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- class Kmer:
- sequence = ''
- def __init__(self,kmer_name):
- self.sequence = kmer_name
- self.counter = 1
- self.lst = []
- self.indxx = {}
- def increase(self):
- self.counter += 1
- def increase_n(self, n):
- self.counter += n
- def add_locus(self, kmer_name):
- self.lst = lst.append(kmer_name)
- def locus_index(self, index, kmer_name):
- #d1["China"]="Beijing"
- self.indxx ["kmer_name"]="index"
- seq = 'ATGGCTAGATCCCTACG'
- seq_lng = len(seq)
- read_lng = 5
- kmer_size = 3
- kmer_dict = {}
- kmer_dict_locus = {}
- kmer_lst = []
- #for read_indx in range(seq_lng-read_lng+1):
- # read = seq[read_indx:(read_indx+read_lng)]
- # print(read)
- for index in range(seq_lng-kmer_size+1):
- current_kmer = seq[index:(index+kmer_size)]
- #print(current_kmer)
- if current_kmer in kmer_dict:
- kmer_dict[current_kmer].increase()
- kmer_dict_locus[current_kmer].locus_index()
- else:
- kmer_dict[current_kmer] = Kmer(current_kmer)
- kmer_lst[current_kmer].add_locus()
- for k,s in kmer_dict.items():
- print(k,s.counter)
- for k,s in kmer_dict_locus.items():
- print(k,s.key)
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