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 _checkTrack(choices,
trackChoiceIndex=1,
genomeChoiceIndex=0,
filetype=None,
validateFirstLine=True):
genome, errorStr = GeneralGuiTool._getGenomeChoice(
choices, genomeChoiceIndex)
if errorStr:
return errorStr
trackName, errorStr = GeneralGuiTool._getTrackChoice(
choices, trackChoiceIndex)
if errorStr:
return errorStr
from quick.application.ExternalTrackManager import ExternalTrackManager
if ExternalTrackManager.isGalaxyTrack(trackName):
errorStr = GeneralGuiTool._checkHistoryTrack(
choices, trackChoiceIndex, genome, filetype, validateFirstLine)
if errorStr:
return errorStr
else:
if not GeneralGuiTool._isValidTrack(choices, trackChoiceIndex,
genomeChoiceIndex):
return 'Please select a valid track'
def _collectTracks(self):
tracks = [self._track, self._track2]
if 'trackNameIntensity' in self._kwArgs:
assert not 'extraTracks' in self._kwArgs
self._kwArgs['extraTracks'] = self._kwArgs['trackNameIntensity']
if 'extraTracks' in self._kwArgs:
from gold.track.Track import PlainTrack
import re
from config.Config import MULTIPLE_EXTRA_TRACKS_SEPARATOR
extraTracks = self._kwArgs['extraTracks']
if type(extraTracks) == str:
extraTracks = extraTracks.split(MULTIPLE_EXTRA_TRACKS_SEPARATOR)
for extraT in extraTracks:
if type(extraT) == str:
#extraT = extraT.split('|')
#extraT = re.split('\^|\|',extraT)
extraT = convertTNstrToTNListFormat(extraT)
if type(extraT) == list:
#print 'TEMP1: ', extraT
from urllib import unquote
extraT = [unquote(part) for part in extraT]
from quick.application.ExternalTrackManager import ExternalTrackManager
if ExternalTrackManager.isGalaxyTrack(extraT):
extraT = ExternalTrackManager.getPreProcessedTrackFromGalaxyTN(self.getGenome(), extraT)
extraT = PlainTrack(extraT)
tracks.append(extraT)
return tracks
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.
'''
genome = choices.genome
trackChoice = choices.history if choices.source == 'history' else choices.track
trackName = trackChoice.split(':')
if ExternalTrackManager.isGalaxyTrack(trackName):
geSource = ExternalTrackManager.getGESourceFromGalaxyOrVirtualTN(
trackName, genome)
if not geSource.hasOrigFile(): #hbfunction
stdTrackName = ExternalTrackManager.getStdTrackNameFromGalaxyTN(
trackName)
ExternalTrackManager.renameExistingStdTrackIfNeeded(
genome, stdTrackName)
geSource = FullTrackGenomeElementSource(genome,
stdTrackName,
allowOverlaps=False)
else:
try:
geSource = FullTrackGenomeElementSource(genome,
trackName,
allowOverlaps=True)
for ge in geSource:
break
except:
geSource = FullTrackGenomeElementSource(genome,
trackName,
allowOverlaps=False)
threshold = float(choices.threshold)
rule = RULE_DICT[choices.rule]
composerCls = getComposerClsFromFileFormatName(choices.format)
geModifier = GEValueThresholder(geSource, genome, threshold, rule)
if choices.merge == 'Yes':
if not geModifier.isSorted():
geModifier = GenomeElementSorter(geModifier)
geModifier = GEAdjacencyClusterer_Segment(geModifier)
composerCls(geModifier).composeToFile(galaxyFn, ignoreEmpty=True)
def _collectTracks(self):
tracks = [self._track, self._track2]
#Map trackNameIntensity over to extraTrack, if extraTrack does not exist in itself (to allow selection of third track in GUI and through some existing code interfaces)
if 'trackNameIntensity' in self._kwArgs:
if not 'extraTracks' in self._kwArgs:
self._kwArgs['extraTracks'] = self._kwArgs[
'trackNameIntensity']
if 'extraTracks' in self._kwArgs:
from gold.util.CommonConstants import MULTIPLE_EXTRA_TRACKS_SEPARATOR
extraTracks = self._kwArgs['extraTracks']
if isinstance(extraTracks, basestring):
extraTracks = extraTracks.split(
MULTIPLE_EXTRA_TRACKS_SEPARATOR)
for extraT in extraTracks:
#HACK for tests
if isinstance(
extraT,
(Track, SampleTrack)): #SampleTrack is used by tests
if str(extraT) not in self._trackDict:
self._trackDict[str(extraT)] = extraT
tracks.append(extraT)
else:
tracks.append(self._trackDict[str(extraT)])
#####################################
else:
if isinstance(extraT, basestring):
#extraT = extraT.split('|')
#extraT = re.split('\^|\|',extraT)
extraT = convertTNstrToTNListFormat(extraT,
doUnquoting=False)
if type(extraT) == list:
from urllib import unquote
extraT = [unquote(part) for part in extraT]
from quick.application.ExternalTrackManager import ExternalTrackManager
if ExternalTrackManager.isGalaxyTrack(extraT):
extraT = ExternalTrackManager.getPreProcessedTrackFromGalaxyTN(
self.getGenome(), extraT)
#extraT = PlainTrack(extraT)
#extraT = Track(extraT)
#tracks.append(extraT)
if str(extraT) not in self._trackDict:
extraTrack = Track(extraT)
self._trackDict[str(extraT)] = extraTrack
tracks.append(extraTrack)
else:
tracks.append(self._trackDict[str(extraT)])
return tracks
def parseBatchLine(batchLine, genome, fullAccess):
if batchLine[0] == '#' or batchLine.strip() == '':
return
from urllib import unquote
#Split and check number of columns
cols = [x for x in batchLine.strip().split(BATCH_COL_SEPARATOR)]
if len(cols) != 6:
results = Results(['N/A'], ['N/A'], 'N/A')
#results.addResultComponent( 'Invalid',InvalidRunResultComponent('Error in batch specification. 6 columns are required, while '\
