()[0]
#if gwasTrackLeaf[0] in ['Malaria','UC']:
#print 'HERE IS WHAT I GOT: ',enrichmentsDict
#print 'ENR: ',enrichments
#print 'One: ', (enrichments.values()[0])['enrichment']['13 - CD4'].getGlobalResult()
#assert 'enrichment' in (enrichments.values()[0]), (enrichments.values()[0])
#disRes[gwasTrackLeaf[0]] = (enrichments.values()[0])['enrichment']
#disRes[gwasTrackLeaf[0]] = (enrichments.values()[0])
#disease = gwasTrackLeaf[0]
#disRes[disease] = [x.getGlobalResult() for x in enrichments]
#print 'DISres: ', disRes[gwasTrackLeaf[0]]
#from quick.util.CommonFunctions import extractIdFromGalaxyFn
res = ResultClass(gwasId=disease, verbose=True, galaxyFn=galaxyFn)
#referenceSubTypes = enrichments.keys()
#referenceSubTypes = [x[0] for x in GalaxyInterface.getSubTrackNames(genome, 'Private:GK:Psych:DHSs'.split(':'), deep=False, username=username) if not x[0] == '-- All subtypes --']
if referenceTrackSource == 'H3K4me3':
refTrackBase = 'Private:GK:Psych:H3K4me3'
refTrackCoverageFunction = 'Private^GK^Psych^H3K4me3CoverageTrack'
elif referenceTrackSource == 'DHS':
refTrackBase = 'Private:GK:Psych:DHSs'
refTrackCoverageFunction = 'Private^GK^Psych^DHSCoverageTrack'
elif referenceTrackSource == 'Chromatin state 1-AP':
refTrackBase = 'Private:Anders:Chromatin State Segmentation:1_Active_Promoter'
refTrackCoverageFunction = 'Private^GWAS^Chromatin^CoverageFunctionTracks^1_Active_PromoterV2'
elif referenceTrackSource == 'Chromatin state 4-SE':
refTrackBase = 'Private:Anders:Chromatin State Segmentation:4_Strong_Enhancer'
refTrackCoverageFunction = 'Private^GWAS^Chromatin^CoverageFunctionTracks^4_Strong_Enhancer'
elif referenceTrackSource == 'Chromatin state 5-SE':
refTrackBase = 'Private:Anders:Chromatin State Segmentation:5_Strong_Enhancer'
refTrackCoverageFunction = 'Private^GWAS^Chromatin^CoverageFunctionTracks^5_Strong_Enhancer'
else:
raise
refTrackSelectType = choices[13]
allReferenceTracks = [
x[0] for x in GalaxyInterface.getSubTrackNames(
genome,
refTrackBase.split(':'),
deep=False,
username=username) if not x[0] == '-- All subtypes --'
]
if refTrackSelectType == 'Use all reference tracks':
referenceSubTypes = allReferenceTracks
elif refTrackSelectType == 'Select single reference track':
referenceSubTypes = [choices[14]]
assert referenceSubTypes[0] in allReferenceTracks
elif refTrackSelectType == 'Select a range among all reference tracks':
try:
firstRefTrack, lastRefTrack = choices[14].split('-')
referenceSubTypes = allReferenceTracks[
int(firstRefTrack):int(lastRefTrack) + 1]
print 'Analyzing %s among a total of %s reference tracks' % (
choices[14], len(allReferenceTracks))
except Exception:
print 'Range format should be e.g. "15-18".'
raise
else:
raise
for referenceSubType in referenceSubTypes:
#if not referenceSubType in ['107 - Adult_Kidney.txt','106 - Adipose_Nuclei.txt']:
# #print 'IGNORING: ',referenceSubType
# continue
#
if analysisType == 'Enrichment':
res[referenceSubType] = directGetEnrichment(
gwasTn, referenceSubType, refTrackBase, kernelType,
kernelParam, useCache, printProgress)
elif analysisType == 'Testing':
res[referenceSubType] = directGetTestResults(
gwasTn, referenceSubType, refTrackBase, kernelType,
kernelParam, refTrackCoverageFunction, nullmodel,
mcDepth, useCache, printProgress)
else:
raise
#print disease, referenceSubType, res[referenceSubType]
#print "ENR: ",enrichments
#res[referenceSubType] = enrichments[referenceSubType]
disRes[disease] = res
#for disease in disRes:
# print 'D FULL %s:' %disease, disRes[disease]
# print 'D DICTS %s:'%disease, disRes[disease].getAllGlobalResultDicts()
# print 'DISEASE %s:'%disease, disRes[disease].getAllGlobalResults()
print 'Total run time (excluding figure generation): %i seconds.' % (
time() - startTime)
print '</pre>'
#print GalaxyInterface.getHtmlBeginForRuns()
print '<h1>Results</h1>'
if len(allDiseases) > 1:
try:
heatMapLink = disRes.getLinkToClusteredHeatmap(
'Heatmap', galaxyFn)
print '<h3>Heatmap</h3>', heatMapLink #, '<br>'
except:
print '<p>Creation of heatmap failed</p>'
tableOutput = disRes.getHtmlResultsTable(includeDetailedResults)
print '<h3>Results table</h3>', tableOutput
if choices[-1]:
print '<h3>Prior coloring table</h3>'
colorFn = ExternalTrackManager.extractFnFromGalaxyTN(
choices[-1].split(':'))
print disRes.getColoredSortedReferencesTable(colorFn)
if includeLocalResults:
print '<h3>Local results</h3>'
print disRes.getLinksToAllLocalHtmlResultsTables(galaxyFn)
