def isInstalled(self):
# Caching added to improve reaction time when displaying genome selection box
if not self.installed:
from quick.application.ProcTrackOptions import ProcTrackOptions
self.installed = self.timeOfInstallation is not None and \
ProcTrackOptions.isValidTrack(self.genome, GenomeInfo.getChrTrackName(self.genome), fullAccess=True) and \
ProcTrackOptions.isValidTrack(self.genome, GenomeInfo.getAssemblyGapsTrackName(self.genome), fullAccess=True)
if self.installed:
self.store()
return self.installed
def getOptionsBoxTrack2Source(prevChoices):
'''
See getOptionsBox1().
'''
if prevChoices[-1] in ['Track','History'] or (prevChoices[-3] == 'Track' and ProcTrackOptions.isValidTrack(prevChoices[0], prevChoices[-2].split(':'), fullAccess=True)) or (prevChoices[-3] == 'History' and prevChoices[-2] != ''):
return ['--- select ---','Track','History']
def _validateGenome(cls, choices, validateBinaryTracksIfPresent=True):
from quick.multitrack.MultiTrackCommon import getGSuiteFromGalaxyTN
from quick.application.ProcTrackOptions import ProcTrackOptions
allGSuiteGalaxyTNs = [
getattr(choices, key) for key in cls.GSUITE_FILE_OPTIONS_BOX_KEYS
]
if all(allGSuiteGalaxyTNs):
if (not cls._allowGenomeOverride(choices)
) and cls._getNumUniquelySpecifiedGenomes(choices) > 1:
return cls.ERROR_GENOME_BUILD_MISMATCH + ', '.join(
cls._getGsuiteGenomes(choices))
errorStr = GeneralGuiTool._checkGenome(choices.genome)
if errorStr:
return errorStr
if not cls._allowMultipleGenomes(
choices) and choices.genome == GSuiteConstants.MULTIPLE:
return cls.ERROR_MULTIPLE_GENOMES_NOT_ALLOWED
if validateBinaryTracksIfPresent:
for galaxyTN in allGSuiteGalaxyTNs:
gSuite = getGSuiteFromGalaxyTN(galaxyTN)
if gSuite.fileFormat == GSuiteConstants.PREPROCESSED and gSuite.location == GSuiteConstants.LOCAL:
for gSuiteTrack in gSuite.allTracks():
if not ProcTrackOptions.isValidTrack(
choices.genome, gSuiteTrack.trackName,
True):
return cls.ERROR_PREPROCESSED_TRACK_INVALID % gSuiteTrack.title
def execute(cls, choices, galaxyFn=None, username=''):
from quick.application.ProcTrackOptions import ProcTrackOptions
#from quick.application.ProcTrackOptions import ProcTrackOptions
#SHELVE_FN = DATA_FILES_PATH + sep + 'TrackInfo.shelve'
#trackInfoShelve = shelve.open(SHELVE_FN, 'c')
#
#cellType = choices.celltype.split('(')[0].strip()
#hg19Keys = [k for k in trackInfoShelve.keys() if k.startswith('hg19:Gene regulation')]
#print 'Size of trackInfo shelve(hg19):', len(hg19Keys)
#
##code for finding candidate tracks for hg19 for selected celltype
#trackCandidateDict = dict()
#for tnStr in hg19Keys:
# value = trackInfoShelve.get(tnStr).description
# if re.search('cell='+cellType+'.*dataType=ChipSeq<.*view=Peaks<', value):
# tn = tnStr.split(':')
# if ProcTrackOptions.isValidTrack(tn[0], tn[1:], True):
# trackCandidateDict[tnStr] = re.sub('[\-\_\s]','', value.split('antibody=')[1].split('<')[0].strip().upper())
genome = choices.genome
mutationTrack = choices.track.split(':')
expand = choices.expand
if choices.datasource == cls.DATA_REPO:
dataFn = DATA_FILES_PATH + 'EncodeBasedTfMappings.txt'
else:
dataFn = ExternalTrackManager.extractFnFromGalaxyTN(
choices.history.split(':'))
gSuiteDict = cls.convertGTrackSuiteToDict(dataFn)
cellTypeList = [k for k, v in choices.celltype.items() if v]
motifFn = HB_SOURCE_CODE_BASE_DIR + '/data/all_PWMs.txt'
motifFn2 = ExternalTrackManager.extractFnFromGalaxyTN(
choices.pwmhistory.split(':')) if choices.pwmhistory else None
motifScanObj = MotifScanner(motifFn, fn2=motifFn2)
resultDict = dict()
for cellType, tfDict in gSuiteDict.items():
if not cellType in cellTypeList:
continue
multiTfDict = MultiExactlySpecifiedTF()
for keyTf, trackPwmList in tfDict.items():
for track, motifId in trackPwmList:
if not ProcTrackOptions.isValidTrack(
genome, track.split(':'), True):
print 'missing or invalid track: ', track
continue
tfObj = ExactlySpecifiedTF(
keyTf, track, motifId,
[track.split(':'), mutationTrack], galaxyFn)
tfObj.getFastaFiles(genome)
tfObj.getPwmScores(motifId, motifScanObj)
multiTfDict[tfObj.tf + '_' + tfObj.chipSeqPeaks + '_' +
motifId] = tfObj
resultDict[cellType] = multiTfDict
for cType, mDict in resultDict.items():
print mDict.getHtmlResultsTable()
def _isValidTrack(prevChoices, tnChoiceIndex=1):
from quick.application.GalaxyInterface import GalaxyInterface
from quick.application.ProcTrackOptions import ProcTrackOptions
genome = prevChoices[0]
tn = prevChoices[tnChoiceIndex].split(':')
return ProcTrackOptions.isValidTrack(genome, tn, True) or \
GalaxyInterface.isNmerTrackName(genome, tn)
def getOptionsBoxTrack6Source(prevChoices):
'''
See getOptionsBox1().
'''
if prevChoices[-1] in [
'Track', 'History'
] or (prevChoices[-3] == 'Track' and ProcTrackOptions.isValidTrack(
prevChoices[0], prevChoices[-2].split(':'),
fullAccess=True)) or (prevChoices[-3] == 'History'
and prevChoices[-2] != ''):
return ['--- select ---', 'Track', 'History']
def _requiredTracksAreValid(self):
from quick.application.ProcTrackOptions import ProcTrackOptions
requiredTrackNames = [
self.getSequenceTrackName(self.genome),
self.getChrTrackName(self.genome),
self.getAssemblyGapsTrackName(self.genome)
]
return all(
ProcTrackOptions.isValidTrack(self.genome, tn, fullAccess=True)
for tn in requiredTrackNames)
def validateAndReturnErrors(choices):
genome, errorStr = CreateSegmentsFromGeneListTool._getGenomeChoice(choices, 0)
if errorStr:
return errorStr
ensemblTn = GenomeInfo.getEnsemblTrackName(genome)
if not ProcTrackOptions.isValidTrack(genome, ensemblTn):
return 'The selected genome have not been set up with a Ensembl gene track. If you require this functionality for the selected genome, please contact the HyperBrowser team.'
if choices[1].strip() == '':
return 'Please enter a list of genes (using Ensembl IDs)'
def _inferTrackName(rawTN, genome, fullAccess):
#genome = DEFAULT_GENOME
if rawTN.lower() in ['blank','none','dummy','_',' ','']:
return None
#trackName = rawTN.replace('_',' ').split(':')
#trackName = rawTN.split(':')
trackName = convertTNstrToTNListFormat(rawTN)
if ProcTrackOptions.isValidTrack(genome, trackName, fullAccess):
return trackName
else:
raise InvalidRunSpecException('Error in trackname specification. \''\
+ rawTN + '\' does not match any tracknames. This may be because of limited user permissions.')
def getAllChosenTracks(choices):
'''
See getOptionsBox1().
'''
allTracks = []
trackParamNames = [('Track1Source', 'Track1'), ('Track2Source', 'Track2'),('Track3Source','Track3'),\
('Track4Source', 'Track4'),('Track5Source', 'Track5'),('Track6Source','Track6')]
#print 'TEMP: ', choices, trackParamNames
for source, trackName in [(getattr(choices, s), getattr(choices,t).split(':')) for s,t in trackParamNames if getattr(choices,t) not in [None,''] ]:
if source == 'History':
allTracks.append(trackName)
elif source == 'Track' and ProcTrackOptions.isValidTrack(choices.Genome, trackName, fullAccess=True):
allTracks.append(trackName)
return allTracks
def _isValidTrack(choices, tnChoiceIndex=1, genomeChoiceIndex=0):
from quick.application.GalaxyInterface import GalaxyInterface
from quick.application.ProcTrackOptions import ProcTrackOptions
genome, errorStr = GeneralGuiTool._getGenomeChoice(
choices, genomeChoiceIndex)
if errorStr or genome is None:
return False
trackName, errorStr = GeneralGuiTool._getTrackChoice(
choices, tnChoiceIndex)
if errorStr:
return False
return ProcTrackOptions.isValidTrack(genome, trackName, True) or \
GalaxyInterface.isNmerTrackName(genome, trackName)
def _inferTrackName(trackName, genome, fullAccess):
if len(trackName) == 0 or \
len(trackName) == 1 and trackName[0].lower() in ['blank', 'none', 'dummy', '_', ' ', '']:
return None
# trackName = rawTN.replace('_',' ').split(':')
# trackName = rawTN.split(':')
#
# trackName = convertTNstrToTNListFormat(rawTN)
if ProcTrackOptions.isValidTrack(genome, trackName, fullAccess):
return trackName
else:
raise InvalidRunSpecException('Error in trackname specification. \'' +\
':'.join(trackName) + '\' does not match any tracknames. ' +\
'This may be because of limited user permissions.')