# + str(len(cols)) + ' are given.'))
results.addError(InvalidRunSpecException('Error in batch specification. 6 columns are required, while '\
+ str(len(cols)) + ' are given: ' + batchLine))
return results, None, None, None, None
bc = BatchContents()
bc.regSpec = cols[1]
bc.binSpec = unquote(cols[2])
from quick.application.ExternalTrackManager import ExternalTrackManager
if ExternalTrackManager.isGalaxyTrack(bc.binSpec.split(':')):
bc.binSpec = ExternalTrackManager.extractFnFromGalaxyTN(
bc.binSpec.split(':'))
try:
from quick.application.GalaxyInterface import GalaxyInterface
bc.trackName1 = [unquote(x) for x in cols[3].split(':')]
bc.trackName2 = [unquote(x) for x in cols[4].split(':')]
bc.cleanedTrackName1, bc.cleanedTrackName2 = GalaxyInterface._cleanUpTracks(
[bc.trackName1, bc.trackName2], genome, realPreProc=True)
bc.cleanedTrackName1 = BatchRunner._inferTrackName(
bc.cleanedTrackName1, genome, fullAccess)
bc.cleanedTrackName2 = BatchRunner._inferTrackName(
bc.cleanedTrackName2, genome, fullAccess)
except (InvalidRunSpecException, IdenticalTrackNamesError), e:
if DebugConfig.PASS_ON_BATCH_EXCEPTIONS:
raise
bc.errorResult = Results(['N/A'], ['N/A'], 'N/A')
bc.errorResult.addError(e)
return bc
def parseBatchLine(batchLine, genome, fullAccess):
if batchLine[0] == '#' or batchLine.strip() == '':
return
from urllib import unquote
# Split and check number of columns
cols = [x for x in batchLine.strip().split(BATCH_COL_SEPARATOR)]
if len(cols) != 6:
results = Results(['N/A'], ['N/A'], 'N/A')
results.addError(InvalidRunSpecException('Error in batch specification. 6 columns are required, while '\
+ str(len(cols)) + ' are given: ' + batchLine))
return results, None, None, None, None
bc = BatchContents()
bc.regSpec = cols[1]
bc.binSpec = unquote(cols[2])
from quick.application.ExternalTrackManager import ExternalTrackManager
if ExternalTrackManager.isGalaxyTrack(bc.binSpec.split(':')):
bc.binSpec = ExternalTrackManager.extractFnFromGalaxyTN(bc.binSpec.split(':'))
bc.statClassName, bc.paramDict = BatchRunner._parseClassAndParams(cols[5])
bc.trackNames = [[unquote(x) for x in cols[i].split(':')] for i in [3, 4]]
if 'trackNameIntensity' in bc.paramDict:
bc.trackNames.append(convertTNstrToTNListFormat(bc.paramDict['trackNameIntensity'], doUnquoting=True))
from quick.application.GalaxyInterface import GalaxyInterface
partlyCleanedTrackNames = GalaxyInterface._cleanUpTracks(bc.trackNames, genome, realPreProc=True)
try:
bc.cleanedTrackNames = BatchRunner._inferTrackNames(partlyCleanedTrackNames, genome, fullAccess)
except (InvalidRunSpecException,IdenticalTrackNamesError), e:
if DebugConfig.PASS_ON_BATCH_EXCEPTIONS:
raise
bc.errorResult = Results(['N/A'],['N/A'],'N/A')
bc.errorResult.addError(e)
return bc
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 runJob(batchLine, genome, fullAccess):
if batchLine[0] == '#' or batchLine.strip()=='':
return
from urllib import unquote
#Split and check number of columns
cols = [x for x in batchLine.strip().split(BATCH_COL_SEPARATOR)]
if len(cols) != 6:
results = Results(['N/A'],['N/A'],'N/A')
#results.addResultComponent( 'Invalid',InvalidRunResultComponent('Error in batch specification. 6 columns are required, while '\
# + str(len(cols)) + ' are given.'))
results.addError(InvalidRunSpecException('Error in batch specification. 6 columns are required, while '\
+ str(len(cols)) + ' are given: ' + batchLine))
return results
#print 'COL2: ',cols[2]
cols[2] = unquote(cols[2])
#print 'COL2: ',cols[2]
from quick.application.ExternalTrackManager import ExternalTrackManager
if ExternalTrackManager.isGalaxyTrack(cols[2].split(':')):
cols[2] = ExternalTrackManager.extractFnFromGalaxyTN(cols[2].split(':'))
#print 'COL2: ',cols[2]
try:
from quick.application.GalaxyInterface import GalaxyInterface
trackName1 = [unquote(x) for x in cols[3].split(':')]
trackName2 = [unquote(x) for x in cols[4].split(':')]
cleanedTrackName1, cleanedTrackName2 = GalaxyInterface._cleanUpTracks([trackName1, trackName2], genome, realPreProc=True)
cleanedTrackName1 = BatchRunner._inferTrackName(':'.join(cleanedTrackName1), genome, fullAccess)
cleanedTrackName2 = BatchRunner._inferTrackName(':'.join(cleanedTrackName2), genome, fullAccess)
except (InvalidRunSpecException,IdenticalTrackNamesError), e:
if DebugConfig.PASS_ON_BATCH_EXCEPTIONS:
raise
results = Results(['N/A'],['N/A'],'N/A')
results.addError(e)
return results
