Sa simple vcf client

batchRequestClient.py

@@ -0,0 +1,85 @@
+#!/usr/bin/env python3
+
+# A simple client application that does the following:
+# - Loads a text file containing one variant per row
+# - Performs a batch lookups to the Saphetor Variant API using N variants at a time. 
+# - Saves the results in a new file.
+#
+# It uses the following module:
+# variantapi.client (https://github.com/saphetor/variant-api-client-python)
+#
+# Note: To sort output json file execute:
+# jq -S '.' output.txt  > output_sorted.txt
+
+import argparse
+import json
+import logging
+import re
+import sys
+import operator
+from sys import argv
+from variantapi.client import VariantAPIClient
+
+__author__ = 'stephanos-androutsellis'
+
+# Declare reference genome as a global variable
+_ref_genome = 1019
+
+
+def main(argv):
+	# Read and parse arguments
+	infile = ''
+	outfile = ''
+	batch_size = 5000
+
+	parser = argparse.ArgumentParser(description='Simple batch lookup Client application')
+	parser.add_argument('-i', help='Input file', type=str, metavar='Input File', required=True)
+	parser.add_argument('-o', help='Output file', type=str, metavar='Output File', required=True)
+	parser.add_argument('-n', help="Number of variants to batch", type=int, metavar='Batch size', required=True,default=5000)
+	parser.add_argument('-k', help='Your key to the API', type=str, metavar='API Key', required=False)
+	parser.add_argument('-g', help='Reference genome either 1019 (default) or 1038', type=int, 
+		metavar='Reference Genome', required=False, default=1019)
+
+	args = parser.parse_args()
+	infile = args.i
+	outfile = args.o
+	batch_size = args.n if args.n is not None else batch_size
+	api_key = args.k
+	ref_genome = args.g if args.g is not None else _ref_genome
+
+	# Open and load input file into list
+	print("Reading input file ", infile)
+	with open(infile) as fi:
+		variants = fi.readlines()
+	variants = [v.strip('\n') for v in variants]
+
+	# Prepare output for writing.
+	print("Opening output file ", outfile)
+	fo = open(outfile,'w')
+
+	# Initialize client connection to API
+	api = VariantAPIClient(api_key)
+	if (api is None):
+		print("Failed to connect to API")
+		sys.exit()
+
+	batch_counter = 0
+	finished = False
+	while not finished:
+		start_index = batch_counter*batch_size
+		end_index = (batch_counter+1)*batch_size
+		if (end_index > len(variants)):
+			end_index = len(variants)
+			finished = True
+		print(start_index, ":", end_index-1)
+		batch_variants = variants[start_index:end_index]
+		print("Lookup for: ", batch_variants, "with ref_genome= ", ref_genome)
+		batch_data = api.batch_lookup(batch_variants, ref_genome=ref_genome)
+
+		fo.write(json.dumps(batch_data, indent=2))
+		batch_counter += 1
+
+	print ("Finished ", batch_counter, " batch lookups")
+
+if __name__ == '__main__':
+    main(argv)