def extract_feature(cls, genome, track, ref, option, regSpec, binSpec, trackFormat) :
#print 'genome, track, ref, option, regSpec, binSpec, trackFormat: ', genome, track, ref, option, regSpec, binSpec, trackFormat
validFeature = FeatureCatalog.getFeaturesFromTracks(genome,track,ref)[option] #validFeature contains analysisDef and the key to get the needed number from the global result
if option == 'Prop. of tr1-points falling inside segments of tr2' and trackFormat in ['Segments', 'Valued segments'] :
analysisDef = 'dummy [tf1=SegmentToMidPointFormatConverter] -> DerivedPointCountsVsSegsStat'
else :
analysisDef = validFeature[0] #or any other statistic from the HB collection
userBinSource = GalaxyInterface._getUserBinSource(regSpec,binSpec,genome)
result = AnalysisDefJob(analysisDef, ref, track, userBinSource).run() if option == 'Prop. of tr2 covered by tr1' else AnalysisDefJob(analysisDef, track, ref, userBinSource).run()
validAnalysisDef = validFeature[1]
assert result.getGlobalResult() is not None, 'Did not get any global result for analysisDef: '+validAnalysisDef
return result.getGlobalResult()[validAnalysisDef]
def extract_feature(self, genome, track, ref, option) :
'''
this function return the relation of clusterTrack to referenceTrack
option is the statistical function used, should be named feature
track, ref is clusterTrack and referenceTrack
'''
validFeature = FeatureCatalog.getFeaturesFromTracks(genome,track,ref)[option] #validFeature contains analysisDef and the key to get the needed number from the global result
if option == 'Prop. of tr1-points falling inside segments of tr2' and cls.getTrackFormat(genome, track) in ['Segments', 'Valued segments'] :
analysisDef = 'dummy [tf1=SegmentToMidPointFormatConverter] -> DerivedPointCountsVsSegsStat'
else :
analysisDef = validFeature[0] #or any other statistic from the HB collection
if self.params.get("compare_in") == "Chromosomes" :
regSpec = "__chrs__"
binSpec = self.params.get("Chromosomes")
elif self.params.get("compare_in") == "Chromosome arms" :
regSpec = "__chrArms__"
binSpec = self.params.get("Chromosome_arms")
elif self.params.get("compare_in") == "Cytobands" :
regSpec = "__chrBands__"
binSpec = self.params.get("Cytobands")
else :
regSpec = self.params.get("region")
binSpec = self.params.get("binsize")
#regSpec = self.params.get("region")
#binSpec = self.params.get("binsize")
#regSpec = 'chr1' #could also be e.g. 'chr1' for the whole chromosome or '*' for the whole genome
#binSpec = '10m' #could also be e.g.'100', '1k' or '*' for whole regions/chromosomes as bins
#genome = 'hg18'
userBinSource = GalaxyInterface._getUserBinSource(regSpec,binSpec,genome)
if option == 'Prop. of tr2 covered by tr1' : #because the confuse of refTrack and clusterTrack in this statistics
result = AnalysisDefJob(analysisDef, ref, track, userBinSource).run()
else :
result = AnalysisDefJob(analysisDef, track, ref, userBinSource).run()
mainResultDict = result.getGlobalResult()
return mainResultDict[validFeature[1]]
def extract_feature(self, genome, track, ref, option) :
'''
this function return the relation of clusterTrack to referenceTrack
option is the statistical function used, should be named feature
track, ref is clusterTrack and referenceTrack
'''
validFeature = FeatureCatalog.getFeaturesFromTracks(genome,track,ref)[option] #validFeature contains analysisDef and the key to get the needed number from the global result
if option == 'Prop. of tr1-points falling inside segments of tr2' and self.getTrackFormat(genome, track) in ['Segments', 'Valued segments'] :
analysisDef = 'dummy [tf1=SegmentToMidPointFormatConverter] -> DerivedPointCountsVsSegsStat'
else :
analysisDef = validFeature[0] #or any other statistic from the HB collection
if self.params.get("compare_in") == "Chromosomes" :
regSpec = "__chrs__"
binSpec = self.params.get("Chromosomes")
elif self.params.get("compare_in") == "Chromosome arms" :
regSpec = "__chrArms__"
binSpec = self.params.get("Chromosome_arms")
elif self.params.get("compare_in") == "Cytobands" :
regSpec = "__chrBands__"
binSpec = self.params.get("Cytobands")
else :
regSpec = self.params.get("region")
binSpec = self.params.get("binsize")
