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)