Removing references to coord col

Roth-Lab · Nov 23, 2024 · 20b8a57 · 20b8a57
1 parent cbf1e9d
commit 20b8a57
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/phyclone/data/cluster_outlier_probabilities.py b/phyclone/data/cluster_outlier_probabilities.py
@@ -73,7 +73,7 @@ def _finalize_loss_prob_on_cluster_df(cluster_df, high_loss_prob, lost_clusters,
         print(
             "{num} potentially lost/outlier cluster{pl} identified,"
             " setting {pos} prior loss prob to {pr}."
-            "\nRemaining cluster(s) will have a prior loss prob of {prl}.".format(
+            "\nRemaining cluster(s) will use a prior loss prob of {prl}.".format(
                 num=len(lost_clusters), pl=pluralize, pr=high_loss_prob, pos=possessive, prl=low_loss_prob
             )
         )
@@ -86,7 +86,7 @@ def _finalize_loss_prob_on_cluster_df(cluster_df, high_loss_prob, lost_clusters,
 
 
 def _get_truncal_chrom_arr(df, truncal_cluster):
-    df = df[["cluster_id", "chrom", "coord", "mutation_id"]].drop_duplicates()
+    df = df[["cluster_id", "chrom", "mutation_id"]].drop_duplicates()
     df = df.loc[df["cluster_id"] == truncal_cluster]
     truncal_dists = list()
     grouped = df.groupby("chrom", sort=False)

diff --git a/phyclone/data/pyclone.py b/phyclone/data/pyclone.py
@@ -123,7 +123,7 @@ def _setup_cluster_df(
             if "chrom" not in cluster_df.columns:
                 data_df = pd.read_table(data_file)
                 if "chrom" in data_df.columns:
-                    data_df = data_df[["mutation_id", "chrom", "coord"]]
+                    data_df = data_df[["mutation_id", "chrom"]]
                     cluster_df = pd.merge(cluster_df, data_df, how="inner", on=["mutation_id"])
                     cluster_df = cluster_df.drop_duplicates()
                 else: