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 validateAndReturnErrors(cls, choices):
'''
Should validate the selected input parameters. If the parameters are not
valid, an error text explaining the problem should be returned. The GUI
then shows this text to the user (if not empty) and greys out the
execute button (even if the text is empty). If all parameters are valid,
the method should return None, which enables the execute button.
'''
errorStr = cls._checkTrack(choices,
trackChoiceIndex='track',
genomeChoiceIndex='genome')
if errorStr:
return errorStr
if choices.track and not choices.attr:
return 'You have chosen a track with no attributes (columns) supported for splitting. ' \
'Attributes that do not support splitting are: ' + ', '.join(cls.UNSUPPORTED_ATTRS)
geSource = etm.getGESourceFromGalaxyOrVirtualTN(
choices.track, choices.genome)
trackFormat = TrackFormat.createInstanceFromGeSource(geSource)
if trackFormat.isDense():
return 'The track format of the selected track file is: %s' % trackFormat.getFormatName() +\
' This tool only supports track types Points, Segments, or variations of these.'
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 _getBasicTrackFormat(choices, tnChoiceIndex=1, genomeChoiceIndex=0):
genome = GeneralGuiTool._getGenomeChoice(choices, genomeChoiceIndex)[0]
tn = GeneralGuiTool._getTrackChoice(choices, tnChoiceIndex)[0]
from quick.application.GalaxyInterface import GalaxyInterface
from gold.description.TrackInfo import TrackInfo
from quick.application.ExternalTrackManager import ExternalTrackManager
from gold.track.TrackFormat import TrackFormat
if ExternalTrackManager.isGalaxyTrack(tn):
geSource = ExternalTrackManager.getGESourceFromGalaxyOrVirtualTN(
tn, genome)
try:
tf = GeneralGuiTool._convertToBasicTrackFormat(
TrackFormat.createInstanceFromGeSource(
geSource).getFormatName())
except Warning:
return genome, tn, ''
else:
if GalaxyInterface.isNmerTrackName(genome, tn):
tfName = 'Points'
else:
tfName = TrackInfo(genome, tn).trackFormatName
tf = GeneralGuiTool._convertToBasicTrackFormat(tfName)
return genome, tn, tf
def getOptionsBoxOutputFormat(cls, prevChoices):
if prevChoices.changeFormat == cls.OUTPUT_FORMAT_CONVERT:
try:
from gold.origdata.GenomeElementSource import GenomeElementSource
from gold.origdata.FileFormatComposer import findMatchingFileFormatComposers
from gold.track.TrackFormat import TrackFormat
gSuite = getGSuiteFromGalaxyTN(prevChoices.gsuite)
selectedTracks = cls._getSelectedTracks(prevChoices, gSuite)
allGeSources = [
GenomeElementSource(track.path,
genome=track.genome,
printWarnings=False,
suffix=track.suffix)
for track in selectedTracks
]
matchingComposersForAllSelectedTracks = \
[findMatchingFileFormatComposers(TrackFormat.createInstanceFromGeSource(geSource)) for geSource in allGeSources]
commonComposers = reduce(
set.intersection,
map(set, matchingComposersForAllSelectedTracks))
return [
composer.fileFormatName for composer in commonComposers
]
except:
return []
def __init__(self, geSource):
GESourceManager.__init__(self, geSource)
self._tf = TrackFormat.createInstanceFromGeSource(geSource)
self._numElements = defaultdict(partial(OrderedDefaultDict, int))
self._valCategories = defaultdict(partial(OrderedDefaultDict, set))
self._edgeWeightCategories = defaultdict(partial(OrderedDefaultDict, set))
self._maxStrLens = defaultdict(partial(OrderedDefaultDict, \
partial(self._initMaxStrLens, self._getMaxStrLensKeys())))
self._maxNumEdges = defaultdict(partial(OrderedDefaultDict, int))
def getOptionsBoxConversion(prevChoices):
if prevChoices.history:
try:
geSource = UniversalConverterTool._getGESource(prevChoices)
matchingComposers = findMatchingFileFormatComposers(TrackFormat.createInstanceFromGeSource(geSource))
return ['%s -> %s (track type: %s)' % \
(geSource.getFileFormatName(), composerInfo.fileFormatName, composerInfo.trackFormatName) \
for composerInfo in matchingComposers if geSource.getFileFormatName() != composerInfo.fileFormatName]
except:
return []
def getOptionsBoxConversion(prevChoices):
if prevChoices.history:
try:
geSource = UniversalConverterTool._getGESource(prevChoices)
matchingComposers = findMatchingFileFormatComposers(
TrackFormat.createInstanceFromGeSource(geSource))
return ['%s -> %s (track type: %s)' % \
(geSource.getFileFormatName(), composerInfo.fileFormatName, composerInfo.trackFormatName) \
for composerInfo in matchingComposers if geSource.getFileFormatName() != composerInfo.fileFormatName]
except:
return []
def _getGESourceManagerFromGESource(self, geSource):
tf = TrackFormat.createInstanceFromGeSource(geSource)
if tf.reprIsDense():
if tf.getValTypeName() in [
'Number', 'Number (integer)', 'Case-control'
]:
return SkipExtraPassDenseGESourceManager(geSource)
else:
raise NotSupportedError
else:
return GESourceManager(geSource)
def __new__(self, geSource, brRegionList):
tf = TrackFormat.createInstanceFromGeSource(geSource)
if tf.reprIsDense():
if tf.getValTypeName() == 'Number':
return NumberFunctionOneChrSortedNoOverlapsGESourceManager.__new__\