def validateTracks(choices):
'''
See getOptionsBox1().
'''
allTracks = []
trackParamNames = [('Track1Source', 'Track1'), ('Track2Source', 'Track2'),('Track3Source','Track3'),\
('Track4Source', 'Track4'),('Track5Source', 'Track5'),('Track6Source','Track6')]
count = 0
for trackNumber, source, trackName in [(t, getattr(choices, s), getattr(choices,t).split(':')) for s,t in trackParamNames if type(getattr(choices,t))==str]:
count+=1
if source == 'Tracks':
if not ProcTrackOptions.isValidTrack(choices.Genome, trackName):
return 'Invalid track: the path for %s is not correctly specified' % trackNumber
if count==0:
return 'No valid tracks chosen'
def getTrackNamesFromFormParameters(cls, choices):
if choices[0] == 'From repository':
genome = choices[2]
trackNames = [
unquote(val).split(':') for val in choices[4].values() if val
]
trackNames += [
v.split(':') for v in choices[5:] if v
and ProcTrackOptions.isValidTrack(genome, v.split(':'), True)
]
return genome, trackNames
else: #if 'From GSuite'
gSuite = getGSuiteFromGalaxyTN(choices[1])
tracks = [
gSuiteTrack.trackName for gSuiteTrack in gSuite.allTracks()
]
genome = gSuite.genome
return genome, tracks
def yielder(self, curTn):
if self._avoidLiterature and curTn == GenomeInfo.getPropertyTrackName(self._genome, 'literature'):
return
for subtype in ProcTrackOptions.getSubtypes(self._genome, curTn, self._fullAccess):
#if self._avoidLiterature and subtype == 'Literature':
if subtype[0] in ['.','_']:
continue
newTn = curTn + [subtype]
doBreak = False
for subTn in self.yielder(newTn):
yield subTn
if ProcTrackOptions.isValidTrack(self._genome, curTn, self._fullAccess):
yield curTn
def validateAndReturnErrors(choices):
'''
Should validate the selected input parameters. If the parameters are not valid,
an error text explaining the problem should be returned. The GUI then shows this text
to the user (if not empty) and greys out the execute button (also if the text isempty).
If all parameters are valid, the method should return None, which enables the execute button.
'''
genome, tn, tf = ExtractIntersectingGenesTool._getBasicTrackFormat(choices)
geneRegsTrackName = GenomeInfo.getStdGeneRegsTn(genome)
if not ExtractIntersectingGenesTool._isValidTrack(choices):
return ""
return "The selected track (%s) is not valid." % ':'.join(tn)
if tf.split()[-1] not in ['points', 'segments']:
return "The track format of the selected track must be either points or segments. Currently: %s" % tf
if not ProcTrackOptions.isValidTrack(genome, geneRegsTrackName, True):
return "The track used for gene ids (%s) is not valid. This is an internal error." % ':'.join(geneRegsTrackName)
def validateTracks(choices):
'''
See getOptionsBox1().
'''
allTracks = []
trackParamNames = [('Track1Source', 'Track1'), ('Track2Source', 'Track2'),('Track3Source','Track3'),\
('Track4Source', 'Track4'),('Track5Source', 'Track5'),('Track6Source','Track6')]
count = 0
for trackNumber, source, trackName in \
[(t, getattr(choices, s),
getattr(choices, t).split(':')) for s,t in trackParamNames
if isinstance(getattr(choices, t), basestring)]:
count += 1
if source == 'Tracks':
if not ProcTrackOptions.isValidTrack(choices.Genome,
trackName):
return 'Invalid track: the path for %s is not correctly specified' % trackNumber
if count == 0:
return 'No valid tracks chosen'
def getAllChosenTracks(choices):
'''
See getOptionsBox1().
