def __init__(self, geSource):
self._geSource = self._decorateGESource(geSource)
self._boundingRegionsAndGEsCorresponds = None
self._areValsCategorical = TrackFormat.createInstanceFromGeSource(geSource).getValTypeName() == 'Category'
self._areEdgeWeightsCategorical = TrackFormat.createInstanceFromGeSource(geSource).getWeightTypeName() == 'Category'
self._valCategories = set()
self._edgeWeightCategories = set()
self._numElements = OrderedDefaultDict(int)
self._maxStrLens = OrderedDefaultDict(partial(self._initMaxStrLens, self._getMaxStrLensKeys()))
self._maxNumEdges = OrderedDefaultDict(int)
self._hasCalculatedStats = False
def __init__(self, geSource):
self._geSource = self._decorateGESource(geSource)
self._boundingRegionsAndGEsCorrespond = None
self._areValsCategorical = TrackFormat.createInstanceFromGeSource(geSource).getValTypeName() == 'Category'
self._areEdgeWeightsCategorical = TrackFormat.createInstanceFromGeSource(geSource).getWeightTypeName() == 'Category'
self._valCategories = set()
self._edgeWeightCategories = set()
self._numElements = OrderedDefaultDict(int)
self._maxStrLens = OrderedDefaultDict(partial(self._initMaxStrLens, self._getMaxStrLensKeys()))
self._maxNumEdges = OrderedDefaultDict(int)
self._hasCalculatedStats = False
def _composeContents(self,
out,
hbColumns,
columns,
geSource,
onlyNonDefault=True,
singleDataLine=False):
tf = TrackFormat.createInstanceFromGeSource(self._geSource)
out.write(self._composeHeaderLines(onlyNonDefault))
out.write(self._composeColSpecLine(columns))
for br, geList in iterateOverBRTuplesWithContainedGEs(
geSource, onlyYieldTwoGEs=singleDataLine):
if br is not None:
out.write(self._composeBoundingRegionLine(br))
for i, ge in enumerate(
self._removeStartElementIfApplicable(tf, geList)):
out.write(
self._composeDataLine(ge, hbColumns, i + 1,
i + 1 == len(geList)))
if singleDataLine:
break
if singleDataLine:
break
def _getGESourceManagerFromGESource(self, geSource):
tf = TrackFormat.createInstanceFromGeSource(geSource)
if tf.reprIsDense():
if tf.getValTypeName() in ['Number', 'Number (integer)', 'Case-control']:
return RegionBasedGESourceManager(geSource, self._regionList, \
calcStatsInExtraPass=False, countElsInBoundingRegions=False)
else:
raise NotSupportedError
else:
return RegionBasedGESourceManager(geSource, self._regionList, \
calcStatsInExtraPass=True, countElsInBoundingRegions=True)
def _getGESourceManagerFromGESource(self, geSource):
tf = TrackFormat.createInstanceFromGeSource(geSource)
if tf.reprIsDense():
if tf.getValTypeName() in [
'Number', 'Number (integer)', 'Case-control'
]:
return RegionBasedGESourceManager(geSource, self._regionList, \
calcStatsInExtraPass=False, countElsInBoundingRegions=False)
else:
raise NotSupportedError
else:
return RegionBasedGESourceManager(geSource, self._regionList, \
calcStatsInExtraPass=True, countElsInBoundingRegions=True)
def _composeContents(self, out, hbColumns, columns, geSource, onlyNonDefault=True, singleDataLine=False):
tf = TrackFormat.createInstanceFromGeSource(self._geSource)
out.write( self._composeHeaderLines(onlyNonDefault) )
out.write( self._composeColSpecLine(columns) )
for br, geList in iterateOverBRTuplesWithContainedGEs(geSource, onlyYieldTwoGEs=singleDataLine):
if br is not None:
out.write( self._composeBoundingRegionLine(br) )
for i, ge in enumerate(self._removeStartElementIfApplicable(tf, geList)):
