QAseq-Fusion_v2.1/py_script/fusion_reads_primer.py

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

import argparse,os


def main(indir):

    infile=indir+"/fusion_breakpoints_primer.txt"
    outfile=indir+"/fusion_breakpoints_primer_stat.txt"
	#out
    count_dict={}
    with open(infile,'r') as inf1:
        for line in inf1:
            info = line.strip("\n").split("\t")
            site = info[0]
            site_rev_temp = site.split("-")
            site_rev=site_rev_temp[1]+"-"+site_rev_temp[0]
            primerID = info[2]
            if site not in count_dict.keys() and site_rev not in count_dict.keys():
                count_dict[site]={primerID:1}
            else:
                if primerID not in count_dict[site].keys():
                    count_dict[site][primerID]=1
                else:
                    count_dict[site][primerID]+=1
                    
    outf=open(outfile,'w')
    for item in count_dict.keys():
        item_dict=count_dict[item]
        primer_num = len(item_dict)
        outf.write(item+"\t"+str(primer_num)+"\n")
    outf.close()


if __name__ == '__main__':
    parser = argparse.ArgumentParser(description='get fusion reads primers')
    parser.add_argument('-i', required=True, type=str, help="indir")
    args = parser.parse_args()
    main(args.i)