Advertisement
Guest User

Untitled

a guest
Mar 13th, 2018
83
0
Never
Not a member of Pastebin yet? Sign Up, it unlocks many cool features!
text 1.22 KB | None | 0 0
  1. class Kmer:
  2. sequence = ''
  3.  
  4. def __init__(self,kmer_name):
  5. self.sequence = kmer_name
  6. self.counter = 1
  7. self.lst = []
  8. self.indxx = {}
  9.  
  10. def increase(self):
  11. self.counter += 1
  12.  
  13. def increase_n(self, n):
  14. self.counter += n
  15.  
  16. def add_locus(self, kmer_name):
  17. self.lst = lst.append(kmer_name)
  18. def locus_index(self, index, kmer_name):
  19. #d1["China"]="Beijing"
  20. self.indxx ["kmer_name"]="index"
  21.  
  22. seq = 'ATGGCTAGATCCCTACG'
  23. seq_lng = len(seq)
  24. read_lng = 5
  25. kmer_size = 3
  26. kmer_dict = {}
  27. kmer_dict_locus = {}
  28. kmer_lst = []
  29.  
  30. #for read_indx in range(seq_lng-read_lng+1):
  31. # read = seq[read_indx:(read_indx+read_lng)]
  32. # print(read)
  33. for index in range(seq_lng-kmer_size+1):
  34. current_kmer = seq[index:(index+kmer_size)]
  35.  
  36. #print(current_kmer)
  37. if current_kmer in kmer_dict:
  38. kmer_dict[current_kmer].increase()
  39. kmer_dict_locus[current_kmer].locus_index()
  40. else:
  41. kmer_dict[current_kmer] = Kmer(current_kmer)
  42. kmer_lst[current_kmer].add_locus()
  43.  
  44. for k,s in kmer_dict.items():
  45. print(k,s.counter)
  46. for k,s in kmer_dict_locus.items():
  47. print(k,s.key)
Advertisement
Add Comment
Please, Sign In to add comment
Advertisement