def execute(cls, choices, galaxyFn=None, username=''):
from quick.application.ExternalTrackManager import ExternalTrackManager
genome = choices[0]
preProcTN1 = ExternalTrackManager.getPreProcessedTrackFromGalaxyTN(
genome, choices[2].split(
':')) if choices[1] == 'history' else choices[2].split(':')
chrSizeDict = dict([(chrom, GenomeInfo.getChrLen(genome, chrom))
for chrom in GenomeInfo.getChrList(genome)])
trackType = choices[3].split(':')[1]
fnSource = ExternalTrackManager.extractFnFromGalaxyTN(
choices[3].split(':'))
if trackType in ['valued.bed', 'category.bed', 'bed']:
geSource = GenomeElementSorter(
BedGenomeElementSource(fnSource, genome=genome)).__iter__()
elif trackType == 'gtrack':
geSource = GenomeElementSorter(
GtrackGenomeElementSource(fnSource, genome=genome)).__iter__()
#headLinesStr = geSource.getHeaderLines().replace('##','\n##')
else:
raise InvalidFormatError(
'The Binning must be of the following formats: gtrack, valued.bed, category.bed ,bed ...'
)
cls.PrintResultToHistItem(galaxyFn, geSource, preProcTN1, genome,
username)
def execute(cls, choices, galaxyFn=None, username=''):
from gold.util.RandomUtil import random
outputFile = open(galaxyFn, 'w')
genome = choices[0]
histItem = choices[2]
trackItem = choices[3]
chromRegsPath = GenomeInfo.getChrRegsFn(genome)
chrSizeDict = dict([(chrom, GenomeInfo.getChrLen(genome, chrom))
for chrom in GenomeInfo.getChrList(genome)])
geSource = headLinesStr = None
if choices[1] == 'history':
trackType = choices[2].split(':')[1]
username = ''.join(
[chr(random.randint(97, 122)) for i in range(6)])
tempFn = createCollectedPath(
genome, [],
username + '_'.join([str(v) for v in time.localtime()[:6]]) +
'.' + trackType)
fnSource = ExternalTrackManager.extractFnFromGalaxyTN(
choices[2].split(':'))
open(tempFn, 'w').write(open(fnSource, 'r').read())
if trackType in ['valued.bed', 'category.bed', 'bed']:
geSource = GenomeElementSorter(
BedGenomeElementSource(tempFn, genome=genome)).__iter__()
#elif trackType == 'gtrack':
# geSource = GenomeElementSorter(GtrackGenomeElementSource(tempFn, genome=genome)).__iter__()
# headLinesStr = geSource.getHeaderLines().replace('##','\n##')
cls.WriteExpandedElementsToFile(geSource,
chrSizeDict,
outputFile,
headLinesStr,
writeHeaderFlag=True)
os.remove(tempFn)
else:
writeHeaderFlag = True
for chrom in GenomeInfo.getChrList(genome):
gRegion = GenomeRegion(genome, chrom, 0, chrSizeDict[chrom])
plTrack = PlainTrack(trackItem.split(':'))
geSource = GenomeElementTvWrapper(
plTrack.getTrackView(gRegion)).__iter__()
cls.WriteExpandedElementsToFile(geSource, chrSizeDict,
outputFile, headLinesStr,
writeHeaderFlag)
writeHeaderFlag = False
outputFile.close()
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
trackChoice = choices.history if choices.source == 'history' else choices.track
trackName = trackChoice.split(':')
if ExternalTrackManager.isGalaxyTrack(trackName):
geSource = ExternalTrackManager.getGESourceFromGalaxyOrVirtualTN(
trackName, genome)
if not geSource.hasOrigFile(): #hbfunction
stdTrackName = ExternalTrackManager.getStdTrackNameFromGalaxyTN(
trackName)
ExternalTrackManager.renameExistingStdTrackIfNeeded(
genome, stdTrackName)
geSource = FullTrackGenomeElementSource(genome,
stdTrackName,
allowOverlaps=False)
else:
try:
geSource = FullTrackGenomeElementSource(genome,
trackName,
allowOverlaps=True)
for ge in geSource:
break
except:
geSource = FullTrackGenomeElementSource(genome,
trackName,
allowOverlaps=False)
threshold = float(choices.threshold)
rule = RULE_DICT[choices.rule]
composerCls = getComposerClsFromFileFormatName(choices.format)
geModifier = GEValueThresholder(geSource, genome, threshold, rule)
if choices.merge == 'Yes':
if not geModifier.isSorted():
geModifier = GenomeElementSorter(geModifier)
