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(choices, galaxyFn=None, username=''):
genome = choices.targetTrackGenome
queryTrackName = choices.targetTrack.split(':')
from quick.multitrack.MultiTrackCommon import getGSuiteDataFromGalaxyTN
trackTitles, refTrackNameList, genome = getGSuiteDataFromGalaxyTN(choices.refTrackCollection)
regSpec = 'track'
binSpec = choices.targetTrack
#future iter1
#regSpec, binSpec = UserBinSelector.getRegsAndBinsSpec(choices)
results = []
for refTrack in refTrackNameList:
analysisDef = '-> ProportionCountStat'
res = GalaxyInterface.runManual([refTrack], analysisDef, regSpec, binSpec, genome, username=username, galaxyFn=galaxyFn) # res is of class Results
segCoverageProp = [res[seg]['Result'] for seg in res.getAllRegionKeys()]#to heatmap
results.append(segCoverageProp)
geSource = FullTrackGenomeElementSource(genome, queryTrackName)
modGeSource = MyElementModifier(geSource, results, genome)
composer = BedComposer(modGeSource, extraTrackLineAttributes={'itemRgb': '"On"'})
composer.composeToFile(galaxyFn)
def getGeSourceList(cls, genome, tracks):
from quick.application.ExternalTrackManager import ExternalTrackManager
from gold.origdata.BedGenomeElementSource import BedGenomeElementSource, BedCategoryGenomeElementSource
from gold.origdata.GtrackGenomeElementSource import GtrackGenomeElementSource
from gold.origdata.TrackGenomeElementSource import FullTrackGenomeElementSource
geSourceList = []
trackNamesWithoutPath = []
for track in tracks:
try:
fileType = ExternalTrackManager.extractFileSuffixFromGalaxyTN(
track)
fn = ExternalTrackManager.extractFnFromGalaxyTN(track)
if fileType == 'category.bed':
geSourceList.append(BedCategoryGenomeElementSource(fn))
elif fileType == 'gtrack':
geSourceList.append(GtrackGenomeElementSource(fn))
else:
geSourceList.append(BedGenomeElementSource(fn))
trackNamesWithoutPath.append(
ExternalTrackManager.extractNameFromHistoryTN(track))
except: # it is not a history, must be in HB track repository
geSourceList.append(
FullTrackGenomeElementSource(genome,
track,
allowOverlaps=True))
trackNamesWithoutPath.append(':'.join(track))
return geSourceList, trackNamesWithoutPath
def __new__(cls,
regSpec,
binSpec,
genome=None,
categoryFilterList=None,
strictMatch=True):
if regSpec in ['file', 'track'] + getSupportedFileSuffixesForBinning():
if genome is None:
genome = DEFAULT_GENOME
from gold.origdata.GenomeElementSource import GenomeElementSource
if regSpec == 'track':
from quick.util.CommonFunctions import convertTNstrToTNListFormat
from gold.origdata.TrackGenomeElementSource import FullTrackGenomeElementSource
trackName = convertTNstrToTNListFormat(binSpec)
geSource = FullTrackGenomeElementSource(genome,
trackName,
allowOverlaps=False)
else:
from quick.application.ExternalTrackManager import ExternalTrackManager
try:
fn = ExternalTrackManager.getGalaxyFnFromEncodedDatasetId(
binSpec)
except:
fn = binSpec
geSource = GenomeElementSource(
fn,
genome=genome,
suffix=regSpec if regSpec != 'file' else None)
if categoryFilterList is not None:
from gold.origdata.GECategoryFilter import GECategoryFilter
geSource = GECategoryFilter(geSource,
categoryFilterList,
strict=strictMatch)
return cls._applyEnvelope(geSource)
else:
if binSpec == '*':
binSize = None
else:
binSize = parseShortenedSizeSpec(binSpec)
from quick.application.AutoBinner import AutoBinner
return AutoBinner(parseRegSpec(regSpec, genome), binSize)
def getGeSource(track, genome=None):
from quick.application.ExternalTrackManager import ExternalTrackManager
from gold.origdata.BedGenomeElementSource import BedGenomeElementSource, BedCategoryGenomeElementSource
from gold.origdata.GtrackGenomeElementSource import GtrackGenomeElementSource
from gold.origdata.TrackGenomeElementSource import FullTrackGenomeElementSource
