Example script using the Gemini query API for custom analysis.

test_gemini_query.py

#!/usr/bin/env python
import sys
from gemini import GeminiQuery

db = sys.argv[1]

# create a GeminiQery instance for the requested database
gq = GeminiQuery(db)


# issue a basic query and iterate over the results.
query  = "select chrom, start, end, gts.NA20814 from variants limit 5"
gq.run(query)
for row in gq:
    print row, row['chrom'], row['gts.NA20814']



# issue a query with filters placed on genotype data.
query  = "select chrom, start, end, gts.NA20814 from variants limit 50"
gt_filter = "gt_types.NA20814 == HET"
gq.run(query, gt_filter)
for row in gq:
    print row, row['chrom'], row['gts.NA20814']
    
    

# grab dict mapping sample to genotype array indices
smp2idx = gq.sample_to_idx

query  = "select chrom, start, end, gts.NA20814 from variants"
gt_filter  = "gt_types.NA20814 == HET"
gq.run(query, gt_filter)

# print a header listing the selected columns
print gq.header
for row in gq:
    # access a NUMPY array of the sample genotypes.
    gts = row['gts']
    # use the sample to index dictionary to access sample genotypes
    idx = smp2idx['NA20814']
    print row, gts[idx]