def isStatisticInChildren(cls, job, statisticName):
for region in job._userBinSource:
stat = job._statClass(region, job._track, job._track2, *job._args, **job._kwArgs)
break
stat.createChildren()
result = cls.searchForStatisticRecursively(stat, statisticName)
MagicStatFactory.resetMemoDict()
return result
def run(self, reset=True, printProgress=PRINT_PROGRESS):
if reset:
MagicStatFactory.resetMemoDict()
results = self._emptyResults()
try:
self._checkNumUserBinsIsValid()
except Exception, e:
results.addError(e)
return results
def isStatisticInChildren(cls, job, statisticName):
for region in job._userBinSource:
stat = job._statClass(region, job._track, job._track2, *job._args, **job._kwArgs)
break
stat.createChildren()
result = cls.searchForStatisticRecursively(stat, statisticName)
MagicStatFactory.resetMemoDict()
return result
def run(self, reset=True, printProgress=PRINT_PROGRESS):
if reset:
MagicStatFactory.resetMemoDict()
results = self._emptyResults()
try:
self._checkNumUserBinsIsValid()
except Exception, e:
results.addError(e)
return results
def __new__(cls, region, track, trackFormatReq, **kwArgs):
assert isinstance(trackFormatReq, TrackFormatReq)
return MagicStatFactory.__new__(cls,
region,
track,
trackFormatReq=trackFormatReq,
**kwArgs)
def _setExtraParams(cls, prevChoices):
methodObj = getattr( MagicStatFactory._getClass(prevChoices[0], 'Unsplittable') , '__init__')
methodParams = ['Region','BinSpec']+[v for v in getargspec(methodObj).args if not v in ['self', 'track', 'track2', 'region']]
defaultVals = ['','']+(list(getargspec(methodObj).defaults) if getargspec(methodObj).defaults and len(methodParams)>0 else [])
lenDifference = len(methodParams)-len(defaultVals)
defaultVals = ['']*(lenDifference)+ defaultVals if lenDifference>=0 else defaultVals[-lenDifference:]
cls._extraParams = [value + ' (default: %s)' % defaultVals[index] for index, value in enumerate(methodParams)]
def _setExtraParams(cls, prevChoices):
methodObj = getattr(
MagicStatFactory._getClass(prevChoices[0], 'Unsplittable'),
'__init__')
methodParams = ['Region', 'BinSpec'] + [
v for v in getargspec(methodObj).args
if not v in ['self', 'track', 'track2', 'region']
]
defaultVals = ['', ''] + (list(getargspec(methodObj).defaults)
if getargspec(methodObj).defaults
and len(methodParams) > 0 else [])
lenDifference = len(methodParams) - len(defaultVals)
defaultVals = [''] * (
lenDifference
) + defaultVals if lenDifference >= 0 else defaultVals[-lenDifference:]
cls._extraParams = [
value + ' (default: %s)' % defaultVals[index]
for index, value in enumerate(methodParams)
]
def __new__(cls, region, track, trackFormatReq, **kwArgs):
assert isinstance(trackFormatReq, TrackFormatReq)
track.addFormatReq(trackFormatReq)
return MagicStatFactory.__new__(cls, region, track, **kwArgs)
def execute(cls, choices, galaxyFn=None, username=''):
shelveDict = {
'track1':
choices[3] if choices[3] != cls.NO_TRACK_SHORTNAME else None
}
shelveDict['track2'] = choices[
5] if choices[5] != cls.NO_TRACK_SHORTNAME else None
print len(choices)
print cls._extraParams
for i in range(len(cls._extraParams)):
index = i * 2 + cls.FIRST_EXTRA_PARAM_BOX_NUMBER + 1
shelveDict[index] = choices[index].strip()
DebugInfoShelve = safeshelve.open(cls.SHELVE_FN)
DebugInfoShelve[choices[0]] = shelveDict
DebugInfoShelve.close()
try:
from gold.application.LogSetup import setupDebugModeAndLogging
setupDebugModeAndLogging()
print 'Getting Unsplittable statClass'
statClassName = choices[0]
#statClass = STAT_CLASS_DICT[statClassName]
#try:
print 'Preparing arguments to init'
unsplittableStatClass = MagicStatFactory._getClass(
statClassName, 'Unsplittable')
