starting sources

tree.py

@@ -0,0 +1,191 @@
+
+import random
+import re
+from itertools import chain
+class node(object):
+    def __init__(self, ndnum):              # initialization function
+        self.rsib = None                    # right sibling
+        self.lchild = None                  # left child
+        self.par = None                     # parent node
+        self.number = ndnum                 # node number (internals negative, tips 0 or positive)
+        self.edgelen = 0.0                  # branch length
+        self.descendants = set([ndnum])     # set containing descendant leaf set
+
+    def __str__(self):
+        # __str__ is a built-in function that is used by print to show an object
+        descendants_as_string = ','.join(['%d' % d for d in self.descendants])
+#         print descendants_as_string
+
+        lchildstr = 'None'
+        if self.lchild is not None:
+            lchildstr = '%d' % self.lchild.number
+
+        rsibstr = 'None'
+        if self.rsib is not None:
+            rsibstr = '%d' % self.rsib.number
+
+        parstr = 'None'
+        if self.par is not None:
+            parstr = '%d' % self.par.number
+
+        return 'node: number=%d edgelen=%g lchild=%s rsib=%s parent=%s descendants=[%s]' % (self.number, self.edgelen, lchildstr, rsibstr, parstr, descendants_as_string)
+
+
+
+tree = '((4,((1,2),3)),5)'
+
+# tree = '((4:3.0,(6:7.0,((1:1.0,2:1.0):5.0,3:6.0):4.0):1.0):7.0,5:2.0)'
+# tree = '((4:3.0,((1:1.0,2:1.0):5.0,3:6.0):4.0):7.0,5:2.0)'
+# tree = '(((14:1.0,((1:1.0,(7:1.0,12:1.0):1.0):1.0,(9:1.0,15:1.0):1.0):1.0):1.0,4:1.0):1.0,((20:1.0,((((18:1.0,11:1.0):1.0,(3:1.0,(24:1.0,(19:1.0,56:1.0):1.0):1.0):1.0):1.0,13:1.0):1.0,((((2:1.0):1.0):1.0):1.0):1.0):1.0):1.0):1.0)'      
+# tree = '((2,(1,7)),((3,6),(4,5)))'
+
+
+ext_br = re.findall('\\(\d+:(\d+\.\d+)' and '\d+:(\d+\.\d+)', tree)    
+int_br = re.findall('\\):(\d+\.\d+)', tree)    
+
+int_br2 = map(float, int_br)
+ext_br2 = map(float, ext_br)
+
+len_int_br = (len(int_br2)-1)
+len_ext_br = (len(ext_br2)-1)
+
+
+
+
+print 'int_nd.edgelen', int_br2
+print 'ext_nd.edgelen', ext_br2
+
+total_length = len(tree)
+internal_node_number = -1
+
+root = node(internal_node_number)
+nd = root
+i = 0
+t= 0
+pre = [root]
+
+try:
+
+    while i < total_length:
+        m = tree[i]
+
+        if m =='(':
+            internal_node_number -= 1
+
+#             print 'internal_node_number=', internal_node_number
+            child = node(internal_node_number)
+            pre.append(child)
+            nd.lchild=child
+
+            child.par=nd
+            nd=child
+#             nd.edgelen = int_br2[len_int_br]
+            len_int_br -=1
+
+#             print 'nd=', nd.number
+#             print 'nd.edgelen', nd.edgelen
+
+            print '*******************'
+
+        elif m == ',':
+            internal_node_number -= 1
+#             print 'internal_node_number=', internal_node_number
+            rsib = node(internal_node_number)
+            pre.append(rsib)
+            nd.rsib = rsib
+            rsib.par=nd.par
+            nd = rsib
+            len_int_br +=1
+
+#             nd.edgelen = int_br2[len_int_br]
+            len_int_br -=1
+
+
+
+#             print 'nd=', nd.number
+            print '...................'
+        elif m == ')':
+            nd = nd.par
+            print '+++++++++++++++++++'
+
+        elif m == ':':
+            edge_len_str = ''
+            i+=1
+            m = tree[i]
+            assert m in ['0','1','2','3','4','5','6','7','8', '9','.']
+            while m in ['0','1','2','3','4','5','6','7','8', '9','.']:
+                edge_len_str += m
+                i+=1
+                m = tree[i]
+            i -=1
+            nd.edgelen = float(edge_len_str)
+
+            print '<<<<<<<<<<<<<<<<<<<<'
+
+        else:
+            internal_node_number += 1
+
+            if True:
+                assert m in ['0','1','2','3','4','5','6','7','8', '9'], 'Error : expecting m to be a digit when in fact it was "%s"' % m
+                mm = ''
+                while m in ['0','1','2','3','4','5','6','7','8', '9' ]:
+
+                    mm += m
+
+                    i += 1
+                    m = tree[i]
+#                     nd.edgelen = ext_br2[t]
+                nd.number = int(mm)
+#                print 'ext_node', mm
+                i -= 1
+
+            print '^^^^^^^^^^^^^^^^^^^^^^^^'
+
+        print 'nd.number=', nd.number
+        print 'nd.edgelen=', nd.edgelen
+        i += 1
+
+        print '#####################################################'
+
+except:
+    "out of range"
+for nd in pre:
+    print nd
+
+
+
+def Makenewick(pre):
+    newickstring = ''
+    for i,nd in enumerate(pre):
+        if nd.lchild:
+            newickstring += '('
+            print nd.number, nd.lchild.number
+
+        elif nd.rsib:
+            print nd.number, nd.rsib.number
+
+            newickstring += '%d' %(nd.number)
+            newickstring += ':%.1f' % nd.edgelen
+
+            newickstring += ','
+
+        else:
+            newickstring += '%d' %(nd.number)
+            newickstring += ':%.1f' % nd.edgelen
+
+            tmpnd = nd
+            while (tmpnd.par is not None) and (tmpnd.rsib is None):
+                newickstring += ')'
+                newickstring += ':%.1f' % tmpnd.par.edgelen
+                tmpnd = tmpnd.par
+
+            if tmpnd.par is not None:
+                newickstring += ','
+
+
+
+    return newickstring
+newick_string = Makenewick(pre)
+print newick_string
+
+