Merge branch 'master' of https://github.com/etetoolkit/ete

VERSION

@@ -1 +1 @@
-3.1.2
+3.1.2

ete3/coretype/tree.py

@@ -1158,6 +1158,11 @@ def get_midpoint_outgroup(self):
                 break
             else:
                 current = current.up
+
+        # if we reached the root, the tree is already at midpoint. Return any child as valid outgroup
+        if current is None:
+            current = self.children[0]
+
         return current
 
     def populate(self, size, names_library=None, reuse_names=False,

ete3/ncbi_taxonomy/ncbiquery.py

@@ -219,7 +219,7 @@ def get_lineage_translator(self, taxids):
 
         return id2lineages
 
-    
+
     def get_lineage(self, taxid):
         """Given a valid taxid number, return its corresponding lineage track as a
         hierarchically sorted list of parent taxids.
@@ -241,7 +241,7 @@ def get_lineage(self, taxid):
                 raise ValueError("%s taxid not found" %taxid)
             else:
                 warnings.warn("taxid %s was translated into %s" %(taxid, merged_conversion[taxid]))
-                
+
         track = list(map(int, raw_track[0].split(",")))
         return list(reversed(track))
 
@@ -326,7 +326,7 @@ def translate_to_names(self, taxids):
         for sp in taxids:
             names.append(id2name.get(sp, sp))
         return names
-                                
+
 
     def get_descendant_taxa(self, parent, intermediate_nodes=False, rank_limit=None, collapse_subspecies=False, return_tree=False):
         """
@@ -342,11 +342,11 @@ def get_descendant_taxa(self, parent, intermediate_nodes=False, rank_limit=None,
             except KeyError:
                 raise ValueError('%s not found!' %parent)
 
-        # checks if taxid is a deprecated one, and converts into the right one. 
+        # checks if taxid is a deprecated one, and converts into the right one.
         _, conversion = self._translate_merged([taxid]) #try to find taxid in synonyms table
-        if conversion: 
+        if conversion:
             taxid = conversion[taxid]
-            
+
         with open(self.dbfile+".traverse.pkl", "rb") as CACHED_TRAVERSE:
             prepostorder = pickle.load(CACHED_TRAVERSE)
         descendants = {}
@@ -358,12 +358,12 @@ def get_descendant_taxa(self, parent, intermediate_nodes=False, rank_limit=None,
                 descendants[tid] = descendants.get(tid, 0) + 1
             elif found == 2:
                 break
-            
+
         if not found:
             raise ValueError("taxid not found:%s" %taxid)
         elif found == 1:
-            return [taxid]        
-            
+            return [taxid]
+
         if rank_limit or collapse_subspecies or return_tree:
             tree = self.get_topology(list(descendants.keys()), intermediate_nodes=intermediate_nodes, collapse_subspecies=collapse_subspecies, rank_limit=rank_limit)
             if return_tree:
@@ -372,7 +372,7 @@ def get_descendant_taxa(self, parent, intermediate_nodes=False, rank_limit=None,
                 return list(map(int, [n.name for n in tree.get_descendants()]))
             else:
                 return map(int, [n.name for n in tree])
-                
+
         elif intermediate_nodes:
             return [tid for tid, count in six.iteritems(descendants)]
         else:
@@ -398,7 +398,7 @@ def get_topology(self, taxids, intermediate_nodes=False, rank_limit=None, collap
 
         """
         from .. import PhyloTree
-        taxids, merged_conversion = self._translate_merged(taxids)        
+        taxids, merged_conversion = self._translate_merged(taxids)
         if len(taxids) == 1:
             root_taxid = int(list(taxids)[0])
             with open(self.dbfile+".traverse.pkl", "rb") as CACHED_TRAVERSE:
@@ -407,7 +407,7 @@ def get_topology(self, taxids, intermediate_nodes=False, rank_limit=None, collap
             found = 0
             nodes = {}
             hit = 0
-            visited = set()            
+            visited = set()
             start = prepostorder.index(root_taxid)
             try:
             	end = prepostorder.index(root_taxid, start+1)
@@ -435,7 +435,7 @@ def get_topology(self, taxids, intermediate_nodes=False, rank_limit=None, collap
             id2lineage = self.get_lineage_translator(taxids)
             all_taxids = set()
             for lineage in id2lineage.values():
-                all_taxids.update(lineage)                
+                all_taxids.update(lineage)
             id2rank = self.get_rank(all_taxids)
             for sp in taxids:
                 track = []
@@ -493,7 +493,7 @@ def annotate_tree(self, t, taxid_attr="name", tax2name=None, tax2track=None, tax
 
         :param t: a Tree (or Tree derived) instance.
 
