Jaccard_index/codescript/rtg_pairs.py

import itertools
import pandas as pd
import sys,argparse,os

parser = argparse.ArgumentParser(description="this script is to preform combination on vcf files, get any two of three replicates for next jaccard index calculation")

parser.add_argument('-vcf', '--vcffile', type=str, help='input vcf file',  required=True)

args = parser.parse_args()

# Rename input:
vcf_input = args.vcffile


file = pd.read_csv(vcf_input,header=None,sep='\t')
location_com = list(itertools.combinations(file[0],2))
name_com = list(itertools.combinations(file[1],2))
num = len(name_com)

outfile = open('rtg_pairs.txt','w')

for i in range(0,num):
	# prepare a
	one = name_com[i][0]
	strings_one = one.split('_')
	sequenceTechA = strings_one[0] + strings_one[1]
	sequenceSiteA = strings_one[2]
	sampleA = strings_one[3]
	repA = strings_one[4]

	# prepare b
	two = name_com[i][1]
	strings_two = two.split('_')
	sequenceTechB = strings_two[0] + strings_two[1]
	sequenceSiteB = strings_two[2]
	sampleB = strings_two[3]
	repB = strings_two[4]

	folder = one + '-' + two
	## add annotation
	# sequencing technology
	if (sequenceTechA == sequenceTechB) and (sequenceSiteA == sequenceSiteB) and (sampleA == sampleB) and (repA != repB):
		outline = location_com[i][0] + '\t' + location_com[i][1] + '\t' + folder + '\n'
		outfile.write(outline)		
	else:
		pass

outfile.close()