for rsid,snp in snpInserts.iteritems():
cursor.execute(snp)
rsidList[rsid] = cursor.fetchone()[0]
# Commit all inserts to pgsql and grab end time
postgresConnection.commit()
# Log completed time, close pgsql cursor
result.snpInsertEnd=time.time()
cursor.close()
# Clear list of SNPs to free up memory
snpInserts.clear()
print "Chromosome " + str(curChr) + ". Reading loci Data."
result.lociLoadStart = time.time()
# Now that we have primary keys for each SNP, read in loci data
with open(curLociFilePath,'r') as csvfile:
data = csv.reader(csvfile,delimiter='\t')
for row in data:
if(len(row) == 4):
# Load loci in pgsql statements
if row[0] in rsidList and rsidList[row[0]] > 0: # If RSID value is present, load with PK
insStr = "INSERT INTO locus (mrna_acc, gene, class, snp_id) VALUES ('{0}', '{1}', '{2}', {3})".format(row[1], row[2], row[3], rsidList[row[0]])
lociInserts.append(insStr)
# Data for reporting
result.lociLoadEnd = time.time()
result.totalLoci = len(lociInserts)
