def run_on_extracted_variables(cls, ts, analysisBins, choices_numberOfTimesToRandomize, choices_randAlg,
choices_randType, galaxyFn, genome):
assert choices_numberOfTimesToRandomize==1 #For now, since ts probably needs to be unique each time..
outputGSuite = GSuite()
for i in range(0, int(choices_numberOfTimesToRandomize)):
print("TF leaf nodes")
print(ts.getLeafNodes())
randTvProvider = cls._createTrackViewProvider(ts, analysisBins, genome, choices_randAlg, choices_randType,
False, None) # the last False and non are temporary..
randomizedTs = getRandomizedVersionOfTs(ts, randTvProvider)
# output files
print("Leaf nodes")
print(randomizedTs.getLeafNodes())
for j, singleTrackTs in enumerate(randomizedTs.getLeafNodes()):
uri = "outputfile"
uri = FileGSuiteTrack.generateURI(path='/home/ivargry/outfile_' + str(randint(0,999999999)) + '_' + str(j) + ".bed", suffix='bed', doQuote=False)
print("URI: " + uri)
title = singleTrackTs.metadata.pop('title')
gSuiteTrack = FileGSuiteTrack(uri, title=title + '.randomized', fileFormat='primary', trackType='segments',
genome=genome, attributes=singleTrackTs.metadata)
outputGSuite.addTrack(gSuiteTrack)
singleTrackTs.metadata['trackFilePath'] = gSuiteTrack.path
singleTrackTs.metadata['randomization_run'] = i
spec = AnalysisSpec(TsWriterStat)
res = doAnalysis(spec, analysisBins, randomizedTs)
assert galaxyFn != ""
GSuiteComposer.composeToFile(outputGSuite, galaxyFn)
def testCreateFileGSuiteTrack(self):
uri = FileGSuiteTrack.generateURI(path='/path/to/file',
suffix='btrack',
trackName=['trackname'],
doQuote=False)
track = GSuiteTrack(uri,
title='MyTrack',
trackType='segments',
genome='unknown',
attributes=OrderedDict([('extra', 'no')]))
self.assertEquals('file:/path/to/file;btrack?track=trackname', uri)
self.assertEquals('file', track.scheme)
self.assertEquals('file:/path/to/file;btrack?track=trackname',
track.uri)
self.assertEquals(None, track.netloc)
self.assertEquals('/path/to/file', track.path)
self.assertEquals('track=trackname', track.query)
self.assertEquals('btrack', track.suffix)
self.assertEquals('MyTrack', track.title)
self.assertEquals(['trackname'], track.trackName)
self.assertEquals('local', track.location)
self.assertEquals('preprocessed', track.fileFormat)
self.assertEquals('segments', track.trackType)
self.assertEquals('unknown', track.genome)
self.assertEquals(OrderedDict([('extra', 'no')]), track.attributes)
def execute(cls, choices, galaxyFn=None, username=''):
from quick.util.CommonFunctions import getFileSuffix
import gold.gsuite.GSuiteComposer as GSuiteComposer
from gold.gsuite.GSuite import GSuite
from gold.gsuite.GSuiteTrack import registerGSuiteTrackClass, GSuiteTrack, FileGSuiteTrack
registerGSuiteTrackClass(FileGSuiteTrack)
gSuite = getGSuiteFromGalaxyTN(choices.gsuite)
outGSuite = GSuite()
for track in gSuite.allTracks():
path = track.path
suffix = track.suffix if track.suffix != getFileSuffix(
path) else ''
uri = FileGSuiteTrack.generateURI(path=path, suffix=suffix)
newTrack = GSuiteTrack(uri,
title=track.title,
trackType=track.trackType,
genome=track.genome,
attributes=track.attributes)
outGSuite.addTrack(newTrack)
GSuiteComposer.composeToFile(outGSuite, galaxyFn)
def testIncorrectTrackType(self):
uri = FileGSuiteTrack.generateURI(path='/path/to/file')
# track = GSuiteTrack(uri, trackType='segment')
self.assertRaises(InvalidFormatError, GSuiteTrack, uri, trackType='segment')
track = GSuiteTrack(uri)
# track.trackType = 'segment'
self.assertRaises(InvalidFormatError, track.__setattr__, 'trackType', 'segment')
def testIncorrectFileFormat(self):
uri = FileGSuiteTrack.generateURI(path='/path/to/file')
# track = GSuiteTrack(uri, fileFormat='doc')
self.assertRaises(InvalidFormatError, GSuiteTrack, uri, fileFormat='doc')
track = GSuiteTrack(uri)
# track.fileFormat = 'doc'
self.assertRaises(InvalidFormatError, track.__setattr__, 'fileFormat', 'doc')
def testQuoteInURLFile(self):
uri = FileGSuiteTrack.generateURI(path='/path/to/file_with ;"[', suffix='btrack',
trackName=['My', 'track ;"[', 'name'], doQuote=True)
track = GSuiteTrack(uri, fileFormat='preprocessed', trackType='segments')
self.assertEquals('file:/path/to/file_with%20%3B%22%5B;btrack?'
'track=My%3Atrack+%3B%22%5B%3Aname', uri)
self.assertEquals('file', track.scheme)
self.assertEquals('file:/path/to/file_with%20%3B%22%5B;btrack?'
'track=My%3Atrack+%3B%22%5B%3Aname', track.uri)
self.assertEquals('/path/to/file_with ;"[', track.path)
self.assertEquals('name', track.title)
self.assertEquals('track=My:track ;"[:name', track.query)
self.assertEquals(['My', 'track ;"[', 'name'], track.trackName)
self.assertEquals('btrack', track.suffix)
def execute(cls, choices, galaxyFn=None, username=''):
inGSuite = getGSuiteFromGalaxyTN(choices.gsuite)
if choices.genome != inGSuite.genome:
inGSuite.setGenomeOfAllTracks(choices.genome)
registerGSuiteTrackClass(FileGSuiteTrack)
outGSuite = GSuite()
for track in inGSuite.allTracks():
origGalaxyTN = ETM.createGalaxyTnFromExternalTn(track.trackName)
uri = FileGSuiteTrack.generateURI(
path=ETM.extractFnFromGalaxyTN(origGalaxyTN),
suffix=ETM.extractFileSuffixFromGalaxyTN(origGalaxyTN))
newTrack = GSuiteTrack(uri,
title=track.title,
trackType=track.trackType,
genome=track.genome,
attributes=track.attributes)
outGSuite.addTrack(newTrack)
GSuiteComposer.composeToFile(outGSuite, galaxyFn)