geModifier = GEAdjacencyClusterer_Segment(geModifier)
composerCls(geModifier).composeToFile(galaxyFn, ignoreEmpty=True)
def execute(cls, choices, galaxyFn=None, username=''):
outputFile = open(galaxyFn, 'w')
genome = choices[0]
histItem = choices[2]
trackItem = choices[3]
chromRegsPath = GenomeInfo.getChrRegsFn(genome)
chrSizeDict = dict([ ( chrom, GenomeInfo.getChrLen(genome, chrom)) for chrom in GenomeInfo.getChrList(genome)])
geSource = headLinesStr = None
if choices[1] == 'History':
trackType = choices[2].split(':')[1]
username = ''.join([chr(random.randint(97,122)) for i in range(6)])
tempFn = createCollectedPath(genome, [], username+'_'.join([str(v) for v in time.localtime()[:6]])+'.'+trackType)
fnSource = ExternalTrackManager.extractFnFromGalaxyTN(choices[2].split(':'))
open(tempFn,'w').write(open(fnSource,'r').read())
if trackType in ['marked.bed', 'category.bed', 'bed']:
geSource = GenomeElementSorter(BedGenomeElementSource(tempFn, genome=genome)).__iter__()
elif trackType == 'gtrack':
geSource = GenomeElementSorter(GtrackGenomeElementSource(tempFn, genome=genome)).__iter__()
headLinesStr = geSource.getHeaderLines().replace('##','\n##')
cls.WriteExpandedElementsToFile(geSource, chrSizeDict, outputFile, headLinesStr, writeHeaderFlag=True)
os.remove(tempFn)
else:
writeHeaderFlag = True
for chrom in GenomeInfo.getChrList(genome):
gRegion = GenomeRegion(genome, chrom, 0, chrSizeDict[chrom])
plTrack = PlainTrack(trackItem.split(':'))
geSource = GenomeElementTvWrapper(plTrack.getTrackView(gRegion)).__iter__()
cls.WriteExpandedElementsToFile(geSource, chrSizeDict, outputFile, headLinesStr, writeHeaderFlag)
writeHeaderFlag = False
outputFile.close()
def execute(cls, choices, galaxyFn=None, username=''):
outputFile = open(galaxyFn, 'w')
genome = choices[0]
histItem = choices[2]
trackItem = choices[3]
chromRegsPath = GenomeInfo.getChrRegsFn(genome)
chrSizeDict = dict([ ( chr, GenomeInfo.getChrLen(genome, chr)) for chr in GenomeInfo.getChrList(genome)])
geSource = headLinesStr = None
if choices[1] == 'history':
trackType = choices[2].split(':')[1]
from proto.hyperbrowser.StaticFile import GalaxyRunSpecificFile
tempFn = GalaxyRunSpecificFile(['fromHistory.'+trackType],galaxyFn).getDiskPath(True)
fnSource = ExternalTrackManager.extractFnFromGalaxyTN(choices[2].split(':'))
open(tempFn,'w').write(open(fnSource,'r').read())
if trackType in ['valued.bed', 'category.bed', 'bed']:
geSource = GenomeElementSorter(BedGenomeElementSource(tempFn, genome=genome)).__iter__()
elif trackType == 'gtrack':
geSource = GenomeElementSorter(GtrackGenomeElementSource(tempFn, genome=genome)).__iter__()
headLinesStr = geSource.getHeaderLines().replace('##','\n##')
cls.WriteExpandedElementsToFile(geSource, chrSizeDict, outputFile, headLinesStr, writeHeaderFlag=True)
os.remove(tempFn)
else:
writeHeaderFlag = True
for chr in GenomeInfo.getChrList(genome):
gRegion = GenomeRegion(genome, chr, 0, chrSizeDict[chr])
plTrack = PlainTrack(trackItem.split(':'))
geSource = GenomeElementTvWrapper(plTrack.getTrackView(gRegion)).__iter__()
cls.WriteExpandedElementsToFile(geSource, chrSizeDict, outputFile, headLinesStr, writeHeaderFlag)
writeHeaderFlag = False
outputFile.close()
def _applyEnvelope(geSource):
from quick.origdata.GERegionBoundaryFilter import GERegionBoundaryFilter
return GERegionBoundaryFilter(GenomeElementSorter(geSource),
GlobalBinSource(geSource.genome))
def _applyEnvelope(geSource):
from gold.origdata.GEMarkRemover import GEMarkRemover
return GenomeElementSorter(GEMarkRemover(geSource))
def _applyEnvelope(geSource):
return GenomeElementSorter(geSource)
def _applyEnvelope(geSource):
from gold.origdata.GEOverlapClusterer import GEOverlapClusterer
return GEOverlapClusterer(GenomeElementSorter(geSource))