Improve numpy calculation speed

KChen-lab · May 8, 2020 · 4e797cb · 4e797cb
1 parent 7c7d8ea
commit 4e797cb
Showing 1 changed file with 5 additions and 0 deletions.
diff --git a/src/utils.py b/src/utils.py
@@ -110,10 +110,15 @@ def Create_Factorial_List(self, max_allele_cnt):
 
     def Create_nCr_mat(self, max_allele_cnt, factorial_list):
         ncr_mat = np.zeros((max_allele_cnt, max_allele_cnt), dtype=np.longdouble)
+        ncr_mat2 = np.zeros((max_allele_cnt, max_allele_cnt), dtype=np.longdouble)
+        factorial_list = np.array(factorial_list)
         for i in range(max_allele_cnt):
+            ncr_mat2[:, i] = factorial_list / \
+                (factorial_list[i] * np.roll(factorial_list, i))
             for j in range(max_allele_cnt):
                 ncr_mat[j, i] = factorial_list[j] / \
                     (factorial_list[i] * factorial_list[j - i])
+        assert np.allclose(ncr_mat, ncr_mat2)
         return ncr_mat
 
     def CheckAltAllele(self, single_cell_dict):