if isinstance(track, basestring):
track = track.split(':')
try:
fileType = ExternalTrackManager.extractFileSuffixFromGalaxyTN(track)
fn = ExternalTrackManager.extractFnFromGalaxyTN(track)
if fileType == 'category.bed':
return BedCategoryGenomeElementSource(fn)
elif fileType == 'gtrack':
return GtrackGenomeElementSource(fn)
else:
return BedGenomeElementSource(fn)
except:
return FullTrackGenomeElementSource(genome, track, allowOverlaps=False)
def execute(cls, choices, galaxyFn=None, username=''):
from quick.application.ExternalTrackManager import ExternalTrackManager
from collections import defaultdict
from gold.origdata.BedGenomeElementSource import BedGenomeElementSource, BedCategoryGenomeElementSource
from gold.origdata.GtrackGenomeElementSource import GtrackGenomeElementSource
from gold.origdata.TrackGenomeElementSource import FullTrackGenomeElementSource
from urllib import unquote
print choices
genome = choices[0]
geSourceList, labelNames = [], []
selectedHists = [
unquote(val).split(':') for id, val in choices[1].iteritems()
if val
]
inorout = [int(x) for x in choices[2].split(',')]
selectedHists += [
v.split(':') for v in choices[3:]
if v not in ['----- Select -----', 'no', 'yes', None, '']
]
for track in selectedHists:
try:
fileType = ExternalTrackManager.extractFileSuffixFromGalaxyTN(
track)
fn = ExternalTrackManager.extractFnFromGalaxyTN(track)
if fileType == 'category.bed':
geSourceList.append(BedCategoryGenomeElementSource(fn))
elif fileType == 'gtrack':
geSourceList.append(GtrackGenomeElementSource(fn))
else:
geSourceList.append(BedGenomeElementSource(fn))
labelNames.append(
ExternalTrackManager.extractNameFromHistoryTN(track))
except:
geSourceList.append(
FullTrackGenomeElementSource(genome,
track,
allowOverlaps=False))
#labelNames.append(track[-1])
labelNames.append(':'.join(track))
primeList = [
2, 3, 5, 7, 11, 13, 17, 19, 23, 29, 31, 37, 41, 43, 47, 53, 59
]
resultCounter = defaultdict(int)
posDict = defaultdict(list)
catDict = defaultdict(list)
debugstring = 'debug out:'
for index, geSource in enumerate(geSourceList):
primeNum = primeList[index]
prevEnd = -1
prevChr = ''
for ge in geSource:
posDict[ge.chr] += [ge.start, ge.end]
catDict[ge.chr] += [primeNum, -primeNum]
prevEnd = ge.end
prevChr = ge.chr
debugstring += 'posDict elements/2: ' + str(
sum(len(v) for v in posDict.itervalues()) / 2) + '\n'
debugstring += 'catDict elements/2: ' + str(
sum(len(v) for v in catDict.itervalues()) / 2) + '\n'
#maxState = reduce( lambda x, y: x*y, primeList[:len(geSourceList)] ) #assuming all tracks are in.
selectedState = 1
for n in range(len(geSourceList)):
if inorout[n]:
selectedState = selectedState * primeList[n]
utfil = open(galaxyFn, 'w')
for chrom in posDict.keys():
indxSortedList = sorted(range(len(posDict[chrom])),
key=posDict[chrom].__getitem__)
posList = posDict[chrom]
catList = catDict[chrom]
catCoverageDepth = defaultdict(int)
currentState = 1
currentPos = 0
for indx in indxSortedList:
pos = posList[indx]
primeVal = catList[indx]
#print 'pos, primeVal: ', pos, primeVal
#print 'resultCounter: ', resultCounter
if currentPos != pos:
if abs(currentState) == selectedState:
print >> utfil, '%s\t%i\t%i' % (chrom, currentPos, pos)
resultCounter[abs(currentState)] += pos - currentPos
#debugstring +='resultCounter='+str(resultCounter)+ ' currentPos='+ str(currentPos) + ' pos='+str(pos)+ ' chrom='+str(chrom)+ ' primeVal='+str(primeVal)+ ' catCoverageDepth='+str(catCoverageDepth) +'<br/>'
#print 'resultCounter,currentState, pos and currentPos',abs(currentState),':', pos, currentPos
currentPos = pos
if primeVal < 0:
catCoverageDepth[abs(primeVal)] -= 1
if catCoverageDepth[abs(primeVal)] == 0:
currentState /= primeVal
else:
catCoverageDepth[primeVal] += 1
if catCoverageDepth[primeVal] == 1:
currentState *= primeVal
utfil.close()