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Shuffle fasta sequences

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  1. #!/usr/bin/env python
  2. # encoding: utf-8
  3. """
  4. 01_shuffle_fa.py
  5.  
  6. Created by SNY of PICB on 2010/12/30 13:01:20.
  7.  
  8. """
  9.  
  10. import sys
  11. import os
  12. import string
  13. import random
  14. from Bio import SeqIO
  15. from Bio.Seq import Seq
  16.  
  17.  
  18. def main():
  19.     in_name = sys.argv[1]
  20.     out_name = sys.argv[2]
  21.  
  22.     in_handle = open(in_name)
  23.     out_handle = open(out_name, "w")
  24.     for seq_record in SeqIO.parse(in_handle, "fasta"):
  25.         l = list(str(seq_record.seq))
  26.         random.shuffle(l)
  27.         seq_record.seq = Seq(''.join(l))
  28.         SeqIO.write(seq_record, out_handle, "fasta")
  29.     in_handle.close()
  30.     out_handle.close()
  31.  
  32.  
  33. if __name__ == '__main__':
  34.     main()

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