IT45200

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Apr 2nd, 2020
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Python 0.42 KB | None | 0 0
  1. from collections import defaultdict
  2.  
  3. kmers = defaultdict(int)
  4.  
  5. def most_frequent_kmer(seq, k):
  6.    
  7.     seq = seq.upper()
  8.     assert set(seq).issubset(set(['A', 'C', 'T', 'G']))
  9.     for i in range(0, len(seq)-(k-1)):
  10.         kmers[seq[i:i+k]] += 1
  11.     for key, val in kmers.items():
  12.         if  val == max(kmers.values()):
  13.             print(str(key), end = ' ')
  14.    
  15. most_frequent_kmer('ACGTTGCATGTCGCATGATGCATGAGAGCT', 4)
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