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 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 execute(cls, choices, galaxyFn=None, username=''):
basisTrackNameAsList = choices.basisTrack.split(':')
extractionOptions = dict(
GalaxyInterface.getTrackExtractionOptions(choices.genome,
basisTrackNameAsList))
extractionFormat = extractionOptions[
choices.extFormatLbl] if extractionOptions else None
gsuite = getGSuiteFromGalaxyTN(choices.gsuite)
outGSuite = GSuite()
for gsTrack in gsuite.allTracks():
# outputTrackFn = cls.extraGalaxyFn[gsTrack.title]
# print '<br>\n<br>\n output track filename: ', outputTrackFn
# print 'path: ', gsTrack.path
# print 'parsed uri: ', gsTrack._parsedUri
newTrackFileName = gsTrack.title + '.' + extractionFormat
outGalaxyFn = ExternalTrackManager.createGalaxyFilesFn(
galaxyFn, newTrackFileName)
ensurePathExists(outGalaxyFn)
uri = GalaxyGSuiteTrack.generateURI(galaxyFn,
extraFileName=newTrackFileName)
GalaxyInterface.parseExtFormatAndExtractTrackManyBins(
choices.genome, basisTrackNameAsList, gsTrack.suffix,
gsTrack.path, True, choices.extFormatLbl, outGalaxyFn)
outGSuite.addTrack(
GSuiteTrack(uri,
title=gsTrack.title,
fileFormat=gsTrack.fileFormat,
trackType=gsTrack.trackType,
genome=choices.genome,
attributes=gsTrack.attributes))
GSuiteComposer.composeToFile(outGSuite, galaxyFn)
def generateSynGSuite(cls, dataOut, galaxyFn, genome):
outGSuite = GSuite()
g = SimulationPointIter()
newData = ''
chrNum = 0
for chr in dataOut:
# fileName = 'syn-chr' + 'iInterR-' + str(chr[0]) + 'st-' + str(chr[1]) + 'end-' + str(
# chr[2]) + 'iInterR-' + str(chr[3]) + 'iIntraR-' + str(chr[4]) + 'prob-' + str(chr[5]) + '--' + str(
# chrNum)
fileName = 'syn-' + str(chr[0]) + ',' + str(chr[1]) + ',' + str(chr[2]) + ',' + str(chr[3]) +',' + str(chr[4]) +',' + str(chr[5])
uri = GalaxyGSuiteTrack.generateURI(galaxyFn=galaxyFn,
extraFileName=fileName,
suffix='bed')
gSuiteTrack = GSuiteTrack(uri)
outFn = gSuiteTrack.path
ensurePathExists(outFn)
g.createChrTrack(genome, chr[0], PointIter, outFn, chr[3], chr[4], chr[5], chr[1], chr[2])
with open(outFn, 'r') as outputFile:
newData += ''.join(outputFile.readlines())
chrNum += 1
if chrNum == len(dataOut):
with open(outFn, 'w') as outputFile:
outputFile.write(newData)
outGSuite.addTrack(GSuiteTrack(uri, title=''.join(fileName), genome=genome))
GSuiteComposer.composeToFile(outGSuite, cls.extraGalaxyFn['synthetic GSuite'])
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.
'''
gSuite = getGSuiteFromGalaxyTN(choices.gsuite)
attrName = choices.attrName
outputGSuite = GSuite()
#Writes the information that has been changed to a new track but jumps over all the empty strings
for i, track in enumerate(gSuite.allTracks()):
if i < cls.MAX_NUM_OF_TRACKS:
newAttrValue = getattr(choices,
'selectAttribute%s' % ((i * 2) + 1))
if (attrName == TITLE_COL):
track.title = newAttrValue
else:
track.setAttribute(attrName, newAttrValue)
outputGSuite.addTrack(track)
#Creates the new GSuite
GSuiteComposer.composeToFile(outputGSuite, galaxyFn)
def addResultsToInputGSuite(gsuite, results, attrNames, outputGSuiteFN):
'''
Add the values from the analysis results as metadata columns and create a new GSuite.
If the new attribute names in attrNames already exist as metadata columns in the GSuite,
attributes with added an appropriate _[index] will be added.
