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 processGeneEntries(xmlFile, dbPath):
con = DB.connect(dbPath)
tableValuePaths = OrderedDict()
inserts = {}
for tableName in sorted(settings.CGI_TABLES.keys()):
columns = getColumns(tableName)
inserts[tableName] = DB.defineSQLInsert(tableName, columns)
columnToElement = {v:k for k, v in settings.CGI_TABLES[tableName]["columns"].items()}
valueElementPaths = []
for i in range(len(columns)):
valueElementPaths.append(columnToElement[columns[i][0]])
tableValuePaths[tableName] = valueElementPaths
for elem in iterparse(xmlFile, tag='GeneEntry'):
for tableName in tableValuePaths:
valuePaths = tableValuePaths[tableName]
valueLists = []
if "elements" in settings.CGI_TABLES[tableName]:
listElemPath = settings.CGI_TABLES[tableName]["elements"]
elemList = elem.findall(listElemPath)
else:
listElemPath = ""
elemList = [elem]
for listElem in elemList:
values = []
for valueElementPath in valuePaths:
valueElementPath = valueElementPath.replace(listElemPath, "").strip("/")
if len(valueElementPath) > 0:
if valueElementPath.startswith("../"):
valueElem = elem.find(valueElementPath.strip("../"))
else:
valueElem = listElem.find(valueElementPath)
else:
valueElem = listElem
if valueElem != None:
values.append(valueElem.text)
else:
values.append(None)
#print inserts[tableName]
#print values
#con.execute(inserts[tableName], values)
valueLists.append(values)
if "preprocess" in settings.CGI_TABLES[tableName]:
valueLists = settings.CGI_TABLES[tableName]["preprocess"](tableName, elem, valueLists)
#print inserts[tableName]
#print valueLists
con.executemany(inserts[tableName], valueLists)
print elem.find("HUGOGeneSymbol").text
con.commit()
con.close()
def initDB(dbPath, clear=True):
# Initialize the database
if clear and os.path.exists(dbPath):
print "Removing existing database", dbPath
os.remove(dbPath)
if not os.path.exists(os.path.dirname(dbPath)):
os.makedirs(os.path.dirname(dbPath))
con = DB.connect(dbPath)
for tableName in sorted(settings.CGI_TABLES.keys()):
columns = getColumns(tableName)
table = settings.CGI_TABLES[tableName]
con.execute(DB.defineSQLTable(tableName, columns, table.get("primary_key", None)))
if "indices" in table:
DB.addIndices(con, tableName, table["indices"])
return con
def makeCountTables(filename):
con = DB.connect(filename)
con.execute("""
CREATE TABLE disease AS
SELECT hugo_gene_symbol, matched_disease_term, nci_disease_concept_code, organism, COUNT(*)
AS term_count
FROM sentence
WHERE matched_disease_term IS NOT NULL
GROUP BY hugo_gene_symbol, matched_disease_term, nci_disease_concept_code, organism
ORDER BY hugo_gene_symbol;
""")
DB.addIndices(con, "disease", ["hugo_gene_symbol"])
con.execute("""
CREATE TABLE drug AS
SELECT hugo_gene_symbol, drug_term, nci_drug_concept_code, organism, COUNT(*)
AS term_count
FROM sentence
WHERE drug_term IS NOT NULL
GROUP BY hugo_gene_symbol, drug_term, nci_drug_concept_code, organism
ORDER BY hugo_gene_symbol;
""")
DB.addIndices(con, "drug", ["hugo_gene_symbol"])
con.commit()
con.close()
