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generate_comphet_tsv.py
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generate_comphet_tsv.py
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from datetime import date
from os.path import exists
from sys import path
import argparse
import os
import sys
import read_resource_jsons as read_resources
def main():
# Parse the command line
args = parse_command_line()
# Define the executable bcftools command
if args.tools_directory:
if not args.tools_directory.endswith('/'):
args.tools_directory = str(args.tools_directory) + '/'
bcftools = args.tools_directory + 'bcftools/bcftools'
else:
bcftools = 'bcftools'
# Open an output tsv file to write annotations to
output_file = open(args.output_tsv, 'w')
# Write the header line to the tsv file
print('CHROM\tSTART\tEND\tREF\tALT\t', str(args.uid), sep = '', file = output_file)
# Parse the vcf file, check the annotations and generate a tsv file for upload to Mosaic
process_vcf(bcftools, args.input_vcf, output_file)
# Close the output tsv file
output_file.close()
# Input options
def parse_command_line():
global version
parser = argparse.ArgumentParser(description='Process the command line')
# Required arguments
parser.add_argument('--input_vcf', '-i', required = True, metavar = 'string', help = 'The input vcf file to annotate')
parser.add_argument('--output_tsv', '-o', required = True, metavar = 'string', help = 'The output tsv file')
parser.add_argument('--tools_directory', '-s', required = True, metavar = 'string', help = 'The path to the directory where the tools live')
parser.add_argument('--uid', '-u', required = True, metavar = 'string', help = 'The uid for the private comp het annotation')
return parser.parse_args()
# The majority of annotations can be processed in a standard way. The type is checked and numerical
# annotations are checked to ensure they fall within the required bounds
def process_vcf(bcftools, vcf, output_file):
# Loop over all records in the vcf file
command = bcftools + ' query -f \'%CHROM\\t%POS\\t%END\\t%REF\\t%ALT\\tPass\\n\' ' + str(vcf)
for record in os.popen(command).readlines():
# Split the record on tabs
fields = record.rstrip().split('\t')
# Update the chromosome and position
fields[0], fields[2] = updateCoords(fields[0], fields[2])
# Build the output record from the updated fields
print('\t'.join(fields), file = output_file)
# Update the chromosome and position in the tsv file
def updateCoords(chrom, pos):
# Check that the chromosome does not include "chr" prefix
if chrom.startswith('chr'): chrom = chrom.strip('chr')
# Add one to the end position
pos = str(int(pos) + 1)
# Return the updated values
return chrom, pos
# If the script fails, provide an error message and exit
def fail(message):
print(message, sep = "")
exit(1)
# Initialise global variables
if __name__ == "__main__":
main()