class AnalysisDefJob(StatJob):
'''
@takes(AnalysisDefJob, str, list, list, UserBinSource)
@returns Results
'''
def __init__(self, analysisDef, trackName1, trackName2, userBinSource,
genome=None, galaxyFn=None, *args, **kwArgs):
from gold.description.Analysis import Analysis
# to be removed later.. Just for convenience with development now..
self._analysisDef = analysisDef
# self._trackName1 = trackName1
# self._trackName2 = trackName2
if genome is None:
genome = userBinSource.genome
self._galaxyFn = galaxyFn
self._analysis = Analysis(analysisDef, genome, trackName1, trackName2)
self._setRandomSeedIfNeeded()
track, track2 = self._analysis.getTracks()
StatJob.__init__(self, userBinSource, track, track2,
self._analysis.getStat(), *args, **kwArgs)
def _setRandomSeedIfNeeded(self):
from gold.util.RandomUtil import getRandomSeed
randSeedChoice = self._analysis.getChoice('randomSeed')
if randSeedChoice == 'Random':
self._analysis.changeChoices('randomSeed', [(str(getRandomSeed()),)*2])
def run(self, printProgress=PRINT_PROGRESS):
'''
Runs the statistic specified in self._analysis (from analysisDef) and returns an object of class Result
'''
#Should be there for batch runs.. Should never happen from GUI..
if self._statClass == None:
self._handleMissingStat()
return None
if DebugConfig.USE_PROFILING:
from gold.util.Profiler import Profiler
profiler = Profiler()
resDict = {}
profiler.run('resDict[0] = StatJob.run(self, printProgress=printProgress)', globals(), locals())
res = resDict[0]
else:
res = StatJob.run(self, printProgress=printProgress)
res.setAnalysis(self._analysis)
res.setAnalysisText(str(self._analysis))
ResultsMemoizer.flushStoredResults()
if DebugConfig.USE_PROFILING:
profiler.printStats()
if DebugConfig.USE_CALLGRAPH and self._galaxyFn:
profiler.printLinkToCallGraph(['profile_AnalysisDefJob'], self._galaxyFn)
return res
def _handleMissingStat(self):
from gold.application.LogSetup import logMessage, logging
from gold.description.RunDescription import RunDescription
import gold.description.Analysis as AnalysisModule
#AnalysisModule.VERBOSE = True
msg = 'Started run with invalid statistic... Please run with debug mode set to "Debug by raising hidden ' \
'exceptions" to see underlying problem. ' \
'Def: ' + self._analysisDef
#+ ', Run description: ' + \
#RunDescription.getRevEngBatchLine( self._trackName1, self._trackName2, self._analysisDef, \
#'Not Available', 'Not Available', self._userBinSource.genome)
logMessage(msg, level=logging.ERROR)
raise Exception(msg)
def getRevEngBatchLine(analysisDef, trackNames, cleanedTrackNames, regSpec,
binSpec, genome, **kwArgs):
#analysisDef is assumed to be unquoted
#if this is to work, must check explicitly against special keywords in regSpec (or check that regSpec is a valid region that is to have region..)...
#if not genome in regSpec:
# regSpec = genome+':'+regSpec
try:
if DebugConfig.VERBOSE:
logMessage('getting RevEngBatchLine:')
#analysisDef =analysisDef.replace('%20PointCountInSegsPvalStat%2C','') #REMOVE
#print 'NOWAG: ',analysisDef
analysis = Analysis(analysisDef, genome, cleanedTrackNames[0],
cleanedTrackNames[1], **kwArgs)
#assert unquote(regSpec) == regSpec
assert unquote(
binSpec
) == binSpec #To assure that unquote can be safely applied to binSpec without any consequences (we don't want to always quote, but still want the possibility to use quoted history track names)
quotedTrackName1 = (':'.join(
[quote(x, safe='') for x in trackNames[0]]))
quotedTrackName2 = (':'.join([
quote(x, safe='') for x in trackNames[1]
])) if trackNames[1] is not None else 'None'
intensityChoice = analysis.getChoice('trackNameIntensity')
if intensityChoice:
quotedIntensityTrackName = quote(intensityChoice, safe='^|')
analysis.changeChoices('trackNameIntensity',
[(quotedIntensityTrackName, ) * 2])
stat = analysis.getStat()
if stat is None:
return 'No corr batch line, as no valid statistic was found.. '
#print 'CAME HERE'
statClassName = stat.__name__
#fixme: Add space, but this is not checked in batchrunner...
