fix(ids): Fix the case where canonical IDs are not supplied.

Author: aaronmussig

.gitignore

@@ -154,3 +154,4 @@ node_modules/
 docs/*.rst
 !docs/index.rst
 
+/test

gtdb_itol_decorate/__main__.py

@@ -7,21 +7,27 @@
 from gtdb_itol_decorate.itol import get_phylum_colours, write_color_datastrip, \
     get_internal_nodes_with_labels, write_internal_node_labels, write_tree_colours, write_collapse_file, \
     write_popup_file
-from gtdb_itol_decorate.newick import load_newick_to_tree, validate_dendropy_namespace, \
+from gtdb_itol_decorate.newick import load_newick_to_tree, assert_no_duplicate_taxa, \
     get_canonical_mapping, validate_sets, strip_tree_labels, set_node_desc_taxa, set_taxon_label_for_internal_nodes
 from gtdb_itol_decorate.util import log
 
 
 def main(tree_path: Path, tax_path: Path, out_dir: Path):
+
+    # Create the output directory
     log(f'Creating output directory: {out_dir}')
     out_dir.mkdir(exist_ok=True)
 
+    # Read and validate the tree
     log(f'Reading tree from: {tree_path}')
     tree = load_newick_to_tree(str(tree_path))
     log(f'Found {len(tree.leaf_nodes()):,} leaf nodes in the tree.')
-    validate_dendropy_namespace((x.label for x in tree.taxon_namespace))
+    assert_no_duplicate_taxa((x.label for x in tree.taxon_namespace))
+
+    # Create a mapping from the canonical genome ID to the tree
     d_canonical_to_gid = get_canonical_mapping((x.label for x in tree.taxon_namespace))
 
+    # Read and validate the taxonomy file
     log(f'Reading taxonomy from: {tax_path}')
     d_tax = load_taxonomy_file(str(tax_path), set(d_canonical_to_gid.keys()))
     log(f'Read the taxonomy for {len(d_tax):,} genomes.')

gtdb_itol_decorate/gtdb.py

@@ -15,7 +15,7 @@ def load_taxonomy_file(path: str, limit_to_gids: set):
     with open(path) as f:
         for line in f.readlines():
             gid, tax = line.strip().split('\t')
-            gid = canonical_gid(gid)
+            # gid = canonical_gid(gid)
             if gid not in limit_to_gids:
                 continue
             if gid in out:

gtdb_itol_decorate/newick.py

@@ -1,3 +1,5 @@
+import sys
+
 from collections import Counter, deque, defaultdict
 
 import dendropy
@@ -27,7 +29,7 @@ def load_newick_to_tree(path: str) -> dendropy.Tree:
                                          preserve_underscores=True)
 
 
-def validate_dendropy_namespace(taxa):
+def assert_no_duplicate_taxa(taxa):
     taxa_count = Counter(taxa)
     duplicates = {k: v for k, v in taxa_count.items() if v > 1}
     if len(duplicates) > 0:
@@ -48,7 +50,8 @@ def get_lca_str(node: dendropy.Node):
 def get_canonical_mapping(gids):
     out = dict()
     for gid in gids:
-        out[canonical_gid(gid)] = gid
+        out[gid] = gid
+        # out[canonical_gid(gid)] = gid
     return out