def execute(cls, choices, galaxyFn=None, username=''):
'''
Is called when execute-button is pushed by web-user. Should print
output as HTML to standard out, which will be directed to a results page
in Galaxy history. If getOutputFormat is anything else than HTML, the
output should be written to the file with path galaxyFn. If needed,
StaticFile can be used to get a path where additional files can be put
(e.g. generated image files). choices is a list of selections made by
web-user in each options box.
'''
if choices[0] == cls.INPUT_FIELD:
batchStr = choices[1]
else:
from quick.application.ExternalTrackManager import ExternalTrackManager
batchStr = open(
ExternalTrackManager.extractFnFromGalaxyTN(
choices[2].split(':'))).read()
batchLines = [x.strip() for x in batchStr.strip().split(os.linesep)]
#batchLines = [x.strip() for x in choices[0].strip().split(os.linesep)]
legalBatchLines = cls._removeIllegalLines(batchLines, username)
if len(legalBatchLines) > 0:
GalaxyInterface.runBatchLines(batchLines=legalBatchLines, galaxyFn=galaxyFn, \
genome=None, username=username)
else:
return 'Your user does not have access to run these command lines.'
def directGetEnrichment(diseaseTrack,
refTrackLeaf,
refTrackBase,
kernelType,
kernelParam,
useCache=True,
printProgress=False):
RETRIEVE_FROM_CACHE = useCache
STORE_TO_CACHE = useCache
if kernelType == 'gaussian':
kernelParamAssignment = ',kernelStdev=%s' % kernelParam
elif kernelType == 'divideByOffset':
kernelParamAssignment = ',minimumOffsetValue=%s' % kernelParam
elif kernelType == 'binSizeNormalized':
kernelParamAssignment = ''
elif kernelType == 'catCoverageNormalized':
kernelParamAssignment = ''
elif kernelType == 'uniform':
kernelParamAssignment = ''
else:
raise #RuntimeError('unre'
batchText = '''
@bins=%s
@TNs=%s:%s
@TNunion=%s
hg19|track|@bins|@TNs|@TNunion|DiffRelCoverageStat(globalSource=chrs,tf1=TrivialFormatConverter,tf2=TrivialFormatConverter,withOverlaps=yes,kernelType=%s%s)
''' % (diseaseTrack, refTrackBase, refTrackLeaf, refTrackBase, kernelType,
kernelParamAssignment)
#print 'BATCHLINE: <br>', batchText
import hashlib
hashName = hashlib.sha1(batchText).hexdigest()
sf = PickleStaticFile(['files', 'Caches', 'Tool7', hashName])
#shelf = safeshelve.open(sf.getDiskPath(True))
#if batchText in shelf:
if RETRIEVE_FROM_CACHE and sf.fileExists():
print ',',
#print 'Retrieving batch result (%s): %s' % (sf.getDiskPath(), batchText)
#return shelf[batchText]
return sf.loadPickledObject()
else:
print '.',
#print 'Running batch: ', batchText
#shelf.close()
batchLines = batchText.split('\n')
from quick.application.GalaxyInterface import GalaxyInterface
res = GalaxyInterface.runBatchLines(batchLines,
username='******',
printResults=False,
printProgress=printProgress)[0]
#global TEMP_NUM_BATCH_RUNS_SO_FAR
#print 'Running batchLines (%s): %s<br>Getting result: %s<br>' % (TEMP_NUM_BATCH_RUNS_SO_FAR, batchLines, res)
#TEMP_NUM_BATCH_RUNS_SO_FAR += 1
#shelf = safeshelve.open(sf.getDiskPath(True))
#shelf[batchText] = res
#shelf.close()
res.batchText = batchText
if STORE_TO_CACHE:
sf.storePickledObject(res)
return res
def execute(choices, galaxyFn=None, username=''):
'''
Is called when execute-button is pushed by web-user. Should print
output as HTML to standard out, which will be directed to a results page
in Galaxy history. If getOutputFormat is anything else than HTML, the
output should be written to the file with path galaxyFn. If needed,
StaticFile can be used to get a path where additional files can be put
(e.g. generated image files). choices is a list of selections made by
web-user in each options box.
'''
if GalaxyInterface._userHasFullAccess(username) or len([i for i in choices[0].split('\n') if len(i.strip())>0 and i.strip()[0]=='$'])==0:
runStr = choices[0]
GalaxyInterface.runBatchLines(batchLines=runStr.split('\n'), galaxyFn=galaxyFn, genome=None, username=username)
else:
print 'Your user does not have access to run this command line.'
def execute(choices, galaxyFn=None, username=''):
'''
Is called when execute-button is pushed by web-user. Should print
output as HTML to standard out, which will be directed to a results page
in Galaxy history. If getOutputFormat is anything else than HTML, the
output should be written to the file with path galaxyFn. If needed,
StaticFile can be used to get a path where additional files can be put
(e.g. generated image files). choices is a list of selections made by
web-user in each options box.
