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a guest Jul 19th, 2019 60 Never
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  1. import pandas as pd
  2. import argparse
  3.  
  4. parser = argparse.ArgumentParser()
  5. parser.add_argument("-in", "--input", help="blast outfmt 6 formata",  required=True)
  6. args = parser.parse_args()
  7. read_file = args.input
  8.  
  9. header_outfmt6 = ['qseqid','sseqid','pident','length','mismatch','gapopen','qstart','qend','sstart','send','evalue','bitscore']
  10. df = pd.read_csv(read_file, sep='t',header = None,names = header_outfmt6)
  11. df_2 = df.drop_duplicates(subset=['sseqid','sstart','send'])
  12.  
  13. out_csv = read_file+'.filtred'
  14. df_2.to_csv(out_csv, sep='t')
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