out.write( self._composeDataLine(ge, hbColumns, i+1, i+1 == len(geList)) )
if singleDataLine:
break
if singleDataLine:
break
def testSorting(self):
geSourceTest = self._commonSetup()
for caseName in geSourceTest.cases:
if not caseName.startswith("gtrack"):
continue
if "no_sort" in caseName:
print "Test case skipped: " + caseName
continue
print caseName
print
case = geSourceTest.cases[caseName]
testFn = self._writeTestFile(case)
print open(testFn).read()
print
sortedContents = sortGtrackFileAndReturnContents(testFn, case.genome)
print sortedContents
sourceClass = GenomeElementSource if case.sourceClass is None else case.sourceClass
forPreProcessor = True if case.sourceClass is None else False
sortedGeSource = GEDependentAttributesHolder(
sourceClass(
"sortedFile.gtrack",
case.genome,
forPreProcessor=forPreProcessor,
printWarnings=False,
strToUseInsteadOfFn=sortedContents,
)
)
reprIsDense = TrackFormat.createInstanceFromGeSource(sortedGeSource).reprIsDense()
if not reprIsDense:
self.assertEquals(sorted(case.assertElementList), [ge for ge in sortedGeSource])
else:
for ge in sortedGeSource:
pass
self.assertEquals(
sorted(case.boundingRegionsAssertList), [br for br in sortedGeSource.getBoundingRegionTuples()]
)
def _compose(self, out):
trackName = self._geSource.getTrackName()
if trackName is not None:
name = ':'.join(self._geSource.getTrackName()).replace(' ', '_')
else:
name = None
print >> out, 'track type=wiggle_0' + (' name=%s' % name
if name is not None else '')
tf = TrackFormat.createInstanceFromGeSource(self._geSource)
span = self._geSource.getFixedLength()
step = self._geSource.getFixedGapSize() + span
isFixedStep = (tf.reprIsDense() or step > 1
or (step == 1 and span != 1))
for brt, geList in iterateOverBRTuplesWithContainedGEs(self._geSource):
if len(geList) == 0:
continue
if isFixedStep:
self._composeFixedStepDeclarationLine(out, brt.region, step,
span)
else:
curChr, curSpan = self._composeVariableStepDeclarationLine(
out, geList[0])
for i, ge in enumerate(geList):
if i==0 and tf.isDense() and tf.isInterval() and \
self._geSource.addsStartElementToDenseIntervals():
continue
val = self._commonFormatNumberVal(ge.val)
if isFixedStep:
cols = [val]
else:
if ge.chr != curChr or self._getVariableSpan(
ge) != curSpan:
curChr, curSpan = self._composeVariableStepDeclarationLine(
out, ge)
cols = [str(ge.start + 1), val]
print >> out, '\t'.join([str(x) for x in cols])
def _allGESourceManagers(self, trackName, allowOverlaps):
collector = PreProcMetaDataCollector(self._genome, trackName)
if allowOverlaps == False and collector.overlapRuleHasBeenFinalized(True):
for i in range(1):
self._status = 'Trying to prepare preprocessing for track "%s"' % ':'.join(trackName) + \
(' (allowOverlaps: %s)' % allowOverlaps)
yield self._getGESourceManagerFromTrack(trackName)
else:
for geSource in self._allGESources(trackName):
if allowOverlaps == True:
tf = TrackFormat.createInstanceFromGeSource(geSource)
if tf.isDense() or geSource.hasNoOverlappingElements():
return
self._status = 'Trying to prepare preprocessing for track "%s"' % ':'.join(trackName) + \
(' (filename: "%s")' % geSource.getFileName() if geSource.hasOrigFile() else '') + \
(' (allowOverlaps: %s)' % allowOverlaps)
if PreProcessUtils.shouldPreProcessGESource(trackName, geSource, allowOverlaps):
yield self._getGESourceManagerFromGESource(geSource)
def _allGESourceManagers(self, trackName, allowOverlaps):
