v1.9.43: fixed reading newick trees with quotes

evolbioinfo · Feb 26, 2024 · 0c8a338 · 0c8a338
1 parent e57266c
commit 0c8a338
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Showing 3 changed files with 9 additions and 4 deletions.
diff --git a/pastml/acr.py b/pastml/acr.py
@@ -34,7 +34,7 @@
 from pastml.visualisation.itol_manager import generate_itol_annotations
 from pastml.visualisation.tree_compressor import REASONABLE_NUMBER_OF_TIPS, VERTICAL, HORIZONTAL, TRIM
 
-PASTML_VERSION = '1.9.42'
+PASTML_VERSION = '1.9.43'
 
 model2class = {F81: F81Model, JC: JCModel, CUSTOM_RATES: CustomRatesModel, HKY: HKYModel, JTT: JTTModel, EFT: EFTModel}
 

diff --git a/pastml/tree.py b/pastml/tree.py
@@ -6,6 +6,7 @@
 
 from Bio import Phylo
 from ete3 import Tree, TreeNode
+from ete3.parser.newick import NewickError
 
 POSTORDER = 'postorder'
 
@@ -176,8 +177,12 @@ def read_tree(tree_path, columns=None):
         try:
             tree = Tree(tree_path, format=f)
             break
-        except:
-            continue
+        except NewickError:
+            try:
+                tree = Tree(tree_path, format=f, quoted_node_names=True)
+                break
+            except NewickError:
+                continue
     if not tree:
         raise ValueError('Could not read the tree {}. Is it a valid newick?'.format(tree_path))
     if columns:

diff --git a/setup.py b/setup.py
@@ -23,7 +23,7 @@
         'Programming Language :: Python :: 3.10',
         'Programming Language :: Python :: 3 :: Only',
     ],
-    version='1.9.42',
+    version='1.9.43',
     description='Ancestral character reconstruction and visualisation for rooted phylogenetic trees.',
     author='Anna Zhukova',
     author_email='anna.zhukova@pasteur.fr',