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 _getAllOutputFormatsForTrack(genome, track):
from quick.application.GalaxyInterface import GalaxyInterface
trackOutputFormats = set()
extractionOptions = \
GalaxyInterface.getTrackExtractionOptions(
genome, track.trackName)
for opt in extractionOptions:
extFormat, suffix = opt
formatInfo = FileFormatInfo(
*TrackExtractor.getAttrsFromExtractionFormat(extFormat),
suffix=suffix)
trackOutputFormats.add(formatInfo)
return trackOutputFormats
def getOptionsBoxExtFormatLbl(prevChoices):
if prevChoices.genome and prevChoices.basisTrack:
extrOpts = GalaxyInterface.getTrackExtractionOptions(
prevChoices.genome, prevChoices.basisTrack.split(':'))
return [x[0] for x in extrOpts if extrOpts]
