augur clades allows attribute name to be specified

Previously the `augur clades` command produced a node-data JSON
which stored clade membership as the node-attr "clade_membership"
and defined the basal nodes of each clade with the node-attr
"clade_annotation". `augur export v2` interpreted the latter as a
special-case and turned it into a branch label of the same name.

The previous commit allowed `augur export` to be supplied node-data
JSONs with a `branch_labels` structure. Here we update `augur clades`
to export data in this structure, which allows the user to specify
the keys to use via the `--attribute-name` arg.

This commit breaks backwards compatibility for pipelines as the default
attribute name is "clade". This will result in dataset (auspice) JSONs
with the same branch labelling as before, but with a different node-attr
(was "clade_membership", now "clade"). As `augur export v2` will make
colorings for all node-attrs in in node-data JSONs, this will be
exported as a "clade" coloring with no changes needed, however auspice
config JSONs may now refer to a non-existent "clade_membership" key.

`augur export v2` has been updated to no longer special-case
`clade_membership` or `clade_annotation` node attrs. We print a
warning if an auspice config JSON refers to `clade_membership` to
help users update their configs.

Functional tests for `augur clades` have been added.

Closes #720

Author: jameshadfield

augur/clades.py

@@ -101,13 +101,12 @@ def assign_clades(clade_designations, all_muts, tree, ref=None):
         mapping of node to clades
     '''
 
-    clade_membership = {}
+    # We add the names of nodes these dictionaries to store which clade they belong to.
+    # all nodes in a clade should appear in `clade_membership` while only one node should
+    # appear in `basal_clade_nodes`
+    (clade_membership, basal_clade_nodes) = ({}, {})
     parents = get_parent_name_by_child_name_for_tree(tree)
 
-    # first pass to set all nodes to unassigned as precaution to ensure attribute is set
-    for node in tree.find_clades(order = 'preorder'):
-        clade_membership[node.name] = {'clade_membership': 'unassigned'}
-
     # count leaves
     for node in tree.find_clades(order = 'postorder'):
         node.leaf_count = 1 if node.is_terminal() else np.sum([c.leaf_count for c in node])
@@ -136,7 +135,7 @@ def assign_clades(clade_designations, all_muts, tree, ref=None):
                     node.sequences[gene][pos] = d
 
 
-    # second pass to assign 'clade_annotation' to basal nodes within each clade
+    # store names of basal nodes of each clade in `basal_clade_nodes` and `clade_membership` dicts.
     # if multiple nodes match, assign annotation to largest
     # otherwise occasional unwanted cousin nodes get assigned the annotation
     for clade_name, clade_alleles in clade_designations.items():
@@ -147,16 +146,17 @@ def assign_clades(clade_designations, all_muts, tree, ref=None):
         sorted_nodes = sorted(node_counts, key=lambda x: x.leaf_count, reverse=True)
         if len(sorted_nodes) > 0:
             target_node = sorted_nodes[0]
-            clade_membership[target_node.name] = {'clade_annotation': clade_name, 'clade_membership': clade_name}
+            basal_clade_nodes[target_node.name] = clade_name
+            clade_membership[target_node.name] = clade_name # basal nodes are members of the clade
 
-    # third pass to propagate 'clade_membership'
+    # propagate 'clade_membership' to children nodes
     # don't propagate if encountering 'clade_annotation'
     for node in tree.find_clades(order = 'preorder'):
         for child in node:
-            if 'clade_annotation' not in clade_membership[child.name]:
-                clade_membership[child.name]['clade_membership'] = clade_membership[node.name]['clade_membership']
-
-    return clade_membership
+            # if the child doesn't define the start of its own clade, but the parent belongs to a clade, then inherit that membership
+            if child.name not in basal_clade_nodes and node.name in clade_membership:
+                clade_membership[child.name] = clade_membership[node.name]
+    return (basal_clade_nodes, clade_membership)
 
 
 def get_reference_sequence_from_root_node(all_muts, root_name):
@@ -181,6 +181,7 @@ def register_arguments(parser):
     parser.add_argument('--mutations', nargs='+', help='JSON(s) containing ancestral and tip nucleotide and/or amino-acid mutations ')
     parser.add_argument('--reference', nargs='+', help='fasta files containing reference and tip nucleotide and/or amino-acid sequences ')
     parser.add_argument('--clades', type=str, help='TSV file containing clade definitions by amino-acid')
+    parser.add_argument('--attribute-name', type=str, default="clade", help="name to use for clade membership & branch labels", required=False)
     parser.add_argument('--output-node-data', type=str, help='name of JSON file to save clade assignments to')
 