(NumberFunctionOneChrSortedNoOverlapsGESourceManager, geSource, brRegionList)
else:
raise NotSupportedError
else:
return SparseOneChrSortedNoOverlapsGESourceManager.__new__\
(SparseOneChrSortedNoOverlapsGESourceManager, geSource, brRegionList)
def getOptionsBoxFormat(prevChoices):
if prevChoices.track:
geSource = etm.getGESourceFromGalaxyOrVirtualTN(
prevChoices.track, prevChoices.genome)
tf = TrackFormat.createInstanceFromGeSource(geSource)
matchingComposers = findMatchingFileFormatComposers(tf)
conversions = [geSource.getFileFormatName() + \
' (no conversion, track type: %s)' % tf.getFormatName()]
conversions += ['%s -> %s (track type: %s)' % (geSource.getFileFormatName(), \
composerInfo.fileFormatName, composerInfo.trackFormatName) \
for composerInfo in matchingComposers \
if geSource.getFileFormatName() != composerInfo.fileFormatName]
return conversions
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, onlyAddTwoGEs=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 _allGESources(self, trackName):
regionList = self._regionList if self._preProcess else [
self._regionList[0]
]
for region in regionList:
self._status = "Trying to create custom track geSource for region: {}".format(
region)
geSource = self._getGeSourceCallBackFunc(self._genome,
self._trackName, region,
**self._callBackArgs)
tf = TrackFormat.createInstanceFromGeSource(geSource)
if tf.reprIsDense():
brList = [BoundingRegionTuple(region, len(region))]
yield BrTuplesGESourceWrapper(geSource, brList)
else:
brList = [BoundingRegionTuple(region, 0)]
yield GEBoundingRegionElementCounter(geSource, brList)
def _calcTrackStatistics(self, chr, allowOverlaps):
if chr not in self._numElements[allowOverlaps]:
# In order to handle the first element of each bounding region for
# genome partitions and step functions correctly
tf = TrackFormat.createInstanceFromGeSource(self._geSource)
if tf.isDense() and tf.isInterval():
geList = self._getGEBuckets(allowOverlaps)[chr]
prevEnd = 0
for br in self._getBRBuckets(allowOverlaps)[chr]:
for i, el in enumerate(geList[prevEnd:prevEnd + br.elCount]):
self._updateTrackStatistics(el, chr, allowOverlaps, \
firstElInPartitionBoundingRegion=(i==0))
prevEnd += br.elCount
else:
for el in self._getGEBuckets(allowOverlaps)[chr]:
self._updateTrackStatistics(el, chr, allowOverlaps)
def _getValueTypeName(choices, tnChoiceIndex=1, genomeChoiceIndex=0):
genome = GeneralGuiTool._getGenomeChoice(choices, genomeChoiceIndex)[0]
tn = GeneralGuiTool._getTrackChoice(choices, tnChoiceIndex)[0]
from quick.application.GalaxyInterface import GalaxyInterface
from gold.description.TrackInfo import TrackInfo
from quick.application.ExternalTrackManager import ExternalTrackManager
from gold.track.TrackFormat import TrackFormat
if ExternalTrackManager.isGalaxyTrack(tn):
geSource = ExternalTrackManager.getGESourceFromGalaxyOrVirtualTN(
tn, genome)
valTypeName = TrackFormat.createInstanceFromGeSource(
geSource).getValTypeName()
else:
if GalaxyInterface.isNmerTrackName(genome, tn):
valTypeName = ''
else:
valTypeName = TrackInfo(genome, tn).markType
return valTypeName.lower()
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 validateAndReturnErrors(choices):
'''
Should validate the selected input parameters. If the parameters are not
valid, an error text explaining the problem should be returned. The GUI
then shows this text to the user (if not empty) and greys out the
execute button (even if the text is empty). If all parameters are valid,
the method should return None, which enables the execute button.
'''
if not choices.genome:
return 'Please select genome'
if not choices.catTrack:
return 'Please select categorical track from history'
geSource = ExternalTrackManager.getGESourceFromGalaxyOrVirtualTN(
choices.catTrack.split(':'), choices.genome)
trackFormat = TrackFormat.createInstanceFromGeSource(geSource)
if trackFormat.getValTypeName() != 'Category':
return 'Please select <b>categorical</b> track from history, current is of type ' + trackFormat.getValTypeName(
)
def _allGESourceManagers(self, trackName, allowOverlaps):
trackNameStr = ':'.join(trackName)
self._status = "Trying to create GESourceManager " \
"(trackName: {}, allowOverlaps: {})".format(trackNameStr, 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"' % trackNameStr + \
(' (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"' % trackNameStr + \
(' (filename: "%s")' % geSource.getFileName() if geSource.hasOrigFile() else '') + \
(' (allowOverlaps: %s)' % allowOverlaps)
if PreProcessUtils.shouldPreProcessGESource(
trackName, geSource, allowOverlaps):
yield self._getGESourceManagerFromGESource(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)
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 __new__(self, geSource):
tf = TrackFormat.createInstanceFromGeSource(geSource)
if tf.reprIsDense():
return DenseStdGESourceManager.__new__(DenseStdGESourceManager, geSource)
else:
return SparseStdGESourceManager.__new__(SparseStdGESourceManager, 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)