'''
assert isinstance(attrNames, (list, tuple)), 'attrNames must be of type list or tuple: %s' % str(attrNames)
newAttrNames = []
for attrName in attrNames:
newAttrNames.append(_updateAttrNameWithIndexIfDuplicate(gsuite, attrName))
outGSuite = GSuite()
for gsTrack in gsuite.allTracks():
currentTrackRes = results[gsTrack.title]
if len(newAttrNames) == 1:
if isinstance(currentTrackRes, (list, tuple)):
if currentTrackRes[0]:
gsTrack.setAttribute(newAttrNames[0], str(currentTrackRes[0]))
else:
if currentTrackRes:
gsTrack.setAttribute(newAttrNames[0], str(currentTrackRes))
else:
assert isinstance(currentTrackRes,
(list, tuple)), 'Expected multiple results per track. Attribute names %s' % str(attrNames)
for i, resultVal in enumerate(currentTrackRes):
if resultVal:
gsTrack.setAttribute(newAttrNames[i], str(resultVal))
outGSuite.addTrack(gsTrack)
GSuiteComposer.composeToFile(outGSuite, outputGSuiteFN)
def execute(cls, choices, galaxyFn=None, username=''):
from gold.gsuite.GSuite import GSuite
from gold.gsuite.GSuiteTrack import GalaxyGSuiteTrack, GSuiteTrack
import gold.gsuite.GSuiteComposer as GSuiteComposer
from quick.application.ExternalTrackManager import ExternalTrackManager
genome = choices.genome if choices.selectGenome == 'Yes' else None
selectedHistories = [
key for key, val in choices.history.iteritems() if val is not None
]
gSuite = GSuite()
for histGalaxyId in selectedHistories:
galaxyTrackName = choices.history[histGalaxyId].split(':')
histGalaxyFn = ExternalTrackManager.extractFnFromGalaxyTN(
galaxyTrackName)
histName = ExternalTrackManager.extractNameFromHistoryTN(
galaxyTrackName)
histSuffix = ExternalTrackManager.extractFileSuffixFromGalaxyTN(
galaxyTrackName)
uri = GalaxyGSuiteTrack.generateURI(galaxyFn=histGalaxyFn,
suffix=histSuffix)
gSuite.addTrack(GSuiteTrack(uri, title=histName, genome=genome))
GSuiteComposer.composeToFile(gSuite, galaxyFn)
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, GalaxyGSuiteTrack
from quick.application.UserBinSource import GlobalBinSource
from quick.extra.ProgressViewer import ProgressViewer
from quick.extra.TrackExtractor import TrackExtractor
genome = choices.genome
fullGenomeBins = GlobalBinSource(genome)
gSuite = getGSuiteFromGalaxyTN(choices.gsuite)
progressViewer = ProgressViewer(
[(cls.PROGRESS_PROCESS_DESCRIPTION, len(gSuite))], galaxyFn)
outGSuite = GSuite()
hiddenStorageFn = cls.extraGalaxyFn[getGSuiteHistoryOutputName(
'storage', datasetInfo=choices.gsuite)]
fileNameSet = set()
for track in gSuite.allTracks():
fileName = cls._getUniqueFileName(fileNameSet, track.trackName)
title = track.title
attributes = track.attributes
fi = cls._getFileFormatInfo(choices, gSuite, genome, track)
uri = GalaxyGSuiteTrack.generateURI(galaxyFn=hiddenStorageFn,
extraFileName=fileName,
suffix=fi.suffix)
gSuiteTrack = GSuiteTrack(uri,
title=title,
genome=genome,
attributes=attributes)
TrackExtractor.extractOneTrackManyRegsToOneFile(
track.trackName,
fullGenomeBins,
gSuiteTrack.path,
fileFormatName=fi.fileFormatName,
globalCoords=True,
asOriginal=fi.asOriginal,
allowOverlaps=fi.allowOverlaps)
outGSuite.addTrack(gSuiteTrack)
progressViewer.update()
primaryFn = cls.extraGalaxyFn[getGSuiteHistoryOutputName(
'primary', datasetInfo=choices.gsuite)]
GSuiteComposer.composeToFile(outGSuite, primaryFn)
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 (cls, e.g. generated image files). choices is a list
of selections made by web-user in each options box.
Mandatory unless isRedirectTool() returns True.
"""
#TODO: add functionality for single gtrack within-track randomization
print 'Executing...'
inputGsuite = getGSuiteFromGalaxyTN(choices.gs)
outputGSuite = GSuite()
genome = inputGsuite.genome
ts = factory.getFlatTracksTS(genome, choices.gs)
randIndex = 0
bins = GlobalBinSource(genome)
if choices.randType == TsRandAlgReg.BETWEEN_TRACKS_CATEGORY and \
choices.category not in [None, 'None']:
ts = ts.getSplittedByCategoryTS(choices.category)
randomizedTs = TrackStructureV2()
for subTsKey, subTs in ts.items():
tvProvider = cls.createTrackViewProvider(
choices, subTs, bins, genome)
randomizedTs[subTsKey] = getRandomizedVersionOfTs(
subTs, tvProvider, randIndex)
randomizedTs = randomizedTs.getFlattenedTS()
else:
tvProvider = cls.createTrackViewProvider(choices, ts, bins, genome)
randomizedTs = getRandomizedVersionOfTs(ts, tvProvider, randIndex)
for singleTrackTs in randomizedTs.getLeafNodes():
uri = GalaxyGSuiteTrack.generateURI(
galaxyFn=galaxyFn,
extraFileName=os.path.sep.join(singleTrackTs.track.trackName) +
'.randomized',
suffix='bed')
title = singleTrackTs.metadata.pop('title')
gSuiteTrack = GSuiteTrack(uri,
title=title + '.randomized',
fileFormat='primary',
trackType='segments',
genome=genome,
attributes=singleTrackTs.metadata)
outputGSuite.addTrack(gSuiteTrack)
singleTrackTs.metadata['trackFilePath'] = gSuiteTrack.path
spec = AnalysisSpec(TsWriterStat)
res = doAnalysis(spec, bins, randomizedTs)
GSuiteComposer.composeToFile(outputGSuite, galaxyFn)
def testComposeLocalUrlGenomeAttributesNonAscii(self):
gSuite = GSuite()
gSuite.addTrack(
GSuiteTrack('galaxy:/12345abc',
genome=u'hg18ø',
attributes=OrderedDict([('one', 'yes')])))
gSuite.addTrack(
GSuiteTrack('file:/path/to/file2',
genome='hg19',
attributes=OrderedDict([('two', u'nø')])))
gSuite.addTrack(
GSuiteTrack(
HbGSuiteTrack.generateURI(trackName=[u'track', u'nøme']),
genome='hg38',
attributes=OrderedDict([('two', 'yes')])))
gSuite.setCustomHeader('my header', u'bø!')
