fixed bug with assigning sequence content in parsimony

phylo.py

@@ -193,37 +193,18 @@ class PhyloNode:
             for i in range(len(stubs) - 1):
                 stubstr += stubs[i] + ','
             return stubstr + stubs[-1] + ')' + label + dist
-        # there is no label
-            '''
-            if not self.left and self.right:
-                return ',' + right
-            elif self.left and not self.right:
-                return left + ','
-            elif self.left and self.right:
-                return '(' + left + ',' + right + ')' + dist
-                '''
-
-    # def __le__(self, other):
-    #     """ Returns indication of less than other node. """
-    #     return other and self.__hash__() <= other.__hash__()
-    #
-    # def __eq__(self, other):
-    #     """ Returns indication of equivalence to other node. """
-    #     return other and self.__hash__() == other.__hash__()
-    #
-    # def __hash__(self):
-    #     """ Returns hash of object. """
-    #     return hash((self.label, self.dist, self.sequence))
 
     def _printSequences(self, start, end):
         """ Returns string with node (incl descendants) in a Newick style. """
         stubs = ['' for _ in range(self.nChildren())]
         label = dist = ''
         for i in range(self.nChildren()):
-            stubs[i] = self._printSequences(self.children[i], start, end)
+            stubs[i] = self.children[i]._printSequences(start, end)
         if self.dist or self.dist == 0.0:
             dist = ':' + str(self.dist)
-        if self.label != None:
+        if self.sequence != None:
+            label = "".join(self.sequence[start:end]) + ""
+        else:  # there is no sequence, just use label
             label = str(self.label)
         if self.nChildren() == 0:
             return label + dist
@@ -263,20 +244,6 @@ class PhyloNode:
                 self.sequence = seq
                 break
 
-    """ # Not sure if this is required (putting nodes into a canonical ordering)
-    def _canonise(self):
-        if self.left == None and self.right == None:  # at leaf
-            return self.label
-        myleft = self.left._canonise()
-        myright = self.right._canonise();
-        if myleft > myright:
-            tmpnode = self.left
-            self.left = self.right
-            self.right = tmpnode
-            return myright
-        return myleft
-    """
-
     def _forwardParsimony(self, aln):
         """ Internal function that operates recursively to first initialise each node (forward),
             stopping only once a sequence has been assigned to the node,
@@ -343,10 +310,10 @@ class PhyloNode:
                     child_symb = [None for _ in range(self.nChildren())]
                     for i in range(self.nChildren()):
                         child_symb[i] = self.backptr[i][col][a_parent]
-                        childbuf.append(aln.alphabet[child_symb[i]])
+                        childbuf[i].append(aln.alphabet[child_symb[i]])
                     col += 1
             for i in range(self.nChildren()):
-                self.children[i]._backwardParsimony(aln, sequence.Sequence(childbuf[i], aln.alphabet, self.label, gappy=True))
+                self.children[i]._backwardParsimony(aln, sequence.Sequence(childbuf[i], aln.alphabet, self.children[i].label or "Child of "+self.label, gappy=True))
         return self.sequence
 
     def getSequence(self):
@@ -623,6 +590,12 @@ def get_unique_tree(tree):
 def unpack_list(list):
     return (" ".join(["%s"] * len(list)) + "!") % (x for x in list)
 
-if __name__ == '__main__':
+if __name__ == '__main__1':
     tree = readNewick('/Users/mikael/simhome/ASR/edge1.nwk')
     print(tree)
+
+if __name__ == '__main__':
+    tree = readNewick('/Users/mikael/simhome/ASR/parsitest.nwk')
+    tree.putAlignment(sequence.Alignment(sequence.readFastaFile('/Users/mikael/simhome/ASR/parsitest.aln', sequence.DNA_Alphabet)))
+    tree.parsimony()
+    print(tree.strSequences())
\ No newline at end of file