#regSpec = self.params.get("region")
#binSpec = self.params.get("binsize")
#regSpec = 'chr1' #could also be e.g. 'chr1' for the whole chromosome or '*' for the whole genome
#binSpec = '10m' #could also be e.g.'100', '1k' or '*' for whole regions/chromosomes as bins
#genome = 'hg18'
userBinSource = GalaxyInterface._getUserBinSource(regSpec,binSpec,genome)
if option == 'Prop. of tr2 covered by tr1' : #because the confuse of refTrack and clusterTrack in this statistics
result = AnalysisDefJob(analysisDef, ref, track, userBinSource).run()
else :
result = AnalysisDefJob(analysisDef, track, ref, userBinSource).run()
mainResultDict = result.getGlobalResult()
return mainResultDict[validFeature[1]]
def computeDistance(cls, genome, track1, track2, feature, regSpec, binSpec): #direct distance between track1, track2
'''
track1 and track2 are two lists like : ['Sequence','Repeating elements','LINE']
feature specifies how the distance between track1 and track2 is defined
'''
validFeature = DirectDistanceCatalog.getValidAnalyses(genome, track1, track2)[feature]
analysisDef = validFeature[0] #'bla bla -> PropFreqOfTr1VsTr2Stat' #or any other statistic from the HB collection
userBinSource = GalaxyInterface._getUserBinSource(regSpec,binSpec,genome)
result = AnalysisDefJob(analysisDef, track1, track2, userBinSource).run()
mainResultDict = result.getGlobalResult()
return mainResultDict[validFeature[1]]
def computeDistance(track1, track2, feature='direct distance'):
'''
track1 and track2 are two lists like : ['Sequence','Repeating elements','LINE']
feature specifies how the distance between track1 and track2 is defined
'''
analysisDef = 'bla bla -> PropFreqOfTr1VsTr2Stat' #or any other statistic from the HB collection
regSpec = 'chr1' #could also be e.g. 'chr1' for the whole chromosome or '*' for the whole genome
binSpec = '10m' #could also be e.g.'100', '1k' or '*' for whole regions/chromosomes as bins
genome = 'hg18' # path /../../..../genome
#allRepeats = GalaxyInterface.getSubTrackNames(genome,['Sequence','Repeating elements'],False) #all elements in 'Repeating elements' directory
#GalaxyInterface.run(trackName1, trackName2, question, regSpec, binSpec, genome='hg18')
userBinSource = GalaxyInterface._getUserBinSource(regSpec,binSpec,genome)
result = AnalysisDefJob(analysisDef, track1, track2, userBinSource).run()
#result er av klassen Results..
#from gold.result.Results import Results
mainResultDict = result.getGlobalResult()
#from PropFreqOfTr1VsTr2Stat:...
#self._result = {'Track1Prop':ratio,'CountTrack1':c1, 'CountTrack2':c2,'Variance':variance}
mainValueOfInterest = mainResultDict['Variance']
return mainValueOfInterest
def computeDistance(self, genome, track1, track2, feature): #direct distance between track1, track2
'''
track1 and track2 are two lists like : ['Sequence','Repeating elements','LINE']
feature specifies how the distance between track1 and track2 is defined
'''
validFeature = DirectDistanceCatalog.getValidAnalyses(genome, track1, track2)[feature]
analysisDef = validFeature[0] #'bla bla -> PropFreqOfTr1VsTr2Stat' #or any other statistic from the HB collection
if self.params.get("compare_in") == "Chromosomes" :
regSpec = "__chrs__"
binSpec = self.params.get("Chromosomes")
elif self.params.get("compare_in") == "Chromosome arms" :
regSpec = "__chrArms__"
binSpec = self.params.get("Chromosome_arms")
elif self.params.get("compare_in") == "Cytobands" :
regSpec = "__chrBands__"
binSpec = self.params.get("Cytobands")
else :
regSpec = self.params.get("region")
binSpec = self.params.get("binsize")
#regSpec = 'chr1' #could also be e.g. 'chr1' for the whole chromosome or '*' for the whole genome
#binSpec = '10m' #could also be e.g.'100', '1k' or '*' for whole regions/chromosomes as bins
#genome = 'hg18' # path /../../..../genome
#allRepeats = GalaxyInterface.getSubTrackNames(genome,['Sequence','Repeating elements'],False)
#GalaxyInterface.run(trackName1, trackName2, question, regSpec, binSpec, genome='hg18')
userBinSource = GalaxyInterface._getUserBinSource(regSpec,binSpec,genome)
result = AnalysisDefJob(analysisDef, track1, track2, userBinSource).run()
#result er av klassen Results..
