#Script to change the barcodes from strings to integers given a containment file output from the Architect workflow.
#Needed because architect.py expects the barcode/well to be an integer.
#Used mappings of each base to a digit to do the transformation.

import sys
import re
import argparse

base_dict = {}
base_dict['A'] = '1'
base_dict['C'] = '2'
base_dict['T'] = '3'
base_dict['G'] = '4'

def make_int_string(barcode):
	new_string = ""
	for char in barcode:
		new_string = new_string + base_dict[char]
	return new_string


if __name__ == "__main__":
	parser = argparse.ArgumentParser(description='Re-format barcodes in containment file so that they are numerical')
	parser.add_argument('containment_file', help='Containment file to re-format', type=str)
	parser.add_argument('output_file', help='Name for the output containment file', type=str)
	args = parser.parse_args()
	
	cont_file = args.containment_file
	infile = open(cont_file, 'r')	
	outfile = open(args.output_file, 'w')
	for line in infile:
		line = line.strip()
		split_line = line.split('\t')
		barcode = split_line[2]
		int_barcode = make_int_string(barcode)
		newline = split_line[0] + '\t' + split_line[1] + '\t' + int_barcode + '\t' + split_line[3] + '\t' + split_line[4] + '\n'
		outfile.write(newline)

	infile.close()
	outfile.close()