Using the GEMINI API¶
The GeminiQuery class¶
Extracting the VCF INFO tags with GEMINI API¶
The GEMINI API is useful to extract the individual tags within the INFO field of a VCF (stored as a compressed dictionary in the variants table). This would be of particular interest to those who want to add custom annotations to their VCF and still be able to access the individual tags programmatically. Here is an example where we try to extract the dbNSFP fields from the ‘INFO’ tag of a VCF, using the API.
#!/usr/bin/env python
import sys
from gemini import GeminiQuery
database = sys.argv[1]
gq = GeminiQuery(database)
query = "SELECT variant_id, chrom, start, end, ref, alt, info \
FROM variants"
gq.run(query)
for row in gq:
try:
print "\t".join([str(row['chrom']), str(row['start']), str(row['end']),
str(row['ref']), str(row['alt']), str(row.info['dbNSFP_SIFT_pred'])])
except KeyError:
pass
# yields
chr1 906272 906273 C T P|D|P
chr1 906273 906274 C A D|D|D
chr1 906276 906277 T C D|D|D
chr1 906297 906298 G T B|B|B
chr1 1959074 1959075 A C D
chr1 1959698 1959699 G A B
chr1 1961452 1961453 C T P
chr1 2337953 2337954 C T D