output = GSuiteComposer.composeToString(gSuite)
targetOutput = \
'##location: local\n' \
'##file format: unknown\n' \
'##track type: unknown\n' \
'##genome: multiple\n' \
'##my header: b%C3%B8!\n' \
'###uri\ttitle\tfile_format\tgenome\tone\ttwo\n' \
'galaxy:/12345abc\t12345abc\tunknown\thg18%C3%B8\tyes\t.\n' \
'file:/path/to/file2\tfile2\tunknown\thg19\t.\tn%C3%B8\n' \
'hb:/track/n%C3%B8me\tn%C3%B8me\tpreprocessed\thg38\t.\tyes\n'
self.assertEquals(targetOutput, output)
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, GalaxyGSuiteTrack
inGSuite = getGSuiteFromGalaxyTN(choices.gsuite)
outGSuite = GSuite()
newSuffix = cls._getNewSuffixIfAny(choices)
for track in cls._getSelectedTracks(choices, inGSuite):
title, suffix = cls._getExportTrackTitleAndSuffix(track, newSuffix)
trackGalaxyFn = cls.extraGalaxyFn[title]
if choices.changeFormat == cls.OUTPUT_FORMAT_CONVERT:
from gold.origdata.FileFormatComposer import getComposerClsFromFileFormatName
geSource = track.getGenomeElementSource(printWarnings=False)
composerCls = getComposerClsFromFileFormatName(
choices.outputFormat)
composer = composerCls(geSource)
composer.composeToFile(trackGalaxyFn)
else:
shutil.copy(track.path, trackGalaxyFn)
uri = GalaxyGSuiteTrack.generateURI(galaxyFn=trackGalaxyFn,
suffix=suffix)
gSuiteTrack = GSuiteTrack(uri,
title=title,
genome=track.genome,
attributes=track.attributes)
outGSuite.addTrack(gSuiteTrack)
GSuiteComposer.composeToFile(outGSuite, galaxyFn)
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.
'''
from gold.gsuite.GSuiteArchiver import ArchiveToGalaxyGSuiteTrackIterator, \
convertArchiveToGSuite
import gold.gsuite.GSuiteComposer as GSuiteComposer
from quick.gsuite.GSuiteHbIntegration import \
writeGSuiteHiddenTrackStorageHtml
from quick.extra.ProgressViewer import ProgressViewer
from quick.util.debug import DebugUtil
# DebugUtil.insertBreakPoint(username=username, currentUser='******')
archive = cls._getArchiveReader(choices)
trackCount = sum(1 for file in archive)
desc = cls._getOutputHistoryDescription(choices)
progressViewer = ProgressViewer([('Extract tracks', trackCount)],
galaxyFn)
storeHierarchy = choices.storeHierarchy == 'Yes'
hiddenStorageFn = cls.extraGalaxyFn[getGSuiteHistoryOutputName(
'storage', desc)]
archiveToGSuiteTrackIter = \
ArchiveToGalaxyGSuiteTrackIterator(archive, hiddenStorageFn, storeHierarchy)
writeGSuiteHiddenTrackStorageHtml(hiddenStorageFn)
gSuite = convertArchiveToGSuite(archiveToGSuiteTrackIter,
progressViewer)
GSuiteComposer.composeToFile(
gSuite,
cls.extraGalaxyFn[getGSuiteHistoryOutputName('primary', desc)])
def testEmptyCompose(self):
gSuite = GSuite()
output = GSuiteComposer.composeToString(gSuite)
targetOutput = \
'##location: unknown\n' \
'##file format: unknown\n' \
'##track type: unknown\n' \
'##genome: unknown\n'
self.assertEquals(targetOutput, output)
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
geSource = etm.getGESourceFromGalaxyOrVirtualTN(choices.track, genome)
#hiddenStorageFn = cls.extraGalaxyFn[cls.HISTORY_HIDDEN_TRACK_STORAGE]
hiddenStorageFn = galaxyFn
composerCls = cls._getComposerCls(choices)
valAttr = choices.attr
gSuite = createGalaxyGSuiteBySplittingInputFileOnAttribute\
(hiddenStorageFn, geSource, genome, composerCls, valAttr)
GSuiteComposer.composeToFile(gSuite, galaxyFn)
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=''):
seqs = [s.strip() for s in choices.seqs.splitlines()]
trackNameList = []
for nmer in seqs:
GalaxyInterface.createNmerTrack(choices.genome, nmer)
trackNameList.append(
['Sequence', 'K-mers',
str(len(nmer)) + '-mers', nmer])
#example trackName = ['Sequence', 'K-mers', '7-mers', 'agagaga']
outGSuite = GSuite()
for trackName in trackNameList:
trackType = TrackInfo(choices.genome,
trackName).trackFormatName.lower()
hbUri = HbGSuiteTrack.generateURI(trackName=trackName)
outGSuite.addTrack(
GSuiteTrack(hbUri,
title=' '.join(['Nmer track'] + trackName[-1:]),
trackType=trackType,
genome=choices.genome))
GSuiteComposer.composeToFile(outGSuite,
cls.extraGalaxyFn['Kmers GSuite'])
def execute(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.
