# Set file paths for current chromosome
curSnpFilePath = snpFilePath.format(curChr)
curLociFilePath = lociFilePath.format(curChr)
if len(path) > 0:
curSnpFilePath = path.rstrip('\\').rstrip('/') + '\\' + curSnpFilePath
curLociFilePath = path.rstrip('\\').rstrip('/') + '\\' + curLociFilePath
# Clear dictionaries for loading multiple chromosomes
snpInserts.clear()
lociInserts = []
rsidList.clear()
# Print status and flush stdout for nohup
print "Chromosome " + str(curChr) + ". Reading SNP Data"
result.snpLoadStart = time.time()
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