 
@@ -205,8 +206,14 @@ def run(args):
 
     clade_designations = read_in_clade_definitions(args.clades)
 
-    clade_membership = assign_clades(clade_designations, all_muts, tree, ref)
+    (basal_clade_nodes, clade_membership) = assign_clades(clade_designations, all_muts, tree, ref)
+
+    # create node_data for export as a JSON
+    node_data = {
+      'nodes': {node: {args.attribute_name: clade} for node,clade in clade_membership.items()},
+      'branch_labels': {node: {args.attribute_name: clade} for node,clade in basal_clade_nodes.items()}
+    }
 
     out_name = get_json_name(args)
-    write_json({'nodes': clade_membership}, out_name)
-    print("clades written to", out_name, file=sys.stdout)
+    write_json(node_data, out_name)
+    print(f"clades written to {out_name} using attribute name {args.attribute_name}", file=sys.stdout)

augur/export_v2.py

@@ -91,17 +91,9 @@ def are_mutations_defined(node_attrs):
             return True
     return False
 
-
-def are_clades_defined(node_attrs):
+def is_node_attr_defined(node_attrs, attr_name):
     for node, data in node_attrs.items():
-        if data.get("clade_membership") or data.get("clade_annotation"):
-            return True
-    return False
-
-
-def are_dates_defined(node_attrs):
-    for node, data in node_attrs.items():
-        if data.get("num_date"):
+        if data.get(attr_name):
             return True
     return False
 
@@ -162,7 +154,7 @@ def set_colorings(data_json, config, command_line_colorings, metadata_names, nod
     def _get_type(key, trait_values):
         # for some keys we know what the type must be
         known_types = {
-            "clade_membership": "categorical",
+            "clade": "categorical",
             "gt": "categorical",
             "author": "categorical",
             "num_date": "continuous"
@@ -199,7 +191,7 @@ def _get_title(key):
             return config_title
 
         # hardcoded fallbacks:
-        if key == "clade_membership":
+        if key == "clade":
             return "Clade"
         if key == "gt":
             return "Genotype"
@@ -251,6 +243,12 @@ def _is_valid(coloring):
         if key == "gt" and not are_mutations_defined(node_attrs):
             warn("[colorings] You asked for mutations (\"gt\"), but none are defined on the tree. They cannot be used as a coloring.")
             return False
+        if key == "clade_membership" and not trait_values:
+            # augur 12 & below defined clades via the key "clade_membership", not "clade".
+            # If an auspice_config file specifies this, and it is not present in any node-data, we print a warning.
+            # (Note that if "clade" is present in node-data, we automatically include it as a colouring.)
+            warn("You asked for a color-by for 'clade_membership' but this is now called 'clade'. You should update your auspice config file.")
+            return False
         if key != "gt" and not trait_values:
             warn("You asked for a color-by for trait '{}', but it has no values on the tree. It has been ignored.".format(key))
             return False
@@ -289,11 +287,10 @@ def _get_colorings():
         # add in genotype as a special case if (a) not already set and (b) the data supports it
         if "gt" not in explicitly_defined_colorings and are_mutations_defined(node_attrs):
             colorings.insert(0,{'key':'gt'})
-        if "num_date" not in explicitly_defined_colorings and are_dates_defined(node_attrs):
+        if "num_date" not in explicitly_defined_colorings and is_node_attr_defined(node_attrs, "num_date"):
             colorings.insert(0,{'key':'num_date'})
-        if "clade_membership" not in explicitly_defined_colorings and are_clades_defined(node_attrs):
-            colorings.insert(0,{'key':'clade_membership'})
-
+        if "clade" not in explicitly_defined_colorings and is_node_attr_defined(node_attrs, "clade"):
+            colorings.insert(0,{'key':'clade'})
         return colorings
 
