outfile="/Users/gerikson/Desktop/CognitiveSNPs/snpID_positiona.txt"
inf = open(infile)
outf = open(outfile, 'w')
diff_coordinates = 0
counter = 0
#desease = ""
for line in inf:
	#print line
	#p_line = line.split("\t")
	#rsID = tp_line[0]

	rsID = line.strip()
	#print rsID
	try:
		counter += 1
		results = Variant.find_by(q=rsID)
		for r in results:
			#print r._id 
			begin = r.dbsnp['hg19']['start']
			temp_id = r._id
			temp_id1 = temp_id.split(":")
			chrom = temp_id1[0]
			outf.write(rsID + "\t" + chrom+"\t" +str(begin)+"\n")

	except:
		print "Not Found " + rsID
		outf.write(rsID)
		continue

#print desease
print "Total variants found " + str(counter)
 def test_find_by(self):
     res = Variant.find_by(q='chr1:69000-70000')
     self.assertEqual(len(res), 3)
     for r in res:
         self.assertEqual(r.cadd['chrom'], 1)
outfile="/Users/gerikson/Desktop/CognitiveSNPs/RegionalPlots/RegionalPlotData_correctSnps.txt"
inf = open(infile)
outf = open(outfile, 'w')
diff_coordinates = 0
counter = 0

dict_pos = {}
for line in inf:

	var = line.strip().split("\t")
	dict_pos[var[2]] = "Y"

inf.close()

counter = 0
results = Variant.find_by(q="chr6:26491708-26530420")
for r in results:
	counter += 1

	try:
		begin = r.dbsnp['hg19']['start']
		found_snp = dict_pos[str(begin)]
		rsID = r.dbsnp["rsid"]
		print rsid
	except:
		print "shit"
		continue

print "Counter " + str(counter)
inf.close()
outf.close()