[export] allow multiple trees

Multiple trees ("subtrees") have been available in Auspice since late
2021¹ and part of the associated schema since early 2022². Despite this
there was no way to produce such datasets within Augur itself, and
despite the schema changes the associated `augur validate` command was
never updated to allow them.

This commit adds multi-tree inputs to `augur export v2` as well as
allowing them to validate with our associated validation commands.

¹ <nextstrain/auspice#1442>
² <#851>

Author: jameshadfield

Diff for: augur/export_v2.py

@@ -118,13 +118,13 @@ def order_nodes(node):
     return od
 
 
-def read_tree(fname):
-    tree = Phylo.read(fname, 'newick')
+def read_trees(filenames):
+    trees = [Phylo.read(fname, 'newick') for fname in filenames]
     # augur export requires unique node names (both terminal and external) as these
     # are used to associate metadata/node-data with nodes. Any duplication is fatal.
     # The exception to this is unlabelled node names, which auspice will handle but
     # won't be associated with any metadata within export.
-    node_names = [clade.name for clade in tree.root.find_clades()]
+    node_names = [clade.name for tree in trees for clade in tree.root.find_clades()]
     if None in node_names:
         raise AugurError(f"Tree contains unnamed nodes. If these are internal nodes you may wish to run "+
                          "`augur refine --tree <newick> --output-tree <newick>` to name them.")
@@ -133,7 +133,7 @@ def read_tree(fname):
         dups = [name for name, count in Counter(node_names).items() if count>1]
         raise AugurError(f"{len(dups)} node names occur multiple times in the tree: " +
                          ", ".join([f"{v!r}" for v in dups[0:5]]) + ("..." if len(dups)>5 else ""))
-    return (tree, node_names)
+    return (trees, node_names)
 
 
 def node_div(T, node_attrs):
@@ -751,7 +751,12 @@ def _recursively_set_data(node):
             node['branch_attrs'] = branch_attrs[node['name']]
         for child in node.get("children", []):
             _recursively_set_data(child)
-    _recursively_set_data(data_json["tree"])
+
+    if isinstance(data_json["tree"], list):
+        for subtree in data_json['tree']:
+            _recursively_set_data(subtree)
+    else:
+        _recursively_set_data(data_json["tree"])
 
 
 def set_node_attrs_on_tree(data_json, node_attrs, additional_metadata_columns):
@@ -840,7 +845,11 @@ def _recursively_set_data(node):
         for child in node.get("children", []):
             _recursively_set_data(child)
 
-    _recursively_set_data(data_json["tree"])
+    if isinstance(data_json["tree"], list):
+        for subtree in data_json['tree']:
+            _recursively_set_data(subtree)
+    else:
+        _recursively_set_data(data_json["tree"])
 
 def node_data_prop_is_normal_trait(name):
     # those traits / keys / attrs which are not "special" and can be exported
@@ -894,7 +903,7 @@ def register_parser(parent_subparsers):
     required = parser.add_argument_group(
         title="REQUIRED"
     )
-    required.add_argument('--tree','-t', metavar="newick", required=True, help="Phylogenetic tree, usually output from `augur refine`")
+    required.add_argument('--tree','-t', metavar="newick", nargs='+', action='extend', required=True, help="Phylogenetic tree(s), usually output from `augur refine`")
     required.add_argument('--output', metavar="JSON", required=True, help="Output file (typically for visualisation in auspice)")
 
     config = parser.add_argument_group(
@@ -1192,7 +1201,7 @@ def run(args):
         metadata_file = {}
 
     # parse input files
-    (T, node_names) = read_tree(args.tree)
+    (trees, node_names) = read_trees(args.tree)
     node_data, node_attrs, node_data_names, metadata_names, branch_attrs = \
             parse_node_data_and_metadata(node_names, node_data_file, metadata_file)
     config = get_config(args)
@@ -1224,7 +1233,8 @@ def run(args):
     set_filters(data_json, config)
 
     # set tree structure
-    data_json["tree"] = convert_tree_to_json_structure(T.root, node_attrs, node_div(T, node_attrs))
+    trees_json = [convert_tree_to_json_structure(tree.root, node_attrs, node_div(tree, node_attrs)) for tree in trees]
+    data_json["tree"] = trees_json[0] if len(trees_json)==1 else trees_json
     set_node_attrs_on_tree(data_json, node_attrs, additional_metadata_columns)
     set_branch_attrs_on_tree(data_json, branch_attrs)
 

Diff for: augur/validate_export.py

@@ -7,7 +7,7 @@
 import sys
 from collections import defaultdict
 
-def ensure_no_duplicate_names(root, ValidateError):
+def ensure_no_duplicate_names(tree, ValidateError):
     """
     Check that all node names are identical, which is required for auspice (v2) JSONs.
     """
@@ -18,10 +18,14 @@ def recurse(node):
         names.add(node["name"])
         if "children" in node:
             [recurse(child) for child in node["children"]]
-    recurse(root)
+    if isinstance(tree, list):
+        for subtree in tree:
+            recurse(subtree)
+    else:
+        recurse(tree)
 
 
-def collectTreeAttrsV2(root, warn):
+def collectTreeAttrsV2(tree, warn):
     """
     Collect all keys specified on `node["node_attrs"]` throughout the tree
     and the values associated with them. Note that this will only look at
@@ -47,7 +51,12 @@ def recurse(node):
             [recurse(child) for child in node["children"]]
         else:
             num_terminal += 1
-    recurse(root)
+
+    if isinstance(tree, list):
+        for subtree in tree:
+            recurse(subtree)
+    else:
+        recurse(tree)
 
     for data in seen.values():
         if data["count"] == num_nodes:
@@ -56,7 +65,7 @@ def recurse(node):
     return(seen, num_terminal)
 
 
-def collectMutationGenes(root):
+def collectMutationGenes(tree):
     """
     Returns a set of all genes specified in the tree in the "aa_muts" objects
     """
@@ -67,17 +76,28 @@ def recurse(node):
             genes.update(mutations.keys())
         if "children" in node:
             [recurse(child) for child in node["children"]]
-    recurse(root)
+
+    if isinstance(tree, list):
+        for subtree in tree:
+            recurse(subtree)
+    else:
+        recurse(tree)
+
     genes -= {"nuc"}
     return genes
 
-def collectBranchLabels(root):
+def collectBranchLabels(tree):
     labels = set()
     def recurse(node):
         labels.update(node.get("branch_attrs", {}).get("labels", {}).keys())
         if "children" in node:
             [recurse(child) for child in node["children"]]
-    recurse(root)
+
+    if isinstance(tree, list):
+        for subtree in tree:
+            recurse(subtree)
+    else:
+        recurse(tree)
     return labels
 
 def verifyMainJSONIsInternallyConsistent(data, ValidateError):

Diff for: tests/functional/export_v2/cram/multi-tree.t

@@ -0,0 +1,53 @@
+
+Setup
+
+  $ source "$TESTDIR"/_setup.sh
+
+Create a small second tree (which has different names/labels than 'tree.nwk')
+  $ cat > tree2.nwk <<~~
+  > (tipG:1,(tipH:1,tipI:1)internalHI:2)SECOND_ROOT:0;
+  > ~~
+
+Minimal export -- no node data, no metadata etc etc
+  $ ${AUGUR} export v2 \
+  >   --tree "$TESTDIR/../data/tree.nwk" tree2.nwk \
+  >   --output minimal.json &> /dev/null
+
+More realistic export - with node_data for all nodes and metadata for some of them
+
+  $ cat > metadata.tsv <<~~
+  > strain	something
+  > tipA	foo
+  > tipB	foo
+  > tipC	foo
+  > tipG	bar
+  > tipH	bar
+  > ~~
+
+
+  $ cat > node-data.json <<~~
+  > {
+  >   "nodes": {
+  >     "ROOT": {"mutation_length": 0},
+  >     "tipA": {"mutation_length": 1},
+  >     "internalBC": {"mutation_length": 2},
+  >     "tipB": {"mutation_length": 1},
+  >     "tipC": {"mutation_length": 1},
+  >     "internalDEF": {"mutation_length": 5},
+  >     "tipD": {"mutation_length": 3},
+  >     "tipE": {"mutation_length": 4},
+  >     "tipF": {"mutation_length": 1},
+  >     "SECOND_ROOT": {"mutation_length": 0},
+  >     "tipG": {"mutation_length": 1},
+  >     "internalHI": {"mutation_length": 2},
+  >     "tipH": {"mutation_length": 1},
+  >     "tipI": {"mutation_length": 1}
+  >   }
+  > }
+  > ~~
+
+  $ ${AUGUR} export v2 \
+  >   --tree "$TESTDIR/../data/tree.nwk" tree2.nwk \
+  >   --metadata metadata.tsv --color-by-metadata something \
+  >   --node-data node-data.json \
+  >   --output output.json &> /dev/null