'''
from quick.gsuite.GSuiteHbIntegration import getSubtracksAsGSuite
import gold.gsuite.GSuiteComposer as GSuiteComposer
genome = choices.genome
parentTrack = choices.parentTrack.split(':')
if parentTrack == ['']:
parentTrack = []
gSuite = getSubtracksAsGSuite(genome, parentTrack, username)
GSuiteComposer.composeToFile(gSuite, galaxyFn)
def execute(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.
'''
from gold.gsuite.GSuite import GSuite
from gold.gsuite.GSuiteTrack import GalaxyGSuiteTrack, GSuiteTrack
import gold.gsuite.GSuiteComposer as GSuiteComposer
from quick.application.ExternalTrackManager import ExternalTrackManager
genome = choices.genome if choices.selectGenome == 'Yes' else None
selectedHistories = [
key for key, val in choices.history.iteritems() if val is not None
]
gSuite = GSuite()
for histGalaxyId in selectedHistories:
galaxyTrackName = choices.history[histGalaxyId].split(':')
histGalaxyFn = ExternalTrackManager.extractFnFromGalaxyTN(
galaxyTrackName)
histName = ExternalTrackManager.extractNameFromHistoryTN(
galaxyTrackName)
histSuffix = ExternalTrackManager.extractFileSuffixFromGalaxyTN(
galaxyTrackName)
uri = GalaxyGSuiteTrack.generateURI(galaxyFn=histGalaxyFn,
suffix=histSuffix)
gSuite.addTrack(GSuiteTrack(uri, title=histName, genome=genome))
GSuiteComposer.composeToFile(gSuite, galaxyFn)
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.
'''
categoryToGenomeElementListDict = defaultdict(list)
genome = choices.genome
outputType = choices.outputType
catTrack = choices.catTrack.split(':')
geSource = ExternalTrackManager.getGESourceFromGalaxyOrVirtualTN(
catTrack, genome)
for ge in geSource:
categoryToGenomeElementListDict[ge.val].append(ge)
for category, genomeElementList in categoryToGenomeElementListDict.iteritems(
):
geSourceWrapper = ListGESourceWrapper(geSource, genomeElementList)
composer = cls.getComposer(geSourceWrapper, outputType)
# staticFile = GalaxyRunSpecificFile(catTrack + [category, outputType], galaxyFn)
composer.composeToFile(cls.extraGalaxyFn[category])
outGSuite = GSuite()
for category, galaxyFileName in OrderedDict([
(x, cls.extraGalaxyFn[x])
for x in categoryToGenomeElementListDict.keys()
]).iteritems():
uri = GalaxyGSuiteTrack.generateURI(galaxyFn=galaxyFileName,
suffix=outputType)
outGSuite.addTrack(GSuiteTrack(uri, title=category, genome=genome))
GSuiteComposer.composeToFile(
outGSuite, cls.extraGalaxyFn['GSuite from categorical'])
print 'Execution done!'
