def testFullCompose(self):
gSuite = GSuite()
gSuite.addTrack(
GSuiteTrack('ftp://server.somewhere.com/path/to/file1.bed',
title='Track',
attributes=OrderedDict([('cell', 'k562'),
('antibody', 'cMyb')])))
gSuite.addTrack(
GSuiteTrack('http://server.other.com/path/to/file2.bed',
title='Track2',
attributes=OrderedDict([('cell', 'GM12878'),
('antibody', 'cMyc')])))
gSuite.addTrack(
GSuiteTrack('https://server.other.com/path/to/file3.bed',
attributes=OrderedDict([('cell', 'GM12878'),
('antibody', 'cMyb')])))
gSuite.addTrack(
GSuiteTrack('rsync://server.other.com/path/to/file4;wig',
title='Track4',
attributes=OrderedDict([('cell', 'NHFL')])))
gSuite.addTrack(GSuiteTrack('hb:/track/name/hierarchy', title='Track'))
gSuite.addTrack(
GSuiteTrack('galaxy:/ad123dd12fg;btrack?track=track:name',
title='Track',
attributes=OrderedDict([('cell', 'k562'),
('antibody', 'cMyb')])))
gSuite.addTrack(
GSuiteTrack('file:/path/to/file.btrack?track=track:name',
title='Track name7',
attributes=OrderedDict([('antibody', 'cMyb'),
('extra', 'yes')])))
gSuite.setGenomeOfAllTracks('hg18')
gSuite.setCustomHeader('My header', 'Some value')
output = GSuiteComposer.composeToString(gSuite)
targetOutput = \
'##location: multiple\n' \
'##file format: multiple\n' \
'##track type: unknown\n' \
'##genome: hg18\n' \
'##my header: Some value\n' \
'###uri\ttitle\tfile_format\tcell\tantibody\textra\n' \
'ftp://server.somewhere.com/path/to/file1.bed\tTrack\tprimary\tk562\tcMyb\t.\n' \
'http://server.other.com/path/to/file2.bed\tTrack2\tprimary\tGM12878\tcMyc\t.\n' \
'https://server.other.com/path/to/file3.bed\tfile3.bed\tprimary\tGM12878\tcMyb\t.\n' \
'rsync://server.other.com/path/to/file4;wig\tTrack4\tprimary\tNHFL\t.\t.\n' \
'hb:/track/name/hierarchy\tTrack (2)\tpreprocessed\t.\t.\t.\n' \
'galaxy:/ad123dd12fg;btrack?track=track%3Aname\tTrack (3)\tpreprocessed\tk562\tcMyb\t.\n' \
'file:/path/to/file.btrack?track=track%3Aname\tTrack name7\tpreprocessed\t.\tcMyb\tyes\n'
self.assertEquals(targetOutput, output)
def execute(cls, choices, galaxyFn=None, username=''):
from quick.webtools.clustering.GSuitePrimaryTrackModifier import GSuitePrimaryTrackModifier
# Set analysis environment
gSuite = getGSuiteFromGalaxyTN(choices.gSuite)
outGSuite = GSuite()
errorGSuite = GSuite()
progressViewer = ProgressViewer([('Manipulate tracks', gSuite.numTracks() + 24)],
cls.extraGalaxyFn[cls.HISTORY_PROGRESS_TITLE])
hiddenStorageFn = cls.extraGalaxyFn[cls.HISTORY_HIDDEN_TRACK_STORAGE]
# Get rsID map for the chosen reference genome
rsidMap = RsidMapper.createRsidMappingFromStaticFiles(progressViewer, choices.refGenome)
# Lift over all tracks
for track in gSuite.allTracks():
fileName = cls.getFilenameWithGTrackSuffix(track.path)
title = getTitleWithSuffixReplaced(track.title, 'gtrack')
try:
uri = GalaxyGSuiteTrack.generateURI(
galaxyFn=hiddenStorageFn,
extraFileName=fileName,
suffix='gtrack'
)
gSuiteTrack = GSuiteTrack(
uri,
title=title,
genome=track.genome,
trackType=track.trackType,
attributes=track.attributes
)
trackFn = gSuiteTrack.path
GSuitePrimaryTrackModifier.liftOverGTrack(track.path, trackFn, rsidMap)
outGSuite.addTrack(gSuiteTrack)
except Exception as e:
track.comment = 'An error occurred for the following track: ' + str(e)
errorGSuite.addTrack(track)
progressViewer.update()
# Update reference genome of all tracks and write to file
outGSuite.setGenomeOfAllTracks(choices.refGenome)
composeToFile(outGSuite, galaxyFn)
composeToFile(errorGSuite, cls.extraGalaxyFn[cls.HISTORY_ERROR_TITLE])
writeGSuiteHiddenTrackStorageHtml(hiddenStorageFn)
def execute(cls, choices, galaxyFn=None, username=''):
from quick.webtools.clustering.CreateLDTrack import CreateLDTrack
from quick.webtools.clustering.RsidMapper import RsidMapper
gSuite = getGSuiteFromGalaxyTN(choices.gSuite)
outGSuite = GSuite()
errorGSuite = GSuite()
progressViewer = ProgressViewer([('Manipulate tracks', gSuite.numTracks() + 24)],
cls.extraGalaxyFn[cls.HISTORY_PROGRESS_TITLE])
ldDict = CreateLDTrack.getLDDict(float(choices.rsquare))
rsidDict = RsidMapper.createRsidMappingFromStaticFiles(progressViewer, choices.refGenome)
hiddenStorageFn = cls.extraGalaxyFn[cls.HISTORY_HIDDEN_TRACK_STORAGE]
for track in gSuite.allTracks():
fileName = cls.getFilenameWithGTrackSuffix(track.path)
title = getTitleWithSuffixReplaced(track.title, 'gtrack')