'''
allTracks = []
trackParamNames = [('Track1Source', 'Track1'), ('Track2Source', 'Track2'),('Track3Source','Track3'),\
('Track4Source', 'Track4'),('Track5Source', 'Track5'),('Track6Source','Track6')]
#print 'TEMP: ', choices, trackParamNames
for source, trackName in [(getattr(choices, s), getattr(choices,
t).split(':'))
for s, t in trackParamNames
if getattr(choices, t) not in [None, '']]:
if source == 'History':
allTracks.append(trackName)
elif source == 'Track' and ProcTrackOptions.isValidTrack(
choices.Genome, trackName, fullAccess=True):
allTracks.append(trackName)
return allTracks
def execute(cls, choices, galaxyFn=None, username=''):
from quick.application.ProcTrackOptions import ProcTrackOptions
from quick.application.GalaxyInterface import GalaxyInterface
import gold.application.StatRunner
analysisDef = 'dummy -> PercentageChangeStat'
genome = choices[0]
binSpec = '*'
regSpec = 'Days_1900_2036:36890-41424'
tnRoot = 'Company stocks:Historical prices:OSE:'
stockList = [k for k, v in choices[1].items() if v]
numStocks = 0
totalPercent = 0.0
for stock in stockList:
tn = tnRoot + stock
if ProcTrackOptions.isValidTrack(genome,
tn.split(':'),
fullAccess=True):
resultDict = GalaxyInterface.runManual(
[tn.split(':'), choices[2].split(':')],
analysisDef,
regSpec,
binSpec,
'days',
galaxyFn,
printResults=False,
printProgress=False)
for k, v in resultDict.items():
print 'increase (from jan. 2001 - jun. 2013) for ', stock, ': ', v
res = v['Result']
if res == 0.0 or res > 10000:
continue
totalPercent += v['Result']
numStocks += 1
else:
print 'this is not a valid track', tn
print 'Average increase (from jan. 2001 - jun. 2013): ', totalPercent / numStocks, ' (number of stocks =', numStocks, ')'
def yielder(self, curTn, level=0):
if self._avoidLiterature and curTn == GenomeInfo.getPropertyTrackName(
self._genome, 'literature'):
return
for subtype in ProcTrackOptions.getSubtypes(self._genome, curTn,
self._fullAccess):
#if self._avoidLiterature and subtype == 'Literature':
if subtype[0] in ['.', '_']:
continue
newTn = curTn + [subtype]
doBreak = False
for subTn in self.yielder(newTn, level=level + 1):
yield subTn
if self._includeParentTrack or level > 0:
if ProcTrackOptions.isValidTrack(self._genome, curTn,
self._fullAccess):
yield curTn
def validateAndReturnErrors(choices):
'''
Should validate the selected input parameters. If the parameters are not valid,
an error text explaining the problem should be returned. The GUI then shows this text
to the user (if not empty) and greys out the execute button (also if the text isempty).
If all parameters are valid, the method should return None, which enables the execute button.
'''
trackChoice = 'history' if choices.trackSource == 'history' else 'track'
errorStr = ExtractIntersectingGenesTool._checkTrack(
choices, trackChoice, 'genome')
if errorStr:
return errorStr
genome, tn, tf = ExtractIntersectingGenesTool._getBasicTrackFormat(
choices, trackChoice)
if tf.split()[-1] not in ['points', 'segments']:
return "The track format of the selected track must be either points or segments. Currently: %s" % tf
geneRegsTrackName = GenomeInfo.getStdGeneRegsTn(genome)
if not ProcTrackOptions.isValidTrack(genome, geneRegsTrackName, True):
return "The track used for gene ids (%s) is not valid. This is an internal error." % ':'.join(
geneRegsTrackName)
def getOptionsBox23(prevChoices): # Alternatively: getOptionsBoxKey()
if prevChoices[0] == 'From repository':
if prevChoices[-2] and ProcTrackOptions.isValidTrack(
prevChoices[2], prevChoices[-2].split(':'), True):
return '__track__'
def getOptionsBox19(prevChoices): # Alternatively: getOptionsBoxKey()
if prevChoices[-2] and ProcTrackOptions.isValidTrack(
prevChoices[2], prevChoices[-2].split(':'), True):
return '__track__'
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)