def plainRun(analysisDef, genome, track1Fn, track2Fn):
'''
Currently under development, not yet functioning.
Note that file names (track1Fn, track2Fn) must either be a valid .dat-file from a Galaxy system,
or be located in a path where the two deepest levels are numerical values above 1000, and unique between different runs by this tool'''
#GalaxyInterface.runManual(trackNames, analysisDef, regSpec, binSpec, genome, galaxyFn=None, trackNameIntensity=None, username='', \
#printResults=True, printProgress=True, printHtmlWarningMsgs=True, applyBoundaryFilter=False, printRunDescription=True, **kwArgs):
from quick.application.ExternalTrackManager import ExternalTrackManager
#fixme: is this correct?
assert all(
idPart > 1000
for idPart in ExternalTrackManager.extractIdFromGalaxyFn(track1Fn))
tn1 = ExternalTrackManager.constructGalaxyTnFromSuitedFn(track1Fn)
assert all(
idPart > 1000
for idPart in ExternalTrackManager.extractIdFromGalaxyFn(track2Fn))
tn2 = ExternalTrackManager.constructGalaxyTnFromSuitedFn(track2Fn)
from quick.application.GalaxyInterface import GalaxyInterface
userBinSource = GalaxyInterface._getUserBinSource('chrs', '*', genome, tn1,
tn2)
from gold.application.StatRunner import AnalysisDefJob
job = AnalysisDefJob(analysisDef, tn1, tn2, userBinSource)
result = job.run(printProgress=False)
return result
def visitGalaxyGSuiteTrack(self, gSuiteTrack):
self.genericVisit(gSuiteTrack)
from quick.application.ExternalTrackManager import ExternalTrackManager
from gold.description.TrackInfo import TrackInfo
if gSuiteTrack.hasExtraFileName():
baseFileName = os.path.basename(gSuiteTrack.uriWithoutSuffix)
else:
baseFileName = gSuiteTrack.title
galaxyTN = ExternalTrackManager.constructGalaxyTnFromSuitedFn(
gSuiteTrack.path, fileEnding=gSuiteTrack.suffix, name=baseFileName)
trackName = ExternalTrackManager.getPreProcessedTrackFromGalaxyTN(
gSuiteTrack.genome,
galaxyTN,
printErrors=False,
printProgress=False,
renameExistingTracksIfNeeded=False)
trackType = TrackInfo(gSuiteTrack.genome,
trackName).trackFormatName.lower()
hbUri = HbGSuiteTrack.generateURI(trackName=trackName)
return GSuiteTrack(hbUri,
title=gSuiteTrack.title,
trackType=trackType,
genome=gSuiteTrack.genome,
attributes=gSuiteTrack.attributes,
comment=gSuiteTrack.comment)
def _createPreprocessedGsuiteTrack(self,
gSuiteTrack,
baseFileName,
doEncodeId,
urlPrefix=None):
from quick.application.ExternalTrackManager import ExternalTrackManager as ETM
from gold.description.TrackInfo import TrackInfo
self.genericVisit(gSuiteTrack)
galaxyTN = ETM.constructGalaxyTnFromSuitedFn(
gSuiteTrack.path, fileEnding=gSuiteTrack.suffix, name=baseFileName)
trackName = ETM.getPreProcessedTrackFromGalaxyTN(
gSuiteTrack.genome,
galaxyTN,
printErrors=False,
printProgress=False,
renameExistingTracksIfNeeded=False,
doEncodeId=doEncodeId,
urlPrefix=urlPrefix)
trackType = TrackInfo(gSuiteTrack.genome,
trackName).trackFormatName.lower()
hbUri = HbGSuiteTrack.generateURI(trackName=trackName)
return GSuiteTrack(hbUri,
title=gSuiteTrack.title,
trackType=trackType,
genome=gSuiteTrack.genome,
attributes=gSuiteTrack.attributes,
comment=gSuiteTrack.comment)
def createLinkedPointTrack(cls, rsids, isUndirected, trackFn, r2):
from quick.webtools.clustering.CreateLDTrack import CreateLDTrack
from quick.application.ExternalTrackManager import ExternalTrackManager
# Create file for GTrack
galaxyTN = ExternalTrackManager.constructGalaxyTnFromSuitedFn(trackFn, fileEnding='gtrack', name='ld_graph')
fn = ExternalTrackManager.extractFnFromGalaxyTN(galaxyTN)
f = open(fn, 'w')
# Get LD information and create linked point track
ldDict = CreateLDTrack.getLDDict(r2)
expansionDict = CreateLDTrack.getExpansionDict(rsids, ldDict)
f.write(CreateLDTrack.formatLinkedPointTrack(expansionDict, isUndirected))