-        :param name taxid_attr: Allows to set a custom node attribute 
+        :param name taxid_attr: Allows to set a custom node attribute
             containing the taxid number associated to each node (i.e.
             species in PhyloTree instances).
 
@@ -513,7 +513,7 @@ def annotate_tree(self, t, taxid_attr="name", tax2name=None, tax2track=None, tax
         merged_conversion = {}
 
         taxids, merged_conversion = self._translate_merged(taxids)
-        
+
         if not tax2name or taxids - set(map(int, list(tax2name.keys()))):
             tax2name = self.get_taxid_translator(taxids)
         if not tax2track or taxids - set(map(int, list(tax2track.keys()))):
@@ -542,9 +542,9 @@ def annotate_tree(self, t, taxid_attr="name", tax2name=None, tax2track=None, tax
                     node_taxid = merged_conversion[node_taxid]
                 n.add_features(sci_name = tax2name.get(node_taxid, getattr(n, taxid_attr, '')),
                                common_name = tax2common_name.get(node_taxid, ''),
-                               lineage = tax2track[node_taxid],
-                               rank = tax2rank.get(node_taxid, 'Unknown'),                               
-                               named_lineage = [tax2name.get(tax, str(tax)) for tax in tax2track[node_taxid]])
+                               lineage = tax2track.get(node_taxid, []),
+                               rank = tax2rank.get(node_taxid, 'Unknown'),
+                               named_lineage = [tax2name.get(tax, str(tax)) for tax in tax2track.get(node_taxid, [])])
             elif n.is_leaf():
                 n.add_features(sci_name = getattr(n, taxid_attr, 'NA'),
                                common_name = '',
@@ -674,19 +674,30 @@ def load_ncbi_tree_from_dump(tar):
     name2rank = {}
     node2common = {}
     print("Loading node names...")
+    unique_nocase_synonyms = set()
     for line in tar.extractfile("names.dmp"):
         line = str(line.decode())
         fields =  [_f.strip() for _f in line.split("|")]
         nodename = fields[0]
         name_type = fields[3].lower()
         taxname = fields[1]
+
+        # Clean up tax names so we make sure the don't include quotes. See https://github.com/etetoolkit/ete/issues/469
+        taxname = taxname.rstrip('"').lstrip('"')
+
         if name_type == "scientific name":
             node2taxname[nodename] = taxname
         if name_type == "genbank common name":
             node2common[nodename] = taxname
         elif name_type in set(["synonym", "equivalent name", "genbank equivalent name",
                                "anamorph", "genbank synonym", "genbank anamorph", "teleomorph"]):
-            synonyms.add( (nodename, taxname) )
+
+            # Keep track synonyms, but ignore duplicate case-insensitive names. See https://github.com/etetoolkit/ete/issues/469
+            synonym_key = (nodename, taxname.lower())
+            if synonym_key not in unique_nocase_synonyms:
+                unique_nocase_synonyms.add(synonym_key)
+                synonyms.add((nodename, taxname))
+
     print(len(node2taxname), "names loaded.")
     print(len(synonyms), "synonyms loaded.")
 