 
@@ -650,8 +647,6 @@ def node_data_prop_is_normal_trait(name):
     # those traits / keys / attrs which are not "special" and can be exported
     # as normal attributes on nodes
     excluded = [
-        "clade_annotation", # Clade annotation is label, not colorby!
-        "clade_membership", # will be auto-detected if it is available
         "authors",          # authors are set as a node property, not a trait property
         "author",           # see above
         "vaccine",          # vaccine info is stored as a "special" node prop
@@ -850,16 +845,6 @@ def transfer_mutations_to_branches(node_attrs, branch_attrs):
                     else:
                         branch_attrs[node_name]["labels"] = { "aa": aa_lab }
 
-def transfer_clade_annotation_to_branches(node_attrs, branch_attrs):
-    for node_name, raw_data in node_attrs.items():
-        if "clade_annotation" in raw_data and is_valid(raw_data["clade_annotation"]):
-            if node_name not in branch_attrs:
-                branch_attrs[node_name] = {}
-            if 'labels' in branch_attrs[node_name]:
-                branch_attrs[node_name]["labels"]['clade'] = raw_data["clade_annotation"]
-            else:
-                branch_attrs[node_name]["labels"] = { "clade": raw_data["clade_annotation"] }
-
 def transfer_branch_labels_to_branch_attrs(branch_labels, branch_attrs):
     for node_name, branch_labels in branch_labels.items():
         if node_name not in branch_attrs:
@@ -899,12 +884,11 @@ def parse_node_data_and_metadata(T, node_data_files, metadata_file):
                 node_attrs[name][corrected_key] = value
                 node_data_names.add(corrected_key)
 
-    # third pass: create `branch_attrs` which includes certain traits supplied in `node_attrs`
-    # (e.g. mutations are coverted to branch attrs, and `clade_annotation` is interpreted as a label)
+    # third pass: create `branch_attrs` which includes a few special-case traits from in `node_attrs`
+    # (e.g. mutations are coverted from node attrs to branch attrs)
     # as well as any branch labels supplied in node-data files.
     branch_attrs = {}
     transfer_mutations_to_branches(node_attrs, branch_attrs)
-    transfer_clade_annotation_to_branches(node_attrs, branch_attrs)
     transfer_branch_labels_to_branch_attrs(node_data.get('branch_labels', {}), branch_attrs)
 
     return (node_data, node_attrs, node_data_names, metadata_names, branch_attrs)

tests/functional/clades.t

@@ -0,0 +1,34 @@
+Integration tests for augur clades.
+
+  $ pushd "$TESTDIR" > /dev/null
+  $ export AUGUR="../../bin/augur"
+
+Run augur clades without --attribute-name. We expect the name to be "clade"
+
+  $ ${AUGUR} clades \
+  >  --tree clades/tree.nwk \
+  >  --clades clades/clades.tsv \
+  >  --mutations clades/nt_muts.json \
+  >  --output-node-data "$TMP/default.json" > /dev/null
+
+  $ python3 "$TESTDIR/../../scripts/diff_jsons.py"  "clades/expected-output-default.json" "$TMP/default.json"
+  {}
+
+Run augur clades with a custom --attribute-name
+
+  $ ${AUGUR} clades \
+  >  --tree clades/tree.nwk \
+  >  --clades clades/clades.tsv \
+  >  --mutations clades/nt_muts.json \
+  >  --attribute-name custom \
+  >  --output-node-data "$TMP/custom-attr.json" > /dev/null
+
+  $ python3 "$TESTDIR/../../scripts/diff_jsons.py"  "clades/expected-output-custom-attr.json" "$TMP/custom-attr.json"
+  {}
+
+# Ensure the only change between runs of `augur clades` is the attr name used
+  $ cat "$TMP/default.json" | sed "s/clade/custom/" > "$TMP/default-now-custom.json"
+  $ diff -u "$TMP/default-now-custom.json" "$TMP/custom-attr.json"
+
+Cleanup
+  $ rm -f "$TMP/default.json" "$TMP/custom-attr.json" "$TMP/default-now-custom.json"

