refactor(updating random.sample to avoid deprecation):

Ecogenomics · Apr 16, 2024 · 501aacc · 501aacc
1 parent 47b5671
commit 501aacc
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Showing 3 changed files with 3 additions and 3 deletions.
diff --git a/gtdbtk/classify.py b/gtdbtk/classify.py
@@ -2188,7 +2188,7 @@ def root_with_outgroup(self, input_tree, taxonomy, outgroup_taxa):
 
         leaves_in_tree = sum([1 for _ in new_tree.leaf_node_iter()])
         while True:
-            rnd_ingroup_leaf = random.sample(ingroup_in_tree, 1)[0]
+            rnd_ingroup_leaf = random.sample(tuple(ingroup_in_tree), 1)[0]
             new_tree.reroot_at_edge(rnd_ingroup_leaf.edge,
                                     length1=0.5 * rnd_ingroup_leaf.edge_length,
                                     length2=0.5 * rnd_ingroup_leaf.edge_length)

diff --git a/gtdbtk/reroot_tree.py b/gtdbtk/reroot_tree.py
@@ -80,7 +80,7 @@ def root_with_outgroup(self, input_tree: str, output_tree: str, outgroup: Set[st
         mrca = tree.mrca(taxa=outgroup_in_tree)
         mrca_leaves = len(mrca.leaf_nodes())
         while True:
-            rnd_ingroup = random.sample(ingroup_leaves, 1)[0]
+            rnd_ingroup = random.sample(tuple(ingroup_leaves), 1)[0]
             tree.reroot_at_edge(rnd_ingroup.edge,
                                 length1=0.5 * rnd_ingroup.edge_length,
                                 length2=0.5 * rnd_ingroup.edge_length)

diff --git a/gtdbtk/trim_msa.py b/gtdbtk/trim_msa.py
@@ -241,7 +241,7 @@ def subsample_msa(self, seqs, markers):
                 lack_cols_marker_ids.append(marker_id)
 
             offset_valid_cols = [i + start for i in valid_cols]
-            sel_cols = random.sample(offset_valid_cols, min(
+            sel_cols = random.sample(tuple(offset_valid_cols), min(
                 self.subset, len(offset_valid_cols)))
             sampled_cols.extend(sel_cols)