def _createChildren(self):
if self._useMC:
rawStat = wrapClass(BasicCustomRStat, {'scriptFn':self._scriptFn})
#self._addChild( RandomizationManagerStat(self._region, self._track, self._track2, rawStat, \
# ReshuffledRandomizedTrack, numResamplings=20 ) )
self._addChild( RandomizationManagerStat(self._region, self._track, self._track2, rawStat, \
PermutedSegsAndSampledIntersegsTrack, numResamplings=20 ) )
else:
self._addChild(BasicCustomRStat(self._region, self._track, self._track2, self._scriptFn))
def test2():
myTrack = Track(['melting'])
myTrack2 = Track(['genes', 'refseq'])
userBinSource = UserBinSource('chr1:0-10', '10')
res = StatRunner.run(userBinSource, myTrack, myTrack2,
wrapClass(CustomRStat, {'scriptFn': fn}))
resColl = ResultsCollection()
resColl.addResults(None, res)
print resColl.getHtmlString()
def doAnalysis(analysisSpec, analysisBins, trackStructure):
'''Performs an analysis,
as specified by analysisSpec object,
in each bin specified by analysisBins,
on data sets specified in tracks.
Typical usage:
analysisSpec = AnalysisSpec(AvgSegLenStat)
analysisSpec.addParameter("withOverlaps","no")
analysisBins = GlobalBinSource('hg18')
tracks = [ Track(['Genes and gene subsets','Genes','Refseq']) ]
results = doAnalysis(analysisSpec, analysisBins, tracks)
'''
# TODO: handle multiple tracks analysis
# assert len(tracks) in [1,2] #for now..
# in an API setting, exceptions should not generally be hidden.
# Maybe this should be optional.
# setupDebugModeAndLogging()
silenceRWarnings()
silenceNumpyWarnings()
if isinstance(trackStructure, TrackStructureV2):
analysisDef = AnalysisDefHandler(analysisSpec.getDefAfterChoices())
statClass = analysisDef._statClassList[0]
validStatClass = wrapClass(
statClass,
keywords=analysisDef.getChoices(filterByActivation=True))
job = StatJob(analysisBins, trackStructure, validStatClass)
else:
tracks = trackStructure
if len(tracks) > 2:
from gold.util.CommonConstants import MULTIPLE_EXTRA_TRACKS_SEPARATOR
analysisSpec.addParameter(
'extraTracks',
MULTIPLE_EXTRA_TRACKS_SEPARATOR.join([
'^'.join([quote(part) for part in x.trackName])
for x in tracks[2:]
]))
job = AnalysisDefJob(analysisSpec.getDefAfterChoices(),
tracks[0].trackName,
tracks[1].trackName if len(tracks) > 1 else None,
analysisBins,
galaxyFn=None)
res = job.run(printProgress=False) # printProgress should be optional?
return res
if getClassName(e) == 'AttributeError' and \
any(x in str(e) for x in ["has no attribute '_track2'", "'NoneType' object has no attribute"]):
if DebugConfig.VERBOSE:
logException(e, level=logging.DEBUG, message='(Warning: error in _determineStatClass for stat: %s)' % statClass.__name__)
else:
logException(e, message='(Error in _determineStatClass, with statClass %s)' % statClass.__name__)
if DebugConfig.PASS_ON_VALIDSTAT_EXCEPTIONS:
raise
else:
#self._reversed = reversed
#self._conversionsUsed = len(trackA.conversionsUsed) > 0 or \
# ((trackB is not None) and len(trackB.conversionsUsed) > 0)
##self._validStatClass = functools.partial(statClass, **self.getChoices())
#functools.update_wrapper(self._validStatClass, statClass)
validStatClass = wrapClass(statClass, keywords=self.getChoices(filterByActivation=True) ) #fixme: Perhaps return validStatClass, self.getChoices() instead?
#self.setConverters( self._track.formatConverters, self._track2.formatConverters if self._track2 is not None else None)
#self._updateOptions()
if DebugConfig.VERBOSE:
logMessage(statClass.__name__ + ': OK')
# print statClass.__name__ + ': OK'
return validStatClass
finally:
self.resetTracks()
return None
def _appendConverterOptions(self, track, labelKey):
if track is None:
return
any(x in str(e) for x in ["has no attribute '_track2'","'NoneType' object has no attribute"]):
if DebugConfig.VERBOSE:
logException(e, message='(Warning: error in _determineStatClass for stat: %s)' % statClass.__name__)
else:
logException(e, message='(Error in _determineStatClass, with statClass %s)' % statClass.__name__)
#if VERBOSE:
# print 'Warning: exception in getStat: ', \
# statClass.__name__ + ': ' + e.__class__.__name__ + ': ' + str(e)
# traceback.print_exc(file=sys.stdout)
else:
#self._reversed = reversed
#self._conversionsUsed = len(trackA.conversionsUsed) > 0 or \
# ((trackB is not None) and len(trackB.conversionsUsed) > 0)
##self._validStatClass = functools.partial(statClass, **self.getChoices())
#functools.update_wrapper(self._validStatClass, statClass)
validStatClass = wrapClass(statClass, keywords=self.getChoices() )
#self.setConverters( self._track.formatConverters, self._track2.formatConverters if self._track2 is not None else None)
#self._updateOptions()
if DebugConfig.VERBOSE:
logMessage(statClass.__name__ + ': OK')
# print statClass.__name__ + ': OK'
return validStatClass
return None
def _appendConverterOptions(self, track, labelKey):
if track is None:
return
if self.getChoice(labelKey) is not None:
assert(self.getChoice(labelKey) == getClassName(track.formatConverters[0]))