Merge pull request #27 from druvus/1.0.10

Change ete2 import

CanSNPer/__main__.py

@@ -4,7 +4,7 @@
 CanSNPer: A toolkit for SNP-typing using NGS data.
 Copyright (C) 2016 Adrian Lärkeryd
 
-VERSION 1.0.9
+VERSION 1.0.10
 
 This program is free software: you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
@@ -35,11 +35,7 @@
 
 from subprocess import Popen
 
-if version_info[0] < 3:
-    from ete2 import Tree, faces, AttrFace, TreeStyle, NodeStyle
-else:
-    from ete3 import Tree, faces, AttrFace, TreeStyle, NodeStyle
-
+import ete2
 
 def parse_arguments():
     '''Parses arguments from the command line and sends them to read_config
@@ -561,9 +557,9 @@ def tree_to_newick(organism, config, c):
 
 def CanSNPer_tree_layout(node):
     '''Layout style for ETE2 trees.'''
-    name_face = AttrFace("name")
+    name_face = ete2.AttrFace("name")
     # Adds the name face to the image at the top side of the branch
-    faces.add_face_to_node(name_face, node, column=0, position="branch-top")
+    ete2.faces.add_face_to_node(name_face, node, column=0, position="branch-top")
 
 
 def draw_ete2_tree(organism, snplist, tree_file_name, config, c):
@@ -576,11 +572,11 @@ def draw_ete2_tree(organism, snplist, tree_file_name, config, c):
 
     '''
     newick = tree_to_newick(organism, config, c)
-    tree = Tree(newick, format=1)
+    tree = ete2.Tree(newick, format=1)
     tree_depth = int(tree.get_distance(tree.get_farthest_leaf()[0]))
     for n in tree.traverse():
         # Nodes are set to red colour
-        nstyle = NodeStyle()
+        nstyle = ete2.NodeStyle()
         nstyle["fgcolor"] = "#BE0508"
         nstyle["size"] = 10
         nstyle["vt_line_color"] = "#000000"
@@ -609,7 +605,7 @@ def draw_ete2_tree(organism, snplist, tree_file_name, config, c):
                     nstyle["vt_line_type"] = 1
                     nstyle["hz_line_type"] = 1
         n.set_style(nstyle)
-    ts = TreeStyle()
+    ts = ete2.TreeStyle()
     ts.show_leaf_name = False  # Do not print(leaf names, they are added in layout)
     ts.show_scale = False  # Do not show the scale
     ts.layout_fn = CanSNPer_tree_layout  # Use the custom layout

changelog

@@ -1,3 +1,7 @@
+2020-05-06 Andreas Sjödin <[email protected]>
+        CanSNPer version 1.0.10
+        * Changing import of ete2
+
 2017-03-29  Emil Hägglund <[email protected]> & Andreas Sjödin <[email protected]>
         CanSNPer version 1.0.9
         * Added Dockerfile

setup.py

@@ -7,7 +7,7 @@
 
 setup(
     name="CanSNPer",
-    version="1.0.9",
+    version="1.0.10",
     url="https://github.com/adrlar/CanSNPer",
     description="CanSNPer: A toolkit for SNP-typing using NGS data.",
     license="GPL'",