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)
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.GSuitePreprocessor import GSuitePreprocessor
from quick.extra.ProgressViewer import ProgressViewer
from quick.multitrack.MultiTrackCommon import getGSuiteFromGalaxyTN
inGSuite = getGSuiteFromGalaxyTN(choices.history)
if choices.genome != inGSuite.genome:
inGSuite.setGenomeOfAllTracks(choices.genome)
progressViewer = ProgressViewer(
[('Preprocess tracks', inGSuite.numTracks())], galaxyFn)
gSuitePreprocessor = GSuitePreprocessor()
outGSuite, errorGSuite = gSuitePreprocessor.visitAllGSuiteTracksAndReturnOutputAndErrorGSuites\
(inGSuite, progressViewer)
#outGSuite, errorGSuite = inGSuite.preProcessAllLocalTracksAndReturnOutputAndErrorGSuites()
nopreprocFn = cls.extraGalaxyFn[getGSuiteHistoryOutputName(
'nopreprocessed', datasetInfo=choices.history)]
GSuiteComposer.composeToFile(errorGSuite, nopreprocFn)
preprocFn = cls.extraGalaxyFn[getGSuiteHistoryOutputName(
'preprocessed', datasetInfo=choices.history)]
GSuiteComposer.composeToFile(outGSuite, preprocFn)
def testComposeRemoteOnlyUrl(self):
gSuite = GSuite()
gSuite.addTrack(
GSuiteTrack('ftp://server.somewhere.com/path/to/file1'))
gSuite.addTrack(GSuiteTrack('http://server.other.com/path/to/file2'))
output = GSuiteComposer.composeToString(gSuite)
targetOutput = \
'##location: remote\n' \
'##file format: unknown\n' \
'##track type: unknown\n' \
'##genome: unknown\n' \
'###uri\ttitle\n' \
'ftp://server.somewhere.com/path/to/file1\tfile1\n' \
'http://server.other.com/path/to/file2\tfile2\n'
self.assertEquals(targetOutput, output)
def testParseAndCompose(self):
inputContents = \
'##location: multiple\n' \
'##file format: multiple\n' \
'##track type: unknown\n' \
'##genome: hg18\n' \
'###uri\ttitle\tfile_format\tcell\tantibody\textra\n' \
'ftp://server.somewhere.com/path/to/file1.bed\tTrack1\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\tTrack5\tpreprocessed\t.\t.\t.\n' \
'galaxy:/ad123dd12fg;btrack?track=track%3Aname\tTrack6\tpreprocessed\tk562\tcMyb\t.\n' \
'file:/path/to/file.btrack?track=track%3Aname\tTrack name7\tpreprocessed\t.\tcMyb\tyes\n'
gSuite = GSuiteParser.parseLines(inputContents.split('\n'))
outputContents = GSuiteComposer.composeToString(gSuite)
self.assertEquals(inputContents, outputContents)
def testComposeUrlTitleLocationTrackType(self):
gSuite = GSuite()
gSuite.addTrack(
GSuiteTrack('ftp://server.somewhere.com/path/to/file1',
title='Track1',
trackType='points'))
gSuite.addTrack(
GSuiteTrack('file:/path/to/file2', trackType='segments'))
output = GSuiteComposer.composeToString(gSuite)
targetOutput = \
'##location: multiple\n' \
'##file format: unknown\n' \
'##track type: multiple\n' \
'##genome: unknown\n' \
'###uri\ttitle\ttrack_type\n' \
'ftp://server.somewhere.com/path/to/file1\tTrack1\tpoints\n' \
'file:/path/to/file2\tfile2\tsegments\n'
self.assertEquals(targetOutput, output)
def testComposeRemoteUrlGenomeFileFormat(self):
gSuite = GSuite()
gSuite.addTrack(
GSuiteTrack('ftp://server.somewhere.com/path/to/file1.bed',
genome='hg18'))
gSuite.addTrack(
GSuiteTrack('http://server.other.com/path/to/file2',
genome='hg18'))
output = GSuiteComposer.composeToString(gSuite)
targetOutput = \
'##location: remote\n' \
'##file format: unknown\n' \
'##track type: unknown\n' \
'##genome: hg18\n' \
'###uri\ttitle\tfile_format\n' \
'ftp://server.somewhere.com/path/to/file1.bed\tfile1.bed\tprimary\n' \
'http://server.other.com/path/to/file2\tfile2\tunknown\n'
self.assertEquals(targetOutput, output)
def testComposeLocalUrlGenomeAttributes(self):
gSuite = GSuite()
gSuite.addTrack(
GSuiteTrack('galaxy:/12345abc',
genome='hg18',
attributes=OrderedDict([('one', 'yes')])))
gSuite.addTrack(
GSuiteTrack('file:/path/to/file2',
genome='hg19',
attributes=OrderedDict([('two', 'no')])))
output = GSuiteComposer.composeToString(gSuite)
targetOutput = \
'##location: local\n' \
'##file format: unknown\n' \
'##track type: unknown\n' \
'##genome: multiple\n' \
'###uri\ttitle\tgenome\tone\ttwo\n' \
'galaxy:/12345abc\t12345abc\thg18\tyes\t.\n' \
'file:/path/to/file2\tfile2\thg19\t.\tno\n'
self.assertEquals(targetOutput, output)
def execute(cls, choices, galaxyFn=None, username=''):
if not choices.source:
return
source = choices.source.split('[')[0].strip()
fileTypes = []
gsm = TrackGlobalSearchModule(cls.useSqlite)
desc = choices.subCategory
if choices.source.find('HyperBrowser') == -1:
#items = gsm.getItems(choices.search,choices.subCategory)
# # allFileTypes = [x.split('[')[0] for x,selected in prevChoices.filetype.iteritems()]
# # fileTypes = [x.split('[')[0] for x,selected in prevChoices.filetype.iteritems() if selected]
##allDataTypes = [x.split('[')[0].strip() for x,selected in choices.dataType.iteritems()]