params = ','.join(['='.join(choicePair) for choicePair in analysis.getAllChoices(filterByActivation=True).items() \
if choicePair[0] not in ['H0','H1_more','H1_less','H1_different','H1_ha1','H1_ha2','H1_ha3','H1_ha4','H1_ha5'] ])
statText = statClassName + '(' + params + ')'
batchElements = [
genome, regSpec, binSpec, quotedTrackName1, quotedTrackName2,
statText
]
#batchElements = [el.replace(BATCH_COL_SEPARATOR, '\\' + BATCH_COL_SEPARATOR) for el in batchElements]
#batchElements = [quote(el, safe='') for el in batchElements]
oneLineBatch = BATCH_COL_SEPARATOR.join(batchElements)
#return oneLineBatch
#Under construction...:
from collections import OrderedDict
#batchVariables = OrderedDict([('@GENOME',genome), ('@REGION',regSpec), ('@BINNING',binSpec), ('@TN1',tn1), ('@TN2',tn2), ('@ANALYSIS',statText)])
batchVariables = OrderedDict([('@REGION', regSpec),
('@BINNING', binSpec),
('@TN1', quotedTrackName1),
('@TN2', quotedTrackName2),
('@ANALYSIS', statText)])
batchComposition = BATCH_COL_SEPARATOR.join([genome] +
batchVariables.keys())
fullBatchList = [
'='.join(assignment) for assignment in batchVariables.items()
] + [batchComposition]
fullBatch = '<br>'.join(fullBatchList)
batchLinkDef = '<a href="%s/hyper?mako=generictool&tool_id=hb_batch_run_tool&command=%s&dbkey=%s">%s</a>'
oneLineBatchLink = batchLinkDef % (URL_PREFIX, quote(oneLineBatch),
genome, 'single line version')
fullBatchLink = batchLinkDef % (URL_PREFIX,
quote('\n'.join(fullBatchList)),
genome, 'variable based version')
#return oneLineBatch + '<br><br>or corresponding spec using variable assignment:<br><br>' + fullBatch + '<br><br>Execute batchline in ' \
#+ oneLineBatchLink + ' / ' + fullBatchLink
return oneLineBatch + '<br><br>Execute batchline in ' + oneLineBatchLink + ' / ' + fullBatchLink
except Exception, e:
#raise
logException(e, logging.WARNING,
'Could not generate corresponding batch line: ')
#if DebugConfig.VERBOSE:
logMessage('analysis, genome, trackName1, trackName2: \n' +
str([analysis, genome, trackNames[0], trackNames[1]]))
return 'Warning: Could not generate corresponding batch line.'
class AnalysisDefJob(StatJob):
#@takes(AnalysisDefJob, str, list, list, UserBinSource)
#@returns Results
def __init__(self, analysisDef, trackName1, trackName2, userBinSource, genome=None, *args, **kwArgs):
from gold.description.Analysis import Analysis
#to be removed later.. Just for convenience with development now..
self._analysisDef = analysisDef
#self._trackName1 = trackName1
#self._trackName2 = trackName2
if genome is None:
genome = userBinSource.genome
self._analysis = Analysis(analysisDef, genome, trackName1, trackName2)
self._setRandomSeedIfNeeded()
track, track2 = self._analysis.getTracks()
StatJob.__init__(self, userBinSource, track, track2, self._analysis.getStat(), *args, **kwArgs)
def _setRandomSeedIfNeeded(self):
from gold.util.RandomUtil import getRandomSeed
randSeedChoice = self._analysis.getChoice('randomSeed')
if randSeedChoice == 'Random':
self._analysis.changeChoices('randomSeed', [(str(getRandomSeed()),)*2])
def run(self, printProgress=PRINT_PROGRESS):
'''
Runs the statistic specified in self._analysis (from analysisDef) and returns an object of class Result
'''
#Should be there for batch runs.. Should never happen from GUI..
if self._statClass == None:
self._handleMissingStat()
return None
if USE_PROFILING:
profiler = Profiler()
resDict = {}
profiler.run('resDict[0] = StatJob.run(self, printProgress=printProgress)', globals(), locals())
res = resDict[0]
else:
res = StatJob.run(self, printProgress=printProgress)
res.setAnalysis(self._analysis)
res.setAnalysisText(str(self._analysis))
ResultsMemoizer.flushStoredResults()
if USE_PROFILING:
profiler.printStats()
return res
def _handleMissingStat(self):
from gold.application.LogSetup import logMessage, logging
from gold.description.RunDescription import RunDescription
import gold.description.Analysis as AnalysisModule
#AnalysisModule.VERBOSE = True
msg = 'Started run with invalid statistic... Def: ' + self._analysisDef
#+ ', Run description: ' + \
#RunDescription.getRevEngBatchLine( self._trackName1, self._trackName2, self._analysisDef, \
#'Not Available', 'Not Available', self._userBinSource.genome)
logMessage(msg, level=logging.ERROR)
raise Exception(msg)
