def handleRegionClustering(self, genome, tracks, clusterMethod, extra_option):
region_cluster_track = self.getHistoryTrackDef('track1')
print region_cluster_track
region_ref_track = self.params.get('reftrack1')
if region_cluster_track[0] == 'galaxy' :
file_type = region_cluster_track[1]
track_path = region_cluster_track[2]
userBinSource = GalaxyInterface._getUserBinSource('bed', track_path, genome)
validFeature = SplittedRegionsAsFeaturesCatalog.getValidAnalyses(genome,region_ref_track,[])
analysisDef = validFeature[0]
result = AnalysisDefJob(analysisDef, region_ref_track, [], userBinSource).run()
print [result[localKey][validFeature[1]] for localKey in sorted(result.keys())]
def handleRegionClustering(self, genome, tracks, clusterMethod, extra_option):
region_cluster_track = self.getHistoryTrackDef('track1')
print region_cluster_track
region_ref_track = self.params.get('reftrack1')
if region_cluster_track[0] == 'galaxy' :
file_type = region_cluster_track[1]
track_path = region_cluster_track[2]
userBinSource = GalaxyInterface._getUserBinSource('bed', track_path, genome)
validFeature = SplittedRegionsAsFeaturesCatalog.getValidAnalyses(genome,region_ref_track,[])
analysisDef = validFeature[0]
result = AnalysisDefJob(analysisDef, region_ref_track, [], userBinSource).run()
print [result[localKey][validFeature[1]] for localKey in sorted(result.keys())]
def build_feature_vector(genome, ctrack, feature, regSpec, binSpec):
'''
this function create a feature vector for ctrack
feature specifies how the vector is constructed
'''
#print 'Feauter:', LocalResultsAsFeaturesCatalog.getValidAnalyses(genome, ctrack, [])
validFeature = LocalResultsAsFeaturesCatalog.getValidAnalyses(genome, ctrack, [])[feature]
analysisDef = validFeature[0]
#regSpec = self.params.get("region")
#binSpec = self.params.get("binsize")
userBinSource = GalaxyInterface._getUserBinSource(regSpec,binSpec,genome)
result = AnalysisDefJob(analysisDef, ctrack, [], userBinSource).run()
return [result[localKey][validFeature[1]] for localKey in sorted(result.keys())]
