fix notebook & code

dib-lab · Nov 3, 2023 · 15fe101 · 15fe101
1 parent b80722c
commit 15fe101
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Showing 2 changed files with 6 additions and 3 deletions.
diff --git a/charcoal/contigs_list_contaminants.py b/charcoal/contigs_list_contaminants.py
@@ -131,7 +131,10 @@ def main(args):
         ident = get_ident(ss)
         lineage = tax_assign[ident]
 
-        lca_db.insert(ss, ident=ident)
+        try:
+            lca_db.insert(ss, ident=ident)
+        except ValueError:
+            continue
         lin_db.insert(ident, lineage)
 
     print(f'loaded {len(siglist)} signatures & created LCA Database')

diff --git a/charcoal/notebooks/report-genome.ipynb b/charcoal/notebooks/report-genome.ipynb
@@ -39,7 +39,7 @@
     "\n",
     "import plotly.graph_objects as go\n",
     "\n",
-    "import sourmash\n",
+    "import sourmash, sourmash.lca.lca_utils\n",
     "from charcoal import utils\n",
     "from charcoal.figs.sourmash_sankey import GenomeSankeyFlow"
    ]
@@ -335,7 +335,7 @@
     "    if genome_lineage[-1].rank != 'genus':\n",
     "        genome_lineage = list(genome_lineage)\n",
     "        for rank in taxlist[len(genome_lineage):]:\n",
-    "            genome_lineage.append(sourmash.lca.LineagePair(rank=rank, name='unassigned'))\n",
+    "            genome_lineage.append(sourmash.lca.lca_utils.LineagePair(rank=rank, name='unassigned'))\n",
     "    \n",
     "    # set the color of the main lineage\n",
     "    genome_lineage = tuple(genome_lineage)\n",