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.'