#from gold.result.Results import Results
mainResultDict = result.getGlobalResult()
#from PropFreqOfTr1VsTr2Stat:...
#self._result = {'Track1Prop':ratio,'CountTrack1':c1, 'CountTrack2':c2,'Variance':variance}
#mainValueOfInterest = mainResultDict['Variance']
return mainResultDict[validFeature[1]]
def computeDistance(self, genome, track1, track2, feature): #direct distance between track1, track2
'''
track1 and track2 are two lists like : ['Sequence','Repeating elements','LINE']
feature specifies how the distance between track1 and track2 is defined
'''
validFeature = DirectDistanceCatalog.getValidAnalyses(genome, track1, track2)[feature]
analysisDef = validFeature[0] #'bla bla -> PropFreqOfTr1VsTr2Stat' #or any other statistic from the HB collection
if self.params.get("compare_in") == "Chromosomes" :
regSpec = "__chrs__"
binSpec = self.params.get("Chromosomes")
elif self.params.get("compare_in") == "Chromosome arms" :
regSpec = "__chrArms__"
binSpec = self.params.get("Chromosome_arms")
elif self.params.get("compare_in") == "Cytobands" :
regSpec = "__chrBands__"
binSpec = self.params.get("Cytobands")
else :
regSpec = self.params.get("region")
binSpec = self.params.get("binsize")
#regSpec = 'chr1' #could also be e.g. 'chr1' for the whole chromosome or '*' for the whole genome
#binSpec = '10m' #could also be e.g.'100', '1k' or '*' for whole regions/chromosomes as bins
#genome = 'hg18' # path /../../..../genome
#allRepeats = GalaxyInterface.getSubTrackNames(genome,['Sequence','Repeating elements'],False)
#GalaxyInterface.run(trackName1, trackName2, question, regSpec, binSpec, genome='hg18')
userBinSource = GalaxyInterface._getUserBinSource(regSpec,binSpec,genome)
result = AnalysisDefJob(analysisDef, track1, track2, userBinSource).run()
#result er av klassen Results..
#from gold.result.Results import Results
mainResultDict = result.getGlobalResult()
#from PropFreqOfTr1VsTr2Stat:...
#self._result = {'Track1Prop':ratio,'CountTrack1':c1, 'CountTrack2':c2,'Variance':variance}
#mainValueOfInterest = mainResultDict['Variance']
return mainResultDict[validFeature[1]]
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 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.
'''
#print 'Executing...'
#print choices
#trackName1 = ['Sequence','Repeating elements','LINE'] #a list of subdirectories from 'genome' to the repeat file
#trackName2 = ['Sequence','Repeating elements','SINE']
#allRepeats = GalaxyInterface.getSubTrackNames(genome,['Sequence','Repeating elements'],False) #all elements in 'Repeating elements' directory
#analysisDef = 'bla bla -> PropFreqOfTr1VsTr2Stat' #or any other statistic from the HB collection
#regSpec = 'chr1' #could also be e.g. 'chr1' for the whole chromosome or '*' for the whole genome
#binSpec = '10m' #could also be e.g.'100', '1k' or '*' for whole regions/chromosomes as bins
genome = 'hg18' # path /../../..../genome
allRepeats = GalaxyInterface.getSubTrackNames(genome,['Sequence','Repeating elements'],False) #all elements in 'Repeating elements' directory
#GalaxyInterface.run(trackName1, trackName2, question, regSpec, binSpec, genome='hg18')
#userBinSource = GalaxyInterface._getUserBinSource(regSpec,binSpec,genome)
#result = AnalysisDefJob(analysisDef, trackName1, trackName2, userBinSource).run()
#result er av klassen Results..
#from gold.result.Results import Results
#mainResultDict = result.getGlobalResult()
#from PropFreqOfTr1VsTr2Stat:...
