def analyze(meta, dbPath=None, resultPath=None, verbose=False):
meta = result.getMeta(meta)
if dbPath == None:
dbPath = settings.CGI_DB_PATH
print "Analyzing", dbPath
con = DB.connect(dbPath)
result.sortFeatures(meta)
features = meta["features"]
count = 1
numFeatures = len(features)
nonSelected = []
for featureName in features:
if not isinstance(features[featureName], int):
if verbose:
print "Processing feature", featureName, str(count) + "/" + str(numFeatures)
geneName = getGeneName(featureName)
if geneName != None:
mappings = getTermAnalysis(con, geneName, "disease")
result.setValue(features[featureName], "CancerGeneIndex", mappings)
mappings = getTermAnalysis(con, geneName, "drug")
result.setValue(features[featureName], "CancerGeneDrug", mappings)
else:
geneName = getGeneName(featureName)
if geneName != None:
nonSelected.append(geneName)
count += 1
result.setValue(meta, "CancerGeneIndex", analyzeTermCoverage(features), "analysis")
result.setValue(meta["analysis"], "non-selected", getCancerGeneCoverage(con, nonSelected), "CancerGeneIndex")
if resultPath != None:
result.saveMeta(meta, resultPath)
return meta
def saveResults(meta, resultPath, results, extras, bestIndex, analyze, hiddenResults=None, hiddenDetails=None, databaseCGI=None, reclassify=False, details=True):
if extras == None:
print "No detailed information for cross-validation"
return
if not os.path.exists(os.path.dirname(resultPath)):
os.makedirs(os.path.dirname(resultPath))
meta = result.getMeta(meta)
# Add general results
meta["results"] = {"best":results[bestIndex], "all":results}
if hiddenResults != None:
meta["results"]["hidden"] = hiddenResults
# Insert detailed results
if details:
featureByIndex = result.getFeaturesByIndex(meta)
if hiddenDetails != None:
saveDetails(meta, hiddenDetails.get("predictions", None), hiddenDetails.get("importances", None), "hidden", featureByIndex, reclassify=reclassify)
fold = 0
for extra in extras:
saveDetails(meta, extra.get("predictions", None), extra.get("importances", None), fold, featureByIndex, reclassify=reclassify)
fold += 1
else:
if "examples" in meta:
del meta["examples"]
if "features" in meta:
del meta["features"]
# Analyze results
if analyze:
print "Analyzing results"
meta = gene.analyze.analyze(meta, databaseCGI)
# Save results
if resultPath != None:
result.saveMeta(meta, resultPath)
def saveResults(meta, resultPath, perfs, selected):
if not os.path.exists(os.path.dirname(resultPath)):
os.makedirs(os.path.dirname(resultPath))
meta = result.getMeta(meta)
featureByIndex = result.getFeaturesByIndex(meta)
for foldIndex in range(len(selected)):
ranks = selected[foldIndex]
for featureRank in range(len(ranks)):
featureIndex = ranks[featureRank]
feature = result.getFeature(meta, featureIndex, featureByIndex)
result.setValue(feature, foldIndex, featureRank, "ranks")
result.setValue(feature, "sort", -sum(feature["ranks"].values()) / len(feature["ranks"]))
result.saveMeta(meta, resultPath)
