ete3 and python3 support

bin/bPTP.py

@@ -5,7 +5,7 @@
 import argparse
 import os
 
-from ete2 import Tree
+from ete3 import Tree
 from nexus import NexusReader
 from summary import partitionparser
 from ptp.ptpllh import lh_ratio_test, exp_distribution, species_setting, exponential_mixture
@@ -180,7 +180,7 @@ def __init__(self, filename, ftype="nexus", reroot=False, method="H1", seed=1234
 
         self.taxa_order = taxa_order
         if len(self.taxa_order) == 0:
-            self.taxa_order = Tree(self.trees[0]).get_leaf_names()
+            self.taxa_order = Tree(self.trees[0], format=1).get_leaf_names()
         self.numtaxa = len(self.taxa_order)
         self.numtrees = len(self.trees)
         self.reroot = reroot
@@ -211,7 +211,7 @@ def remove_outgroups(self, ognames, remove = False, output = ""):
                 with open(output, "w") as fout:
                     for t in self.trees:
                         fout.write(t + "\n") 
-        except ValueError, e:
+        except ValueError as e:
             print(e)
             print("")
             print("")

bin/summary.py

@@ -1,4 +1,6 @@
 #! /usr/bin/env python
+import matplotlib
+matplotlib.use('agg')
 import matplotlib.pyplot as plt
 import sys
 import argparse
@@ -242,7 +244,8 @@ def summary(self, fout = "", region = 1.0, bnmi = False, ML_par = None, ml_spe_s
                     pmap[par]= pmap.get(par, 0) + 1
 
             """Output partition summary"""
-            for key, value in sorted(pmap.iteritems(), reverse = True, key=lambda (k,v): (v,k)):
+            # kv: (-kv[1], kv[0])
+            for key, value in sorted(pmap.items(), reverse = True, key=lambda kv: (kv[1],kv[0])):
                 onespe = ""
                 for idx in key:
                     onespe = onespe + ", " + self.taxaorder[idx]

nexus/__init__.py

@@ -92,8 +92,8 @@
 """
 __author__ = 'Simon Greenhill <simon@simon.net.nz>'
 
-from reader import *
-from writer import NexusWriter
+from .reader import *
+from .writer import NexusWriter
 
 __version__ = "0.87"
 PACKAGE_NAME = "python-nexus"

nexus/writer.py

@@ -14,7 +14,7 @@
 ;
 END;
 """
-from reader import NexusReader
+from .reader import NexusReader
 
 class NexusWriter:
 

ptp/ptpllh.py

@@ -4,8 +4,8 @@
 
 from scipy import stats
 
-from ete2 import Tree, NodeStyle, TreeStyle, TextFace
-
+from ete3 import Tree, NodeStyle, TreeStyle, TextFace
+from ete3.treeview.main import  _FaceAreas
 #except ImportError:
 #print("Please install the matplotlib and other dependent package first.")
 #print("If your OS is ubuntu or has apt installed, you can try the following:") 
@@ -212,7 +212,7 @@ def output_species(self, taxa_order = []):
             print("#taxa_order != num_taxa!")
             print(repr(num_taxa) + "    " + repr(len(taxa_order)))
             for sp in self.spe_list:
-                print sp
+                print(sp)
             sys.exit()
             return None, None
         else: 
@@ -650,11 +650,12 @@ def showTree(delimitation, scale = 500, render = False, fout = "", form = "svg",
     style0["hz_line_type"] = 0
     style0["size"] = 0
 
-    tree.clear_face()
+    #tree.clear_face()
     for node in tree.get_descendants():
         node.set_style(style0)
         node.img_style["size"] = 0
-        node.clear_face()
+        node._faces = _FaceAreas()
+        #node.clear_face()
 
     tree.set_style(style0)
     tree.img_style["size"] = 0
@@ -692,7 +693,7 @@ def showTree(delimitation, scale = 500, render = False, fout = "", form = "svg",
                 node.add_face(TextFace("0", fsize = 8), column=0, position = "branch-top")
             else:
                 node.add_face(TextFace("{0:.2f}".format(node.bs), fsize = 8), column=0, position = "branch-top")
-            
+
     ts = TreeStyle()
     """scale pixels per branch length unit"""
     ts.scale =  scale 

requirements.txt

@@ -6,3 +6,4 @@ pytest
 matplotlib
 lxml
 MySQL-python
+PyQt5