#dataTypes = [x.split('[')[0].strip() for x,selected in choices.dataType.iteritems() if selected]
dataTypes = [choices.dataType.split('[')[0].strip()]
##Was made to speadup so that there will be no filetype comparisons,
##but deactivated for now since there is hardcoded filtering in
##prevChoices.fileType
#if len(allFileTypes) == len(fileTypes):
# fileTypes = []
if 'all tracks' in choices.outputType:
remoteGSuite = gsm.getGSuite(choices.search,
choices.subCategory,
source,
dataTypes,
filterFileSuffix=True)
elif choices.outputType == 'Select tracks manually':
remoteGSuite = gsm.getGSuite(choices.search,choices.subCategory,source,dataTypes,\
filterFileSuffix = True,selectedFileIDs = choices.results)
elif choices.outputType == 'Select 10 random tracks':
remoteGSuite = gsm.getRandomGSuite(choices.search,choices.subCategory,source,dataTypes,\
filterFileSuffix = True,count = 10)
elif choices.outputType == 'Select 50 random tracks':
remoteGSuite = gsm.getRandomGSuite(choices.search,choices.subCategory,source,dataTypes,\
filterFileSuffix = True,count = 50)
if choices.downloadAndPreprocess == 'Yes' and choices.source.find(
'HyperBrowser') == -1:
trackCount = remoteGSuite.numTracks()
progressViewer = \
ProgressViewer([('Download tracks', trackCount),
('Preprocess tracks', trackCount)], galaxyFn)
#from gold.gsuite.GSuiteDownloader import GSuiteMultipleGalaxyFnDownloader
#gSuiteDownloader = GSuiteMultipleGalaxyFnDownloader()
#localGSuite, errorLocalGSuite = \
# gSuiteDownloader.visitAllGSuiteTracksAndReturnOutputAndErrorGSuites\
# (remoteGSuite, progressViewer, cls.extraGalaxyFn)
from gold.gsuite.GSuiteDownloader import GSuiteSingleGalaxyFnDownloader
from quick.gsuite.GSuiteHbIntegration import \
writeGSuiteHiddenTrackStorageHtml
gSuiteDownloader = GSuiteSingleGalaxyFnDownloader()
hiddenStorageFn = cls.extraGalaxyFn[getGSuiteHistoryOutputName(
'storage', desc)]
localGSuite, errorLocalGSuite = \
gSuiteDownloader.visitAllGSuiteTracksAndReturnOutputAndErrorGSuites \
(remoteGSuite, progressViewer, hiddenStorageFn, [])
writeGSuiteHiddenTrackStorageHtml(hiddenStorageFn)
progressViewer.updateProgressObjectElementCount(
'Preprocess tracks', localGSuite.numTracks())
gSuitePreprocessor = GSuitePreprocessor()
preProcessedGSuite, errorPreProcessGSuite = \
gSuitePreprocessor.visitAllGSuiteTracksAndReturnOutputAndErrorGSuites\
(localGSuite, progressViewer)
#preProcessedGSuite, errorPreProcessGSuite = localGSuite.preProcessAllLocalTracksAndReturnOutputAndErrorGSuites(progressViewer)
GSuiteComposer.composeToFile(
remoteGSuite,
cls.extraGalaxyFn[getGSuiteHistoryOutputName('remote', desc)])
GSuiteComposer.composeToFile(
errorLocalGSuite, cls.extraGalaxyFn[getGSuiteHistoryOutputName(
'nodownload', desc)])
GSuiteComposer.composeToFile(
localGSuite,
cls.extraGalaxyFn[getGSuiteHistoryOutputName('primary', desc)])
GSuiteComposer.composeToFile(
errorPreProcessGSuite,
cls.extraGalaxyFn[getGSuiteHistoryOutputName(
'nopreprocessed', desc)])
GSuiteComposer.composeToFile(
preProcessedGSuite,
cls.extraGalaxyFn[getGSuiteHistoryOutputName(
'preprocessed', desc)])
else:
GSuiteComposer.composeToFile(remoteGSuite, galaxyFn)
def __str__(self):
import gold.gsuite.GSuiteComposer as GSuiteComposer
return GSuiteComposer.composeToString(self)
class MultiTrackIntersectTool(GeneralGuiTool, GenomeMixin):
GSUITE_FILE_OPTIONS_BOX_KEYS = ['gSuite']
ALLOW_UNKNOWN_GENOME = False
ALLOW_GENOME_OVERRIDE = False
ALLOW_MULTIPLE_GENOMES = False
WHAT_GENOME_IS_USED_FOR = 'the output GSuite file' # Other common possibility: 'the analysis'
FROM_HISTORY_TEXT = 'From history'
FROM_HYPERBROWSER_TEXT = 'From HyperBrowser repository'
WITH_OVERLAPS = 'Allow multiple overlapping points/segments within the same track'
NO_OVERLAPS = 'Merge any overlapping points/segments within the same track'
GSUITE_ALLOWED_FILE_FORMATS = [GSuiteConstants.PREPROCESSED]
GSUITE_ALLOWED_LOCATIONS = [GSuiteConstants.LOCAL]
GSUITE_ALLOWED_TRACK_TYPES = [GSuiteConstants.POINTS,
GSuiteConstants.VALUED_POINTS,
GSuiteConstants.SEGMENTS,
GSuiteConstants.VALUED_SEGMENTS]
GSUITE_DISALLOWED_GENOMES = [GSuiteConstants.UNKNOWN,
GSuiteConstants.MULTIPLE]
OUTPUT_TRACKS_SUFFIX = 'bed'
GSUITE_OUTPUT_LOCATION = GSuiteConstants.LOCAL
GSUITE_OUTPUT_FILE_FORMAT = GSuiteConstants.PREPROCESSED
GSUITE_OUTPUT_TRACK_TYPE = GSuiteConstants.SEGMENTS
OUTPUT_GSUITE_DESCRIPTION = ', intersected'
PROGRESS_INTERSECT_MSG = 'Intersect tracks'
PROGRESS_PREPROCESS_MSG = 'Preprocess tracks'
@staticmethod
def getToolName():
'''
Specifies a header of the tool, which is displayed at the top of the
page.
