QAseq-Fusion_v2.1/py_script/fusion_primer_stat.py

#!/usr/bin/python
# -*- coding:utf-8 -*-

import argparse,time,os

def main(indir):

	infile=indir+"/fusion_breakpoints_primer.txt"
	outfile=indir+"/fusion_breakpoints_primer_stat.txt"
	outf=open(outfile,'w')

	site_dict={}
	with open(infile,'r') as inf1:
		for line in inf1:
			info = line.strip("\n").split("\t")
			if info[0] not in site_dict.keys():
				site_dict[info[0]] = 0
			else:
				site_dict[info[0]] +=1
	
	for site in site_dict.keys():
		outf.write(site+"\t"+str(site_dict[site])+"\n")

if __name__ == '__main__':
	parser = argparse.ArgumentParser(description='Filter FusionGene results,by target parterner gene,blacklist file,fusion reads num')
	parser.add_argument('-i', required=True, type=str, help="indir")
	args = parser.parse_args()
	main(args.i)