'''
genome = choices[0]
batchLines = choices[1].split('\n')
assert choices[2] in ['False','True']
verbose = (choices[2] == 'True')
DebugAnalysisTool.setupDebugModeAndLogging(verbose=False) #set from selection box..
try:
GalaxyInterface.runBatchLines(batchLines, galaxyFn, genome, username)
except Exception, e:
print '</div>'
print traceback.format_exc()
print e
raise
def execute(cls, choices, galaxyFn=None, username=''):
'''
Is called when execute-button is pushed by web-user. Should print
output as HTML to standard out, which will be directed to a results page
in Galaxy history. If getOutputFormat is anything else than HTML, the
output should be written to the file with path galaxyFn. If needed,
StaticFile can be used to get a path where additional files can be put
(e.g. generated image files). choices is a list of selections made by
web-user in each options box.
'''
batchLines = choices[0].split('\n')
assert choices[1] in ['False','True']
verbose = (choices[1] == 'True')
from gold.application.LogSetup import setupDebugModeAndLogging
setupDebugModeAndLogging()
try:
GalaxyInterface.runBatchLines(batchLines, galaxyFn, username=username)
except Exception, e:
print '</div>'
print traceback.format_exc()
print e
raise
def execute_batch(cls, choices, galaxyFn=None, username=''):
print GalaxyInterface.getHtmlBeginForRuns(galaxyFn)
html = HtmlCore()
html.header('Batch run results')
refSnps = cls.get_ref_snp(choices)
#print refSnps
batchMal = "$Tool[hb_variant_melting_profiles](" + '|'.join(
["'%s'"] * len(choices)) + ")"
cmdList = []
for rs in refSnps:
#if len(rs[4]) > 1:
# rs = list(rs)
# rs[4] = list(rs[4])[0]
# rs = tuple(rs)
fakeChoices = (choices.genome, 'Single',
'__batch__') + rs + choices[8:]
#print rs
cmdList.append(batchMal % fakeChoices)
#print cmdList
GalaxyInterface.runBatchLines(cmdList,
galaxyFn,
username=username,
printResults=False,
printProgress=True)
#print HtmlCore().styleInfoEnd()
results_tsv = GalaxyRunSpecificFile(['results.tsv'], galaxyFn)
results = results_tsv.getFile()
dir = os.path.dirname(results_tsv.getDiskPath())
for i in range(0, len(cmdList)):
header = True
ri = 0
for resultline in open(os.path.join(dir, str(i), 'results.tsv')):
if header:
header = False
if i == 0:
headertxt = '#run\t' + resultline
results.write(headertxt)
html.tableHeader(headertxt.split('\t'))
else:
results.write(str(i) + '\t' + resultline)
if resultline.count('?') == 0:
link = '<a href="%d/html/chart-%d.html">%d (graph)</a>' % (
i, ri, i)
else:
link = str(i)
html.tableLine([link] + resultline.split('\t'))
ri += 1
results.close()
html.tableFooter()
# XXX: temp fix for HB/stable bug
if URL_PREFIX == '/hb':
print '</div>'
print '<p><b>' + results_tsv.getLink('Download results') + '</b></p>'
print html
print GalaxyInterface.getHtmlEndForRuns()
def directGetTestResults(diseaseTrack,
refTrackLeaf,
refTrackBase,
kernelType,
kernelParam,
refTrackCoverageFunction,
nullmodel,
mcDepth='high',
useCache=True,
printProgress=False):
RETRIEVE_FROM_CACHE = useCache
STORE_TO_CACHE = useCache
if mcDepth == 'high':
mcParams = 'fdrThreshold=1.0,globalPvalThreshold=0.00002,maxSamples=50000,numResamplings=100,numSamplesPerChunk=50,mThreshold=20,fdrCriterion=simultaneous'
elif mcDepth == 'relatively high':
mcParams = 'fdrThreshold=1.0,globalPvalThreshold=0.0001,maxSamples=10000,numResamplings=100,numSamplesPerChunk=50,mThreshold=20,fdrCriterion=simultaneous'
elif mcDepth == 'moderate':
mcParams = 'fdrThreshold=1.0,globalPvalThreshold=0.001,maxSamples=1000,numResamplings=50,numSamplesPerChunk=50,mThreshold=10,fdrCriterion=simultaneous'
elif mcDepth == 'low':
mcParams = 'fdrThreshold=1.0,globalPvalThreshold=1.0,maxSamples=10,numResamplings=10,numSamplesPerChunk=10,mThreshold=20,fdrCriterion=simultaneous'
elif mcDepth == 'extremely low':
mcParams = 'fdrThreshold=1.0,globalPvalThreshold=1.0,maxSamples=2,numResamplings=2,numSamplesPerChunk=10,mThreshold=20,fdrCriterion=simultaneous'
else:
raise
if kernelType == 'gaussian':
kernelParamAssignment = ',kernelStdev=%s' % kernelParam
spreadParamAssignment = ',spreadParam=%s' % kernelParam
elif kernelType == 'divideByOffset':
kernelParamAssignment = ',minimumOffsetValue=%s' % kernelParam
spreadParamAssignment = ',spreadParam=%s' % kernelParam
elif kernelType == 'binSizeNormalized':
kernelParamAssignment = ''
spreadParamAssignment = ''
elif kernelType == 'catCoverageNormalized':
kernelParamAssignment = ''
spreadParamAssignment = ''
elif kernelType == 'binSizeNormalizedV2':
kernelParamAssignment = ''
spreadParamAssignment = ''
assert nullmodel in [
'RandomGenomeLocationTrack_',
'PermutedSegsAndSampledIntersegsTrack_'
] #with last option, the end result would be about the same in the corresponding three track version..
