Update markov_for_dinuc.py

Hugenotte585 · Jun 21, 2023 · 2173fb6 · 2173fb6
1 parent cce34b3
commit 2173fb6
Showing 1 changed file with 0 additions and 13 deletions.
diff --git a/models/baseline/markov_for_dinuc.py b/models/baseline/markov_for_dinuc.py
@@ -88,19 +88,6 @@ def __init__(self, kmercount, dinucdist):
         self.kmer_counts_dict = kmercount.kmer_counts_dict
         self.markov_matrix = dinucdist
 
-    def compile_from_counts(self):
-        for k in range(1,self.max_k+1):
-            for kmer in self.kmer_dict[k]:
-                state = [self.kmer_dict[k-1][kmer[:k-1]]]
-                next_nt = [self.kmer_dict[1][kmer[k-1]]]
-                counts = self.kmer_counts_dict[k][self.kmer_dict[k][kmer]]
-                self.markov_matrix[k-1, state, next_nt] = counts
-            # normalize rows
-            if k == 1:
-                self.markov_matrix[k-1,:,:] = self.markov_matrix[k-1,:,:]/np.sum(self.markov_matrix[k-1,:,:])
-            else:
-                self.markov_matrix[k-1,:,:] = self.markov_matrix[k-1,:,:]/np.sum(self.markov_matrix[k-1,:,:],axis=1)[:,np.newaxis]
-
     def impute_for_seq(self, seq, order=None):
         probs = []
         if not order and not order == 0: