1.7.6: bug fix

4i0n · May 2, 2017 · 0b007b5 · 0b007b5
1 parent a19885e
commit 0b007b5
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Showing 5 changed files with 13 additions and 8 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,3 +1,6 @@
+- Version 1.7.6: 
+        - ** Bug Fix **: PASTA used to sometimes fail due to troubles with new dendropy rooting
+
 - Version 1.7.4:
         - ** Bug Fix **: fixed a bug that eliminated one sequence 
 

diff --git a/README.md b/README.md
@@ -252,9 +252,9 @@ Debug
 -------
 To show debug information, set the following environmental variables: 
 ```
-PASTA_DEBUG=TRUE
-PASTA_LOGGING_LEVEL=DEBUG
-PASTA_LOGGING_FORMAT=RICH
+export PASTA_DEBUG=TRUE
+export PASTA_LOGGING_LEVEL=DEBUG
+export PASTA_LOGGING_FORMAT=RICH
 ```
 (last line is optional)
 

diff --git a/pasta/__init__.py b/pasta/__init__.py
@@ -12,7 +12,7 @@
 PROGRAM_NAME = "PASTA"
 PROGRAM_AUTHOR = ["Siavash Mirarab","Nam Nguyen","Jiaye Yu", "Mark T. Holder", "Jeet Sukumaran", "Jamie Oaks"]
 PROGRAM_LICENSE = "GNU General Public License, version 3"
-PROGRAM_VERSION = "1.7.5"
+PROGRAM_VERSION = "1.7.6"
 PROGRAM_YEAR = "2013-2017"
 PROGRAM_DESCRIPTION = "Practical Alignment using SATe and TrAnsitivity"
 PROGRAM_WEBSITE = "http://www.cs.utexas.edu/~phylo/software/pasta/"

diff --git a/pasta/pastajob.py b/pasta/pastajob.py
@@ -333,8 +333,10 @@ def build_subsets_tree(self, curr_tmp_dir_par):
         #_LOG.debug("fake taxa inferred")                   
         #Then make sure the tree is rooted at a branch (not at a node). 
         if len(subsets_tree._tree.seed_node.child_nodes()) > 2:
-            subsets_tree._tree.reroot_at_edge(subsets_tree._tree.seed_node.child_nodes()[0].edge)                        
-        _LOG.debug("Subset Labeling (start):\n%s" %str(subsets_tree.compose_newick())[0:200])
+            c = subsets_tree._tree.seed_node.child_nodes()[0]
+            subsets_tree._tree.reroot_at_edge(c.edge,length1=c.edge.length/2., length2=c.edge.length/2.)                        
+        _LOG.debug("Subset Labeling (start):\n%s" %str(subsets_tree.compose_newick(suppress_rooting=False)))
+        #_LOG.debug("Subset Labeling (start):\n%s" %str(len(subsets_tree._tree.seed_node.child_nodes())))
         # Then label internal branches based on their children, and collapse redundant edges. 
         for node in subsets_tree._tree.postorder_internal_node_iter():
             # my label is the intersection of my children, 

diff --git a/pasta/tree.py b/pasta/tree.py
@@ -172,8 +172,8 @@ def leaf_node_names(self):
     def __str__(self):
         return self.compose_newick()
 
-    def compose_newick(self):
-        return self._tree.as_string(schema="newick",suppress_rooting = True)
+    def compose_newick(self,suppress_rooting = True):
+        return self._tree.as_string(schema="newick",suppress_rooting)
         #return self._tree.compose_newick()
 
     def read_tree_from_file(self, treefile, file_format):