def test_get_multiple(self):
ids = ','.join(['chr16:g.28883241A>G', 'chr1:g.35367G>A'])
res = Variant.get_multiple(ids=ids)
self.assertTrue(res is not None)
for r in res:
self.assertTrue(r._id in ids)
def test_get(self):
res = Variant.get('chr1:g.35367G>A')
self.assertTrue(res is not None)
self.assertEqual(res.cadd['chrom'], 1)
def test_find_multiple_by(self):
rsids = ','.join(['rs58991260', 'rs2500'])
res = Variant.find_multiple_by(q=rsids, scopes='dbsnp.rsid')
for r in res:
self.assertTrue(r.dbsnp['rsid'] in rsids)
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/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)
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()