def process(indir, outdir, projectFilter, numTopFeatures=30, actions=""): if isinstance(projectFilter, basestring): projectFilter = projectFilter.split(",") projects = result.getProjects(indir, {"filename":projectFilter, "features":"ALL_FEATURES"}, numTopFeatures) if "PROJECTS" in actions: print "----------------------------", "Projects", "----------------------------" print makeProjectTable(projects) print if "GENES" in actions: print "----------------------------", "Genes", "----------------------------" print makeGenesTable(projects) print if "GENE_LIST" in actions: print "----------------------------", "Genes List", "----------------------------" print listTopGenes(projects) if outdir: makeCGIFigure(projects, ["CANCER_OR_CONTROL", "REMISSION"], outdir)
def processDir(database, inputDir, inputFilter, resultDir, cutoff=30, verbose=3, parallel=1, preDispatch='2*n_jobs', randomize=False, slurm=False, limit=1, debug=False, dummy=False, rerun=None, hideFinished=False): # _, _, _, argDict = inspect.getargvalues(inspect.currentframe()) # output = OrderedDict() # output["call"] = argDict # results = OrderedDict() # output["results"] = results projects = result.getProjects(inputDir, inputFilter, returnPaths=True) for projectName in sorted(projects.keys()): print "---------", "Processing project", projectName, "---------" for experiment in projects[projectName]: for classifier in projects[projectName][experiment]: # initialize results structure project = projects[projectName][experiment][classifier] # determine subdirectory for results #resultSubDir = None #if resultDir != None: # resultSubDir = os.path.join(resultDir, "_".join([projectName, experiment, classifier])) #points = process(database, project, resultDir, cutoff, verbose=verbose, parallel=parallel, preDispatch=preDispatch, randomize=randomize, limit=limit, debug=debug, dummy=dummy, rerun=rerun, hideFinished=hideFinished, slurm=slurm)