Commit bdf447e8 by Blaise Li

### Fix print, comment solution for kmer counting.

parent f7903932
Pipeline #58185 passed with stages
in 13 seconds
 ... @@ -391,7 +391,7 @@ Compute the 6 mers occurences of the sequence above, and print each 6mer and it' ... @@ -391,7 +391,7 @@ Compute the 6 mers occurences of the sequence above, and print each 6mer and it' >>> s = s.replace('\n', '') >>> s = s.replace('\n', '') >>> kmers = get_kmer_occurences(s, 6) >>> kmers = get_kmer_occurences(s, 6) >>> for kmer in kmers: >>> for kmer in kmers: >>> print kmer[0], '..', kmer[1] >>> print(kmer[0], '..', kmer[1]) gcagag .. 2 gcagag .. 2 aacttc .. 1 aacttc .. 1 gcaact .. 1 gcaact .. 1 ... ...
 def get_kmer_occurences(seq, kmer_len): def get_kmer_occurences(seq, kmer_len): """ """ return a list of tuple return a list of tuple each tuple contains a kmers present in seq and its occurence each tuple contains a kmers present in seq and its occurence """ """ # Counter dictionary (keys will be kmers, values will be counts) kmers = {} kmers = {} stop = len(seq) - kmer_len stop = len(seq) - kmer_len for i in range(stop + 1): for i in range(stop + 1): # Extract kmer starting at position i kmer = seq[i: i + kmer_len] kmer = seq[i: i + kmer_len] # Increment the count for kmer # or create the entry the first time this kmer is seen # using default value 0, plus 1 kmers[kmer] = kmers.get(kmer, 0) + 1 kmers[kmer] = kmers.get(kmer, 0) + 1 return kmers.items() # pairs (kmer, count) \ No newline at end of file return kmers.items()
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