tests/functional/clades/clades.tsv

@@ -0,0 +1,12 @@
+clade	gene	site	alt
+
+# the 1b mutation only once, on the branch leading to tips B and C
+# thus we expect the clade label to be on node `internalAB`
+cladeCB	nuc	1	B
+# the 2c mutation appears twice -- on branch `internalAB` and `internalDEF`
+# as the latter has 3 descendants, it is chosen over the former
+cladeDEF	nuc	2	C
+# mutation 3e appears only on a terminal node (tipE)
+# but we still expect both a branch label and a node_attr
+# this means that tipE should be annotated "cladeE" and _not_ "cladeDEF"
+cladeE	nuc	3	E

tests/functional/clades/expected-output-custom-attr.json

@@ -0,0 +1,40 @@
+{
+  "branch_labels": {
+    "internalBC": {
+      "custom": "cladeCB"
+    },
+    "internalDEF": {
+      "custom": "cladeDEF"
+    },
+    "tipE": {
+      "custom": "cladeE"
+    }
+  },
+  "generated_by": {
+    "program": "augur",
+    "version": "12.0.0"
+  },
+  "nodes": {
+    "internalBC": {
+      "custom": "cladeCB"
+    },
+    "internalDEF": {
+      "custom": "cladeDEF"
+    },
+    "tipB": {
+      "custom": "cladeCB"
+    },
+    "tipC": {
+      "custom": "cladeCB"
+    },
+    "tipD": {
+      "custom": "cladeDEF"
+    },
+    "tipE": {
+      "custom": "cladeE"
+    },
+    "tipF": {
+      "custom": "cladeDEF"
+    }
+  }
+}

tests/functional/clades/expected-output-default.json

@@ -0,0 +1,40 @@
+{
+  "branch_labels": {
+    "internalBC": {
+      "clade": "cladeCB"
+    },
+    "internalDEF": {
+      "clade": "cladeDEF"
+    },
+    "tipE": {
+      "clade": "cladeE"
+    }
+  },
+  "generated_by": {
+    "program": "augur",
+    "version": "12.0.0"
+  },
+  "nodes": {
+    "internalBC": {
+      "clade": "cladeCB"
+    },
+    "internalDEF": {
+      "clade": "cladeDEF"
+    },
+    "tipB": {
+      "clade": "cladeCB"
+    },
+    "tipC": {
+      "clade": "cladeCB"
+    },
+    "tipD": {
+      "clade": "cladeDEF"
+    },
+    "tipE": {
+      "clade": "cladeE"
+    },
+    "tipF": {
+      "clade": "cladeDEF"
+    }
+  }
+}

tests/functional/clades/nt_muts.json

@@ -0,0 +1,19 @@
+{
+  "nodes": {
+    "tipA": {"muts": [], "aa_muts": {}},
+    "tipB": {"muts": [], "aa_muts": {}},
+    "tipC": {"muts": [], "aa_muts": {}},
+    "tipD": {"muts": [], "aa_muts": {}},
+    "tipE": {"muts": ["A3E"], "aa_muts": {}},
+    "tipF": {"muts": [], "aa_muts": {}},
+    "internalBC": {
+      "muts": ["A1B", "A2C"],
+      "aa_muts": {}
+    },
+    "internalDEF": {
+      "muts": ["A2C"],
+      "aa_muts": {}
+    },
+    "ROOT":{"muts": [], "aa_muts": {}}
+  }
+}

tests/functional/clades/tree.nwk

@@ -0,0 +1 @@
+(tipA:1,(tipB:1,tipC:1)internalBC:2,(tipD:3,tipE:4,tipF:1)internalDEF:5)ROOT:1;