def testSetProperties(self):
track = GSuiteTrack('http://server.com/path/to/file.bed')
self.assertRaises(AttributeError, track.__setattr__, 'uri',
'http://server.comm/path/to/other.bed')
self.assertRaises(AttributeError, track.__setattr__, 'uriWithoutSuffix',
'http://server.com/path/to/other')
self.assertRaises(AttributeError, track.__setattr__, 'scheme', 'https')
self.assertRaises(AttributeError, track.__setattr__, 'netloc', 'other.com')
self.assertRaises(AttributeError, track.__setattr__, 'path', '/path/to/other.bed')
self.assertRaises(AttributeError, track.__setattr__, 'query', 'download=true')
self.assertRaises(AttributeError, track.__setattr__, 'trackName', ['track', 'name'])
self.assertRaises(AttributeError, track.__setattr__, 'suffix', 'wig')
self.assertRaises(AttributeError, track.__setattr__, 'location', 'local')
track.title = 'Title'
self.assertEquals('Title', track.title)
track.fileFormat = 'unknown'
self.assertEquals('unknown', track.fileFormat)
track.trackType = 'segments'
self.assertEquals('segments', track.trackType)
track.genome = 'hg19'
self.assertEquals('hg19', track.genome)
track.attributes = OrderedDict([('a', '123'), ('b', '234'), ('C', '345')])
self.assertEquals(OrderedDict([('a', '123'), ('b', '234'), ('c', '345')]),
track.attributes)
self.assertEquals('123', track.a)
self.assertEquals('234', track.getAttribute('b'))
self.assertEquals('345', track.c)
self.assertEquals('345', track.getAttribute('c'))
track.setAttribute('D', '456')
self.assertEquals('456', track.getAttribute('d'))
with self.assertRaises(ArgumentValueError):
track.attributes = OrderedDict([('a', '123'), ('A', '234')])
track.comment = 'Comment'
self.assertEquals('Comment', track.comment)
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.
'''
import gold.gsuite.GSuiteComposer as GSuiteComposer
from gold.gsuite.GSuite import GSuite
from gold.gsuite.GSuiteTrack import GSuiteTrack, HbGSuiteTrack
from gold.origdata.TrackGenomeElementSource import TrackViewListGenomeElementSource
from gold.origdata.FileFormatComposer import getComposerClsFromFileSuffix
from quick.multitrack.MultiTrackCommon import getGSuiteFromGalaxyTN
from quick.application.ExternalTrackManager import ExternalTrackManager
from quick.application.GalaxyInterface import GalaxyInterface
from quick.application.UserBinSource import UserBinSource
from quick.extra.TrackExtractor import TrackExtractor
genome = choices.genome
gSuite = getGSuiteFromGalaxyTN(choices.gSuite)
if choices.withOverlaps == cls.NO_OVERLAPS:
if choices.trackSource == cls.FROM_HISTORY_TEXT:
filterTrackName = ExternalTrackManager.getPreProcessedTrackFromGalaxyTN(genome, choices.trackHistory)
else:
filterTrackName = choices.track.split(':')
else:
if choices.trackSource == cls.FROM_HISTORY_TEXT:
regSpec = ExternalTrackManager.extractFileSuffixFromGalaxyTN(choices.trackHistory)
binSpec = ExternalTrackManager.extractFnFromGalaxyTN(choices.trackHistory)
else:
regSpec = 'track'
binSpec = choices.track
userBinSource = UserBinSource(regSpec, binSpec, genome)
desc = cls.OUTPUT_GSUITE_DESCRIPTION
emptyFn = cls.extraGalaxyFn \
[getGSuiteHistoryOutputName('nointersect', description=desc, datasetInfo=choices.gSuite)]
primaryFn = cls.extraGalaxyFn \
[getGSuiteHistoryOutputName('primary', description=desc, datasetInfo=choices.gSuite)]
errorFn = cls.extraGalaxyFn \
[getGSuiteHistoryOutputName('nopreprocessed', description=desc, datasetInfo=choices.gSuite)]
preprocessedFn = cls.extraGalaxyFn \
[getGSuiteHistoryOutputName('preprocessed', description=desc, datasetInfo=choices.gSuite)]
hiddenStorageFn = cls.extraGalaxyFn \
[getGSuiteHistoryOutputName('storage', description=desc, datasetInfo=choices.gSuite)]
analysisDef = '-> TrackIntersectionStat'
# analysisDef = '-> TrackIntersectionWithValStat'
numTracks = gSuite.numTracks()
progressViewer = ProgressViewer([(cls.PROGRESS_INTERSECT_MSG, numTracks),
(cls.PROGRESS_PREPROCESS_MSG, numTracks)], galaxyFn)
emptyGSuite = GSuite()
primaryGSuite = GSuite()
for track in gSuite.allTracks():
newSuffix = cls.OUTPUT_TRACKS_SUFFIX
extraFileName = os.path.sep.join(track.trackName)
extraFileName = changeSuffixIfPresent(extraFileName, newSuffix=newSuffix)
title = getTitleWithSuffixReplaced(track.title, newSuffix)
primaryTrackUri = GalaxyGSuiteTrack.generateURI(
galaxyFn=hiddenStorageFn, extraFileName=extraFileName,
suffix=newSuffix if not extraFileName.endswith(newSuffix) else '')
primaryTrack = GSuiteTrack(primaryTrackUri, title=title,
genome=track.genome, attributes=track.attributes)
if choices.withOverlaps == cls.NO_OVERLAPS:
res = GalaxyInterface.runManual([track.trackName, filterTrackName], analysisDef, '*', '*',
genome=genome, galaxyFn=galaxyFn, username=username)
trackViewList = [res[key]['Result'] for key in sorted(res.keys())]
tvGeSource = TrackViewListGenomeElementSource(genome, trackViewList)
composerCls = getComposerClsFromFileSuffix(cls.OUTPUT_TRACKS_SUFFIX)
composerCls(tvGeSource).composeToFile(primaryTrack.path)
else:
TrackExtractor.extractOneTrackManyRegsToOneFile( \
track.trackName, userBinSource, primaryTrack.path, fileFormatName=cls.OUTPUT_TRACKS_SUFFIX, \
globalCoords=True, asOriginal=False, allowOverlaps=True)
# Temporary hack until better solution for empty result tracks have been implemented
from gold.origdata.GenomeElementSource import GenomeElementSource
geSource = GenomeElementSource(primaryTrack.path, genome=genome, suffix=cls.OUTPUT_TRACKS_SUFFIX)
try:
geSource.parseFirstDataLine()
primaryGSuite.addTrack(primaryTrack)
except Exception, e: # Most likely empty file
primaryTrack.comment = e.message
emptyGSuite.addTrack(primaryTrack)
numTracks -= 1
progressViewer.updateProgressObjectElementCount(
cls.PROGRESS_PREPROCESS_MSG, numTracks)
#
progressViewer.update()