try:
uri = GalaxyGSuiteTrack.generateURI(
galaxyFn=hiddenStorageFn,
extraFileName=fileName,
suffix='gtrack'
)
gSuiteTrack = GSuiteTrack(
uri,
title=title,
genome=track.genome,
trackType='points',
attributes=track.attributes
)
trackFn = gSuiteTrack.path
CreateLDTrack.parseFileIntoPointTrack(track.path, trackFn, ldDict, rsidDict)
outGSuite.addTrack(gSuiteTrack)
except Exception as e:
track.comment = 'An error occurred for the following track: ' + str(e)
errorGSuite.addTrack(track)
progressViewer.update()
outGSuite.setGenomeOfAllTracks(choices.refGenome)
composeToFile(outGSuite, galaxyFn)
composeToFile(errorGSuite, cls.extraGalaxyFn[cls.HISTORY_ERROR_TITLE])
writeGSuiteHiddenTrackStorageHtml(hiddenStorageFn)
def testAddGSuiteTracks(self):
gSuite = GSuite()
gSuite.setGenomeOfAllTracks('hg18')
self.assertEqual('unknown', gSuite.genome)
gSuite.addTrack(GSuiteTrack('ftp://server.somewhere.com/path/to/file1.bed',
title='Track1', \
attributes=OrderedDict([('cell', 'k562'),
('antibody', 'cMyb')])))
gSuite.addTrack(GSuiteTrack('http://server.other.com/path/to/file2.bed',
title='Track2', \
attributes=OrderedDict([('cell', 'GM12878'),
('antibody', 'cMyc')])))
gSuite.addTrack(
GSuiteTrack('https://server.other.com/path/to/file3.bed',
attributes=OrderedDict([('cell', 'GM12878'),
('antibody', 'cMyb')])))
gSuite.addTrack(
GSuiteTrack(
'rsync://server.other.com/other/path/to/file3.bed;bed9',
attributes=OrderedDict([('cell', 'NHFL')])))
gSuite.setGenomeOfAllTracks('hg18')
self.assertEqual('remote', gSuite.location)
self.assertEqual('primary', gSuite.fileFormat)
self.assertEqual('unknown', gSuite.trackType)
self.assertEqual('hg18', gSuite.genome)
self.assertEqual(['cell', 'antibody'], gSuite.attributes)
self.assertEqual(False, gSuite.isPreprocessed())
self.assertEqual(True, gSuite.hasCustomTitles())
self.assertEqual(4, gSuite.numTracks())
self.assertEqual(['hg18'] * 4, [x.genome for x in gSuite.allTracks()])
self.assertEqual(['Track1', 'Track2', 'file3.bed', 'file3.bed (2)'],
gSuite.allTrackTitles())
self.assertEqual(['unknown'], gSuite.allTrackTypes())
gSuite.addTrack(
GSuiteTrack('hb:/track/name/hierarchy',
title='Track1',
genome='hg19',
trackType='segments'))
self.assertEqual('multiple', gSuite.genome)
gSuite.addTrack(GSuiteTrack('galaxy:/ad123dd12fg;btrack?track=track:name',
title='Track2', \
attributes=OrderedDict([('cell', 'k562'),
('antibody', 'cMyb')])))
gSuite.addTrack(GSuiteTrack('file:/path/to/file.btrack?track=track:name',
title='Track2', \
attributes=OrderedDict([('antibody', 'cMyb'),
('extra', 'yes')])))
self.assertEqual('multiple', gSuite.location)
self.assertEqual('multiple', gSuite.fileFormat)
self.assertEqual('unknown', gSuite.trackType)
self.assertEqual('unknown', gSuite.genome)
self.assertEqual(['cell', 'antibody', 'extra'], gSuite.attributes)
self.assertEqual(False, gSuite.isPreprocessed())
self.assertEqual(True, gSuite.hasCustomTitles())
self.assertEqual(7, gSuite.numTracks())
self.assertEqual(['hg18'] * 4 + ['hg19'] + ['unknown'] * 2,
[x.genome for x in gSuite.allTracks()])
self.assertEqual(['Track1', 'Track2', 'file3.bed', 'file3.bed (2)', \
'Track1 (2)', 'Track2 (2)', 'Track2 (3)'],
gSuite.allTrackTitles())
self.assertEqual(['segments', 'unknown'], gSuite.allTrackTypes())
self.assertRaises(
InvalidFormatError,
gSuite.addTrack,
GSuiteTrack('https://server.third.com/path/to/file3.bed'),
allowDuplicateTitles=False)
import gold.gsuite.GSuiteParser as GSuiteParser
gSuite = GSuite()
uri1 = FtpGSuiteTrack.generateURI(netloc='server.com', path='file.bed')
gSuite.addTrack(
GSuiteTrack(uri1,
title='Track1',
attributes=OrderedDict([('a', 'yes'), ('b', 'no')])))
uri2 = HbGSuiteTrack.generateURI(
trackName=['Genes and gene subsets', 'Genes', 'Refseq'])
gSuite.addTrack(
GSuiteTrack(uri2, attributes=OrderedDict([('b', 'no'), ('c', 'yes')])))
gSuite.setGenomeOfAllTracks('hg19')
contents = GSuiteComposer.composeToString(gSuite)
print 'GSuite file contents'
print '--------------------'
print contents
gSuite2 = GSuiteParser.parseFromString(contents)
print 'Various ways of direct access'
print '-----------------------------'
print "genome=%s, location=%s, file format=%s, track type=%s, attributes=%s" % \
(gSuite.genome, gSuite.location, gSuite.fileFormat, gSuite.trackType, gSuite.attributes)
for track in gSuite2.allTracks():