#self._result = {'Track1Prop':ratio,'CountTrack1':c1, 'CountTrack2':c2,'Variance':variance}
#mainValueOfInterest = mainResultDict['Variance']
#print 'first repeat', allRepeats[0]
#print '\n all repeats', allRepeats
#minValue = HiepsTool.computeDistance(trackName1,trackName2)
#print minValue
#choicedTracks = [['Sequence','Repeating elements',name] for name in choices]
#print '\n choiced tracks', choicedTracks
#d_matrix = HiepsTool.constructDistMatrix(choicedTracks)
#tree = treecluster(distancematrix=d_matrix, method='s')
#print tree
#figure = StaticFile(['hiepln','dendro'],'jpg')
#filepath = figure.getDiskPath()
#print filepath
#draw_dendrogram(tree,choices,filepath)
#print figure.getLink('clustring result')
track1 = ['Sequence','Repeating elements', 'DNA']
track2 = ['Gene regulation', 'TFBS', 'High Throughput']
analysisDef = 'bla bla -> DerivedOverlapStat' #or any other statistic from the HB collection
regSpec = 'chr1' #could also be e.g. 'chr1' for the whole chromosome or '*' for the whole genome
binSpec = '10m' #could also be e.g.'100', '1k' or '*' for whole regions/chromosomes as bins
genome = 'hg18' # path /../../..../genome
#allRepeats = GalaxyInterface.getSubTrackNames(genome,['Sequence','Repeating elements'],False) #all elements in 'Repeating elements' directory
#GalaxyInterface.run(trackName1, trackName2, question, regSpec, binSpec, genome='hg18')
userBinSource = GalaxyInterface._getUserBinSource(regSpec,binSpec,genome)
result = AnalysisDefJob(analysisDef, track1, track2, userBinSource).run()
#result er av klassen Results..
#from gold.result.Results import Results
mainResultDict = result.getGlobalResult()
#keys = result.getResDictKeys()
#print keys
#print mainResultDict['2in1']
print '<ol>'
for key in mainResultDict.keys() :
print '<li>key:%s,value:%s </li>'%(key,mainResultDict[key])
print '</ol>'
from gold.application.GalaxyInterface import GalaxyInterface
from gold.application.StatRunner import AnalysisDefJob
trackName1 = ['Sequence', 'Repeating elements', 'LINE']
trackName2 = ['Sequence', 'Repeating elements', 'SINE']
#GalaxyInterface.getSubTrackNames(['Sequence','Repeating elements'],False)
analysisDef = 'bla bla -> PropFreqOfTr1VsTr2Stat' #or any other statistic from the HB collection
regSpec = 'chr1' #could also be e.g. 'chr1' for the whole chromosome or '*' for the whole genome
binSpec = '10m' #could also be e.g.'100', '1k' or '*' for whole regions/chromosomes as bins
genome = 'hg18'
#GalaxyInterface.run(trackName1, trackName2, question, regSpec, binSpec, genome='hg18')
userBinSource = GalaxyInterface._getUserBinSource(regSpec, binSpec, genome)
result = AnalysisDefJob(analysisDef, trackName1, trackName2,
userBinSource).run()
#result er av klassen Results..
#from gold.result.Results import Results
mainResultDict = result.getGlobalResult()
#from PropFreqOfTr1VsTr2Stat:...
#self._result = {'Track1Prop':ratio,'CountTrack1':c1, 'CountTrack2':c2,'Variance':variance}
mainValueOfInterest = mainResultDict['Variance']
print 'The ..variance..: ', mainValueOfInterest
from gold.application.GalaxyInterface import GalaxyInterface
from gold.application.StatRunner import AnalysisDefJob
trackName1 = ['Sequence','Repeating elements','LINE']
trackName2 = ['Sequence','Repeating elements','SINE']
#GalaxyInterface.getSubTrackNames(['Sequence','Repeating elements'],False)
analysisDef = 'bla bla -> PropFreqOfTr1VsTr2Stat' #or any other statistic from the HB collection
regSpec = 'chr1' #could also be e.g. 'chr1' for the whole chromosome or '*' for the whole genome
binSpec = '10m' #could also be e.g.'100', '1k' or '*' for whole regions/chromosomes as bins
genome = 'hg18'
#GalaxyInterface.run(trackName1, trackName2, question, regSpec, binSpec, genome='hg18')
userBinSource = GalaxyInterface._getUserBinSource(regSpec,binSpec,genome)
result = AnalysisDefJob(analysisDef, trackName1, trackName2, userBinSource).run()
#result er av klassen Results..
#from gold.result.Results import Results
mainResultDict = result.getGlobalResult()
#from PropFreqOfTr1VsTr2Stat:...
#self._result = {'Track1Prop':ratio,'CountTrack1':c1, 'CountTrack2':c2,'Variance':variance}
mainValueOfInterest = mainResultDict['Variance']
print 'The ..variance..: ', mainValueOfInterest