'''
return "Intersect preprocessed tracks in GSuite with a single track"
@classmethod
def getInputBoxNames(cls):
'''
Specifies a list of headers for the input boxes, and implicitly also the
number of input boxes to display on the page. The returned list can have
two syntaxes:
1) A list of strings denoting the headers for the input boxes in
numerical order.
2) A list of tuples of strings, where each tuple has
two items: a header and a key.
The contents of each input box must be defined by the function
getOptionsBoxK, where K is either a number in the range of 1 to the
number of boxes (case 1), or the specified key (case 2).
Note: the key has to be camelCase (e.g. "firstKey")
'''
return [('Select GSuite file from history:', 'gSuite')] +\
cls.getInputBoxNamesForGenomeSelection() +\
[('Select source of filtering track:', 'trackSource'),
('Select track from history:', 'trackHistory'),
('Select track:', 'track'),
('Overlap handling:', 'withOverlaps')]
#@staticmethod
#def getInputBoxOrder():
# '''
# Specifies the order in which the input boxes should be displayed, as a
# list. The input boxes are specified by index (starting with 1) or by
# key. If None, the order of the input boxes is in the order specified by
# getInputBoxNames.
# '''
# return None
@classmethod
def getOptionsBoxGSuite(cls): # Alternatively: getOptionsBox2()
'''
See getOptionsBoxFirstKey().
prevChoices is a namedtuple of selections made by the user in the
previous input boxes (that is, a namedtuple containing only one element
in this case). The elements can accessed either by index, e.g.
prevChoices[0] for the result of input box 1, or by key, e.g.
prevChoices.key (case 2).
'''
return cls.getHistorySelectionElement('gsuite')
@classmethod
def getOptionsBoxTrackSource(cls, prevChoices):
return [cls.FROM_HISTORY_TEXT, cls.FROM_HYPERBROWSER_TEXT]
@classmethod
def getOptionsBoxTrackHistory(cls, prevChoices):
if prevChoices.trackSource == cls.FROM_HISTORY_TEXT:
from gold.application.DataTypes import getSupportedFileSuffixesForPointsAndSegments
return cls.getHistorySelectionElement(*getSupportedFileSuffixesForPointsAndSegments())
@classmethod
def getOptionsBoxTrack(cls, prevChoices):
if prevChoices.trackSource == cls.FROM_HYPERBROWSER_TEXT:
return cls.TRACK_SELECT_ELEMENT
@classmethod
def getOptionsBoxWithOverlaps(cls, prevChoices):
if prevChoices.trackHistory or prevChoices.track:
return [cls.NO_OVERLAPS, cls.WITH_OVERLAPS]
#@staticmethod
#def getInfoForOptionsBoxKey(prevChoices):
# '''
# If not None, defines the string content of an clickable info box beside
# the corresponding input box. HTML is allowed.
# '''
# return None
#@staticmethod
#def getDemoSelections():
