check if input tree is rooted

lib/pipeline.ml

@@ -121,7 +121,7 @@ let derive_from_model ~model ~input_tree ~tree_dataset ~tree_prefix ~profile ~pr
 let derive_from_tree ~tree_dir ~tree ~profile ~preview ~use_concat ~ns ~no_Ne ~no_HaPC ~ne_test =
   let tree_prefix = Filename.chop_extension tree in
   let input_tree = input (Filename.concat tree_dir tree) in
-  let tree_dataset = Tree_dataset.prepare input_tree in
+  let tree_dataset = Tree_dataset.prepare ~descr:tree_prefix input_tree in
   let models = Convergence_hypothesis.[
       [
         H0_NeG1  ;

lib/scripts/parse_input_tree.py

@@ -105,6 +105,12 @@ if t:
         features = list(set(features)) # list(set(*)) = remove duplicates
     logger.info("No detected tag" if not features else "Detected tags: "+", ".join([f for f in features]))
     
+    #check rooted tree
+    nb_root_children = len(t.get_children())
+    if nb_root_children > 2:
+        logger.error("Unrooted tree")
+        sys.exit(1)
+
     if "ND" in features:
         logger.warning("\"ND\" is in the detected tags but it will be removed by the programm")
         features.remove("ND")

lib/tree_dataset.ml

@@ -5,8 +5,8 @@ open File_formats
 
 let env = docker_image ~account:"carinerey" ~name:"python_basics" ~tag:"07252018" ()
 
-let prepare tree =
-  workflow ~descr:"utils.parse_input_tree" [
+let prepare ?(descr="") tree =
+  workflow ~descr:("utils.parse_input_tree." ^ descr) [
     cmd "python" ~env [
       file_dump (string Scripts.parse_input_tree) ;
       opt "-t" dep tree ;

lib/tree_dataset.mli

 open Bistro.Std
 open File_formats
 
-val prepare : nhx workflow -> [`tree_dataset] directory workflow
+val prepare :
+    ?descr : string -> 
+    nhx workflow -> [`tree_dataset] directory workflow
 val nodes :
   [`tree_dataset] directory workflow ->
   Convergence_hypothesis.t ->