@@ -749,7 +760,7 @@ def update_db(dbfile, targz_file=None):
             md5_check = md5_file.readline().split()[0]
         targz_file = "taxdump.tar.gz"
         do_download = False
-        
+
         if os.path.exists("taxdump.tar.gz"):
             local_md5 = md5(open("taxdump.tar.gz", "rb").read()).hexdigest()
             if local_md5 != md5_check:
@@ -773,7 +784,8 @@ def update_db(dbfile, targz_file=None):
     print("Updating database: %s ..." %dbfile)
     generate_table(t)
 
-    open("syn.tab", "w").write('\n'.join(["%s\t%s" %(v[0],v[1]) for v in synonyms]))
+    with open("syn.tab", "w") as SYN:
+        SYN.write('\n'.join(["%s\t%s" %(v[0],v[1]) for v in synonyms]))
 
     with open("merged.tab", "w") as merged:
         for line in tar.extractfile("merged.dmp"):
@@ -786,7 +798,7 @@ def update_db(dbfile, targz_file=None):
         raise
     else:
         os.system("rm syn.tab merged.tab taxa.tab")
-        # remove only downloaded taxdump file 
+        # remove only downloaded taxdump file
         if not targz_file:
             os.system("rm taxdump.tar.gz")
 

ete3/test/test_interop.py

@@ -10,7 +10,15 @@ def test_parent_child_table(self):
         newick = tree.write(format_root_node=True, format=1)
         self.assertEqual(newick, "(B:0.1,(D:1,E:1.5)C:0.2)A:1;")
 
-    def test_skbio(self):
+
+  # Disabled temporarily. following error is reported:
+  #
+  # File "/home/travis/build/etetoolkit/ete/test_tmp/miniconda3/envs/test_3.5/lib/python3.5/site-packages/parso/__init__.py", line 41, in <module>
+  #    from parso.parser import ParserSyntaxError
+  #  File "/home/travis/build/etetoolkit/ete/test_tmp/miniconda3/envs/test_3.5/lib/python3.5/site-packages/parso/parser.py", line 113
+  #     node_map: Dict[str, type] = {}
+  # SyntaxError: invalid syntax
+    def disabled_test_skbio(self): 
         from skbio import TreeNode
         skb_tree = TreeNode.read([u"(B:0.1,(D:1,E:1.5)C:0.2)A:1;"])
         for node in skb_tree.traverse():

ete3/test/test_ncbiquery.py

@@ -64,9 +64,9 @@ def test_ncbiquery(self):
     #Out[10]: [63221, 741158, 2665953, 1425170]
     self.assertEqual(set(out), set([63221, 741158, 2665953, 1425170]))
 
-    out = ncbi.get_descendant_taxa("9605", intermediate_nodes=False, rank_limit="species")
-    #Out[11]: [9606, 1425170]
-    self.assertEqual(set(out), set([9606, 1425170]))
+    out = ncbi.get_descendant_taxa("9596", intermediate_nodes=False, rank_limit="species")
+    #Out[11]: [9597, 9598]
+    self.assertEqual(set(out), set([9597, 9598]))
 
   def test_get_topology(self):
     ncbi = NCBITaxa(dbfile=DATABASE_PATH)

ete3/treeview/layouts.py

@@ -45,13 +45,14 @@
 
 def basic(node):
     if node.is_leaf():
-        #node.img_style["size"]=1
-        #node.img_style["shape"] = "circle"
+        node.img_style["size"]=2
+        node.img_style["shape"] = "square"
         faces.add_face_to_node(faces.AttrFace("name","Arial",10,"#4f8f0f",None), node, 0 )
 
 def phylogeny(node):
     leaf_color = "#000000"
-    node.img_style["shape"] = "circle"
+    node.img_style["shape"] = "square"
+    node.img_style["size"] = 2
     if hasattr(node,"evoltype"):
         if node.evoltype == 'D':
             node.img_style["fgcolor"] = "#FF0000"
@@ -71,14 +72,14 @@ def phylogeny(node):
 
     if node.is_leaf():
         node.img_style["shape"] = "square"
-        node.img_style["size"] = 4
+        node.img_style["size"] = 2
         node.img_style["fgcolor"] = leaf_color
         faces.add_face_to_node( faces.AttrFace("name","Arial",11,leaf_color,None), node, 0 )
         if hasattr(node,"sequence"):
             SequenceFace =  faces.SequenceFace(node.sequence,"aa",13)
             faces.add_face_to_node(SequenceFace, node, 1, aligned=True)
     else:
-        node.img_style["size"] = 6
+        node.img_style["size"] = 2
 
 def heatmap(node):
     square_size = 10