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)
track, track2 = self._analysis.getTracks()
statistic = self._analysis.getStat()
self._analysis.initRandomUtilAndUpdateSeedIfNeeded()
StatJob.__init__(self, userBinSource, track, track2, statistic, *args,
**kwArgs)
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.updateFromAnalysis(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... 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)
