final script that simulates DNA sequnces for a given tree under Jukes…

… Cantor model

simSequences.py

@@ -34,17 +34,17 @@ def simulateSequences(self, num_sites):
 
                 ran_nm = random.random()
                 if ran_nm < freq[0]:
-                    self.state = 'A'
+#                     self.state = 'A'
                     self.states[i] = 'A'
                 elif ran_nm <= freq[0]+freq[1]:
-                    self.state = 'C'
+#                     self.state = 'C'
                     self.states[i] = 'C'
                 elif ran_nm <= freq[0]+freq[1]+freq[2]:
-                    self.state = 'G'
+#                     self.state = 'G'
                     self.states[i] = 'G'
 
                 else: 
-                    self.state = 'T'
+#                     self.state = 'T'
                     self.states[i] = 'T'
 
         else:
@@ -62,19 +62,19 @@ def simulateSequences(self, num_sites):
                 for i in prob:
 
                     if ran_nm <= prob[0]:
-                        self.state = 'A'
+#                         self.state = 'A'
                         self.states[m] = 'A'
 
                     elif ran_nm <= prob[0]+ prob[1]:
-                        self.state = 'C'
+#                         self.state = 'C'
                         self.states[m] = 'C'
 
                     elif ran_nm <= prob[0]+ prob[1]+ prob[2]:
-                        self.state = 'G'
+#                         self.state = 'G'
                         self.states[m] = 'G'
 
                     else:
-                        self.state = 'T'
+#                         self.state = 'T'
                         self.states[m] = 'T'
 
         return self.states
@@ -98,7 +98,7 @@ def __str__(self):
         return 'node: number=%d edgelen=%g lchild=%s rsib=%s parent=%s descendants=[%s]' % (self.number, self.edgelen, lchildstr, rsibstr, parstr, descendants_as_string)
 
 
-def simulate2(preorder, ntax,  num_sites, out):
+def simulate(preorder, ntax,  num_sites, out):
     newf = open(out, 'w')
     newf.write('#nexus\n\n')
     newf.write('begin data;\n')
@@ -182,5 +182,5 @@ def readnewick(tree):
     ntax = 10
     num_sites = 10000
 
-    result = simulate2(preorder, ntax, num_sites, output_filename)
+    result = simulate(preorder, ntax, num_sites, output_filename)