nullmodel = 'RandomGenomeLocationTrack_'
elif kernelType == 'binSizeNormalizedV3':
kernelParamAssignment = ''
spreadParamAssignment = ''
elif kernelType == 'uniform':
kernelParamAssignment = ''
spreadParamAssignment = ''
else:
raise #RuntimeError('unre'
#if nullmodel=='SegsSampledByDistanceToReferenceTrack_':
# exonRefTrack = ',trackNameIntensity=Genes and gene subsets^Exons^Ensembl exons'
#else:
# exonRefTrack = ''
import urllib
if kernelType == 'binSizeNormalizedV2':
batchText = '''
@TraitBins = %s
@TN1=%s:%s
@TN2=%s
@rawStat=rawStatistic=DiffRelCoverageMainValueStat
@assump=assumptions=%s
@randParams=randomSeed=Random,tail=more,@assump
@mcParams=%s
@conv=tf1=TrivialFormatConverter,tf2=TrivialFormatConverter
@kernelParams=kernelType=binSizeNormalized
hg19|track|@TraitBins|@TN1|@TN2|RandomizationManagerStat(@rawStat,globalSource=userbins,@mcParams,@randParams,@conv,@kernelParams,includeFullNullDistribution=yes)
''' % (urllib.quote(diseaseTrack), refTrackBase, refTrackLeaf, refTrackBase,
nullmodel, mcParams, kernelType, spreadParamAssignment,
kernelParamAssignment)
else:
batchText = '''
@TN1= %s
@TN2s=%s:%s
@extraTracks=%s
@binning=__chrArms__|*
@rawStat=rawStatistic=ThreeTrackT2inT1vsT3inT1KernelVersionStat
@assump=assumptions=%s
@randParams=randomSeed=Random,tail=more,@assump
@mcParams=%s
@conv=tf1=TrivialFormatConverter,tf2=TrivialFormatConverter
@kernelParams=kernelType=%s%s%s
hg19|@binning|@TN1|@TN2s|RandomizationManagerStat(@rawStat,globalSource=userbins,@mcParams,@randParams,@conv,extraTracks=@extraTracks,@kernelParams,silentProgress=yes)
''' % (diseaseTrack, refTrackBase, refTrackLeaf, refTrackCoverageFunction,
nullmodel, mcParams, kernelType, spreadParamAssignment,
kernelParamAssignment)
# '''
#@bins=%s
#@TNs=%s:%s
#@TNunion=%s
#hg19|track|@bins|@TNs|@TNunion|DiffRelCoverageStat(globalSource=chrs,tf1=TrivialFormatConverter,tf2=TrivialFormatConverter,withOverlaps=yes,kernelType=%s%s)
#''' % (diseaseTrack, refTrackBase, refTrackLeaf, refTrackBase,kernelType, kernelParamAssignment)
#print 'BATCHLINE: <br>', batchText
import hashlib
hashName = hashlib.sha1(batchText).hexdigest()
sf = PickleStaticFile(['files', 'Caches', 'Tool7', hashName])
if RETRIEVE_FROM_CACHE and sf.fileExists():
print ',',
#print 'Retrieving batch result (%s): %s' % (sf.getDiskPath(), batchText)
#return shelf[batchText]
return sf.loadPickledObject()
else:
print '.',
#print 'Running batch: ', batchText
#shelf.close()
batchLines = batchText.split('\n')
from quick.application.GalaxyInterface import GalaxyInterface
res = GalaxyInterface.runBatchLines(batchLines,
username='******',
printResults=False,
printProgress=printProgress)[0]
#print 'Running batchLines (%s): %s<br>Getting result: %s<br>' % ('', batchLines, res) #TEMP_NUM_BATCH_RUNS_SO_FAR
res.batchText = batchText
if STORE_TO_CACHE:
sf.storePickledObject(res)
return res