# return ['testChoice1','..']
@classmethod
def getExtraHistElements(cls, choices):
desc = cls.OUTPUT_GSUITE_DESCRIPTION
return [HistElement(getGSuiteHistoryOutputName(
'nointersect', description=desc, datasetInfo=choices.gSuite),
GSuiteConstants.GSUITE_SUFFIX),
HistElement(getGSuiteHistoryOutputName(
'primary', description=desc, datasetInfo=choices.gSuite),
GSuiteConstants.GSUITE_SUFFIX),
HistElement(getGSuiteHistoryOutputName(
'nopreprocessed', description=desc, datasetInfo=choices.gSuite),
GSuiteConstants.GSUITE_SUFFIX),
HistElement(getGSuiteHistoryOutputName(
'preprocessed', description=desc, datasetInfo=choices.gSuite),
GSuiteConstants.GSUITE_SUFFIX),
HistElement(getGSuiteHistoryOutputName(
'storage', description=desc, datasetInfo=choices.gSuite),
GSuiteConstants.GSUITE_STORAGE_SUFFIX, hidden=True)]
@classmethod
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()
gSuitePreprocessor = GSuitePreprocessor()
preprocessedGSuite, errorGSuite = gSuitePreprocessor.\
visitAllGSuiteTracksAndReturnOutputAndErrorGSuites \
(primaryGSuite, progressViewer)
GSuiteComposer.composeToFile(emptyGSuite, emptyFn)
GSuiteComposer.composeToFile(primaryGSuite, primaryFn)
GSuiteComposer.composeToFile(preprocessedGSuite, preprocessedFn)
GSuiteComposer.composeToFile(errorGSuite, errorFn)
writeGSuiteHiddenTrackStorageHtml(hiddenStorageFn)
def printGSuite(cls, choices, cols, rows, colListString, outFile):
#print cols
from quick.extra.ProgressViewer import ProgressViewer
from gold.gsuite.GSuite import GSuite
from gold.gsuite.GSuiteTrack import GSuiteTrack, GalaxyGSuiteTrack
import gold.gsuite.GSuiteComposer as GSuiteComposer
from gold.origdata.GtrackGenomeElementSource import GtrackGenomeElementSource
from gold.origdata.GtrackComposer import ExtendedGtrackComposer
from gold.origdata.GESourceWrapper import ListGESourceWrapper
from gold.origdata.GenomeElement import GenomeElement
from collections import defaultdict
from copy import copy
from urllib import quote
from unidecode import unidecode
from pyliftover import LiftOver
gSuite = GSuite()
diseaseColIndex = cols.index(cls.DISEASE_COLUMN_NAME)
chrColIndex = cols.index(cls.CHR_COLUMN_NAME)
startColIndex = cols.index(cls.START_COLUMN_NAME)
valColIndex = cols.index(cls.VAL_COLUMN_NAME)
orderedExtraKeys = copy(cols)
extraIndexes = range(len(cols))
for colName in [cls.DISEASE_COLUMN_NAME, cls.CHR_COLUMN_NAME,
cls.START_COLUMN_NAME, cls.VAL_COLUMN_NAME]:
extraIndexes.remove(cols.index(colName))
orderedExtraKeys.remove(colName)
orderedExtraKeys = [cls._fixColNameForGTrack(key) for key in orderedExtraKeys]
diseaseToRowsDict = defaultdict(list)
for row in rows:
disease = row[diseaseColIndex]
if isinstance(disease, unicode):
disease = unidecode(disease).replace('\x00', '')
diseaseToRowsDict[disease].append(row)
progressViewer = ProgressViewer([('Create GWAS tracks for diseases/traits', len(diseaseToRowsDict))],
cls.extraGalaxyFn[cls.HISTORY_PROGRESS_TITLE] )
for disease in sorted(diseaseToRowsDict.keys()):
uri = GalaxyGSuiteTrack.generateURI(galaxyFn=cls.extraGalaxyFn[cls.HISTORY_HIDDEN_TRACK_STORAGE],
extraFileName=disease.replace('/', '_') + '.gtrack')
gSuiteTrack = GSuiteTrack(uri, title=disease, genome=cls.OUTPUT_GENOME)
gSuite.addTrack(gSuiteTrack)
shouldLiftOver = cls.DATABASE_GENOME != cls.OUTPUT_GENOME
if shouldLiftOver:
liftOver = LiftOver(cls.DATABASE_GENOME, cls.OUTPUT_GENOME)
geList = []
for row in diseaseToRowsDict[disease]:
extra = {}
for col, index in zip(orderedExtraKeys, extraIndexes):
cell = row[index].strip()
if isinstance(cell, unicode):
cell = unidecode(cell)
extra[col] = cell if cell != '' else '.'
chrom = 'chr' + row[chrColIndex]
if chrom == 'chr23':
chrom = 'chrX'
if chrom == 'chr24':
chrom = 'chrY'
if chrom == 'chrMT':
chrom = 'chrM'
start = int(row[startColIndex])
if shouldLiftOver:
newPosList = liftOver.convert_coordinate(chrom, start)
if newPosList is None or len(newPosList) != 1:
print 'SNP with position %s on chromosome %s ' % (chrom, start) +\
'could not be lifted over from reference genome ' +\
'%s to %s (for disease/trait "%s")' % \
(cls.DATABASE_GENOME, cls.OUTPUT_GENOME, disease)
else:
chrom, start = newPosList[0][0:2]
#print extra
geList.append(GenomeElement(chr=chrom, start=start,
val=row[valColIndex], orderedExtraKeys=orderedExtraKeys,
extra=extra))
geSource = GtrackGenomeElementSource(cls.GTRACK_BLUEPRINT_PATH)
wrappedGeSource = ListGESourceWrapper(geSource, geList)
composer = ExtendedGtrackComposer(wrappedGeSource)
composer.composeToFile(gSuiteTrack.path)
progressViewer.update()
GSuiteComposer.composeToFile(gSuite, outFile)
