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- #!/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)
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