sys.stdout.flush()
# Read in data from SNP file and create insert statements
with open(curSnpFilePath,'r') as csvfile:
data = csv.reader(csvfile,delimiter='\t')
for row in data:
if(len(row) == 3):
hasSig = False
if row[2] != '' and row[2] != 'false':
hasSig = True
rsidList[row[0]] = 0
insStr = "INSERT INTO snp (rsid, chr, has_sig) VALUES ('{0}', '{1}', {2}) RETURNING id".format(row[0], row[1], hasSig)
snpInserts[row[0]] = insStr
# Data for reporting
result.snpLoadEnd = time.time()
result.totalSnps = len(snpInserts)
# Insert SNP data into postgres
cursor = postgresConnection.cursor()
print "Chromosome " + str(curChr) + ". Inserting SNP Data."
sys.stdout.flush()
# Log current run start time
result.snpInsertStart = time.time()
# For each snp, insert record and then grab primary key
for rsid,snp in snpInserts.iteritems():
cursor.execute(snp)
rsidList[rsid] = cursor.fetchone()[0]