genome = choices[1]
from gold.track.Track import PlainTrack
prefixTN1 = cls.STD_PREFIX_TN if choices[2] == 'yes' else []
tn1 = prefixTN1 + choices[3].split(':')
track1 = PlainTrack(
tn1) if choices[3] != cls.NO_TRACK_SHORTNAME else None
prefixTN2 = cls.STD_PREFIX_TN if choices[4] == 'yes' else []
tn2 = prefixTN2 + choices[5].split(':')
track2 = PlainTrack(
tn2) if choices[5] != cls.NO_TRACK_SHORTNAME else None
from gold.track.GenomeRegion import GenomeRegion
#region = GenomeRegion(genome, 'chr1',1000,2000)
#region2 = GenomeRegion(genome, 'chr1',5000,6000)
kwArgs = {}
regVal = choices[cls.FIRST_EXTRA_PARAM_BOX_NUMBER + 1]
binSpecVal = choices[cls.FIRST_EXTRA_PARAM_BOX_NUMBER + 3]
ubSource = UserBinSource(regVal, binSpecVal, genome=genome)
region = list(ubSource)[0]
if len(cls._extraParams) > 3:
for i in range(len(cls._extraParams)):
paramName = choices[i * 2 +
cls.FIRST_EXTRA_PARAM_BOX_NUMBER]
param = paramName[:paramName.find('(')].strip()
val = choices[i * 2 + cls.FIRST_EXTRA_PARAM_BOX_NUMBER +
1].strip()
if val != '':
kwArgs[param] = val
shelveDict[i * 2 + cls.FIRST_EXTRA_PARAM_BOX_NUMBER +
1] = val
print 'Calling __init__'
#
statObj = unsplittableStatClass(region, track1, track2, **kwArgs)
print 'Calling createChildren'
statObj.createChildren()
print 'Calling getResult'
statObj.getResult()
#except:
# raise
#print 'Preparing arguments to init'
#genome = 'hg18'
#prefixTN = ['DNA structure'] if choices[2] == 'yes' else []
#from gold.track.Track import PlainTrack
#tn1 = prefixTN + choices[3].split(':')
#track1 = PlainTrack(tn1)
#tn2 = prefixTN + choices[5].split(':')
#track2 = PlainTrack(tn2)
#from gold.track.GenomeRegion import GenomeRegion
##region = GenomeRegion(genome, 'chr1',1000,2000)
##region2 = GenomeRegion(genome, 'chr1',5000,6000)
#
#kwArgs = {}
#regVal = choices[cls.FIRST_EXTRA_PARAM_BOX_NUMBER+1]
#binSpecVal = choices[cls.FIRST_EXTRA_PARAM_BOX_NUMBER+3]
#ubSource = UserBinSource(regVal, binSpecVal, genome=choices[1])
#region = list(UserBinSource)[0]
#
#if len(cls._extraParams)>2:
# for i in range(2,len(cls._extraParams)):
# paramName = choices[i*2+cls.FIRST_EXTRA_PARAM_BOX_NUMBER]
# param = paramName[:paramName.find('(')].strip()
# val = choices[i*2+cls.FIRST_EXTRA_PARAM_BOX_NUMBER+1].strip()
# if val !='':
# kwArgs[param] = val
# shelveDict[i*2+cls.FIRST_EXTRA_PARAM_BOX_NUMBER+1] = val
#
#
##extraParams += [v.strip() for v in choices.kwArgs.split(',')] if choices.kwArgs.strip() != '' else []
##args = [region, track1, track2]
#
#print 'Calling __init__'
##
#statObj = unsplittableStatClass(region, track1, track2, **kwArgs)
#
#print 'Calling createChildren'
#statObj.createChildren()
#
#print 'Calling getResult'
#statObj.getResult()
print 'Running StatJob'
magicStatClass = STAT_CLASS_DICT[statClassName]
#res = StatJob([region,region2],track1,track2,magicStatClass,**kwArgs).run()
res = StatJob(ubSource, track1, track2, magicStatClass,
**kwArgs).run()
from quick.application.GalaxyInterface import GalaxyInterface
GalaxyInterface._viewResults([res], galaxyFn)
except Exception, e:
print 'Error: ', e
raise
def _updateInMemoDict(self, statKwUpdateDict):
from gold.statistic.MagicStatFactory import MagicStatFactory
MagicStatFactory.updateMemoDict(self, statKwUpdateDict)
def execute(cls, choices, galaxyFn=None, username=''):
shelveDict = {'track1':choices[3] if choices[3]!=cls.NO_TRACK_SHORTNAME else None}
shelveDict['track2'] = choices[5] if choices[5]!=cls.NO_TRACK_SHORTNAME else None
print len(choices)
print cls._extraParams
for i in range(len(cls._extraParams)):
index = i*2+cls.FIRST_EXTRA_PARAM_BOX_NUMBER+1
shelveDict[index] = choices[index].strip()
DebugInfoShelve = safeshelve.open(cls.SHELVE_FN)
DebugInfoShelve[choices[0]] = shelveDict
DebugInfoShelve.close()
try:
cls.setupDebugModeAndLogging(verbose=False) #add box to select this
print 'Getting Unsplittable statClass'
statClassName = choices[0]
#statClass = STAT_CLASS_DICT[statClassName]
#try:
print 'Preparing arguments to init'
unsplittableStatClass = MagicStatFactory._getClass(statClassName, 'Unsplittable')
genome = choices[1]
from gold.track.Track import PlainTrack
prefixTN1 = cls.STD_PREFIX_TN if choices[2] == 'yes' else []
tn1 = prefixTN1 + choices[3].split(':')
track1 = PlainTrack(tn1) if choices[3]!=cls.NO_TRACK_SHORTNAME else None
prefixTN2 = cls.STD_PREFIX_TN if choices[4] == 'yes' else []
tn2 = prefixTN2 + choices[5].split(':')
track2 = PlainTrack(tn2) if choices[5]!=cls.NO_TRACK_SHORTNAME else None
from gold.track.GenomeRegion import GenomeRegion
#region = GenomeRegion(genome, 'chr1',1000,2000)
#region2 = GenomeRegion(genome, 'chr1',5000,6000)
kwArgs = {}
regVal = choices[cls.FIRST_EXTRA_PARAM_BOX_NUMBER+1]
binSpecVal = choices[cls.FIRST_EXTRA_PARAM_BOX_NUMBER+3]
ubSource = UserBinSource(regVal, binSpecVal, genome=genome)
region = list(ubSource)[0]
if len(cls._extraParams)>3:
for i in range(len(cls._extraParams)):
paramName = choices[i*2+cls.FIRST_EXTRA_PARAM_BOX_NUMBER]
param = paramName[:paramName.find('(')].strip()
val = choices[i*2+cls.FIRST_EXTRA_PARAM_BOX_NUMBER+1].strip()
if val !='':
kwArgs[param] = val
shelveDict[i*2+cls.FIRST_EXTRA_PARAM_BOX_NUMBER+1] = val
print 'Calling __init__'
#
statObj = unsplittableStatClass(region, track1, track2, **kwArgs)
print 'Calling createChildren'
statObj.createChildren()
print 'Calling getResult'
statObj.getResult()
#except:
# raise
#print 'Preparing arguments to init'
#genome = 'hg18'
#prefixTN = ['DNA structure'] if choices[2] == 'yes' else []
#from gold.track.Track import PlainTrack
#tn1 = prefixTN + choices[3].split(':')
#track1 = PlainTrack(tn1)
#tn2 = prefixTN + choices[5].split(':')
#track2 = PlainTrack(tn2)
#from gold.track.GenomeRegion import GenomeRegion
##region = GenomeRegion(genome, 'chr1',1000,2000)
##region2 = GenomeRegion(genome, 'chr1',5000,6000)
#
#kwArgs = {}
#regVal = choices[cls.FIRST_EXTRA_PARAM_BOX_NUMBER+1]
#binSpecVal = choices[cls.FIRST_EXTRA_PARAM_BOX_NUMBER+3]
#ubSource = UserBinSource(regVal, binSpecVal, genome=choices[1])
#region = list(UserBinSource)[0]
#
#if len(cls._extraParams)>2:
# for i in range(2,len(cls._extraParams)):
# paramName = choices[i*2+cls.FIRST_EXTRA_PARAM_BOX_NUMBER]
# param = paramName[:paramName.find('(')].strip()
# val = choices[i*2+cls.FIRST_EXTRA_PARAM_BOX_NUMBER+1].strip()
# if val !='':
# kwArgs[param] = val
# shelveDict[i*2+cls.FIRST_EXTRA_PARAM_BOX_NUMBER+1] = val
#
#
##extraParams += [v.strip() for v in choices.kwArgs.split(',')] if choices.kwArgs.strip() != '' else []
##args = [region, track1, track2]
#
#print 'Calling __init__'
##
#statObj = unsplittableStatClass(region, track1, track2, **kwArgs)
#
#print 'Calling createChildren'
#statObj.createChildren()
#
#print 'Calling getResult'
#statObj.getResult()
print 'Running StatJob'
magicStatClass = STAT_CLASS_DICT[statClassName]
#res = StatJob([region,region2],track1,track2,magicStatClass,**kwArgs).run()
res = StatJob(ubSource,track1,track2,magicStatClass,**kwArgs).run()
from quick.application.GalaxyInterface import GalaxyInterface
GalaxyInterface._viewResults([res],galaxyFn)
except Exception, e:
print 'Error: ',e
raise
def _updateInMemoDict(self, statKwUpdateDict):
from gold.statistic.MagicStatFactory import MagicStatFactory
MagicStatFactory.updateMemoDict(self, statKwUpdateDict)