collector = PreProcMetaDataCollector(self._genome, trackName)
if allowOverlaps == False and collector.overlapRuleHasBeenFinalized(
True):
for i in range(1):
self._status = 'Trying to prepare preprocessing for track "%s"' % ':'.join(trackName) + \
(' (allowOverlaps: %s)' % allowOverlaps)
yield self._getGESourceManagerFromTrack(trackName)
else:
for geSource in self._allGESources(trackName):
if allowOverlaps == True:
tf = TrackFormat.createInstanceFromGeSource(geSource)
if tf.isDense() or geSource.hasNoOverlappingElements():
return
self._status = 'Trying to prepare preprocessing for track "%s"' % ':'.join(trackName) + \
(' (filename: "%s")' % geSource.getFileName() if geSource.hasOrigFile() else '') + \
(' (allowOverlaps: %s)' % allowOverlaps)
if PreProcessUtils.shouldPreProcessGESource(
trackName, geSource, allowOverlaps):
yield self._getGESourceManagerFromGESource(geSource)
def _compose(self, out):
trackName = self._geSource.getTrackName()
if trackName is not None:
name = ':'.join(self._geSource.getTrackName()).replace(' ','_')
else:
name = None
print >>out, 'track type=wiggle_0' + (' name=%s' % name if name is not None else '')
tf = TrackFormat.createInstanceFromGeSource(self._geSource)
span = self._geSource.getFixedLength()
step = self._geSource.getFixedGapSize() + span
isFixedStep = (tf.reprIsDense() or step > 1 or (step == 1 and span != 1))
for brt, geList in iterateOverBRTuplesWithContainedGEs(self._geSource):
if len(geList) == 0:
continue
if isFixedStep:
self._composeFixedStepDeclarationLine(out, brt.region, step, span)
else:
curChr, curSpan = self._composeVariableStepDeclarationLine(out, geList[0])
for i,ge in enumerate(geList):
if i==0 and tf.isDense() and tf.isInterval() and \
self._geSource.addsStartElementToDenseIntervals():
continue
val = self._commonFormatNumberVal(ge.val)
if isFixedStep:
cols = [val]
else:
if ge.chr != curChr or self._getVariableSpan(ge) != curSpan:
curChr, curSpan = self._composeVariableStepDeclarationLine(out, ge)
cols = [str(ge.start+1), val]
print >>out, '\t'.join([str(x) for x in cols])
testFn = self._writeTestFile(case)
print open(testFn).read()
print
sortedContents = sortGtrackFileAndReturnContents(
testFn, case.genome)
print sortedContents
sourceClass = GenomeElementSource if case.sourceClass is None else case.sourceClass
forPreProcessor = True if case.sourceClass is None else False
sortedGeSource = GEDependentAttributesHolder(sourceClass('sortedFile.gtrack', case.genome, \
forPreProcessor=forPreProcessor, \
printWarnings=False, \
strToUseInsteadOfFn=sortedContents))
reprIsDense = TrackFormat.createInstanceFromGeSource(
sortedGeSource).reprIsDense()
if not reprIsDense:
self.assertEquals(sorted(case.assertElementList),
[ge for ge in sortedGeSource])
else:
for ge in sortedGeSource:
pass
self.assertEquals(
sorted(case.boundingRegionsAssertList),
[br for br in sortedGeSource.getBoundingRegionTuples()])
def runTest(self):
pass
def _init(self):
self._allValsAreBedVals = False
tf = TrackFormat.createInstanceFromGeSource(self._geSource)
if tf.getValTypeName() == 'Number (integer)':
self._allValsAreBedVals = all(
(0 <= ge.val <= 1000) for ge in self._geSource)
def _init(self):
self._allValsAreBedVals = False
tf = TrackFormat.createInstanceFromGeSource(self._geSource)
if tf.getValTypeName() == 'Number (integer)':
self._allValsAreBedVals = all((0 <= ge.val <= 1000) for ge in self._geSource)
