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BU-ISCIII · Apr 1, 2024 · 7aea641 · 7aea641
1 parent 8817b27
commit 7aea641
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Showing 2 changed files with 32 additions and 32 deletions.
diff --git a/taranis/eval_cluster.py b/taranis/eval_cluster.py
@@ -173,9 +173,9 @@ def evaluate_clusters(
                         "alleles_not_found"
                     ]
                 if len(result_eval["alleles_not_in_cluster"]) > 0:
-                    evaluation_alleles[cluster_id]["alleles_not_in_cluster"] = (
-                        result_eval["alleles_not_in_cluster"]
-                    )
+                    evaluation_alleles[cluster_id][
+                        "alleles_not_in_cluster"
+                    ] = result_eval["alleles_not_in_cluster"]
             else:
                 evaluation_alleles[cluster_id]["result"] = "OK"
         return self.summary(evaluation_alleles)
diff --git a/taranis/seq_cluster.py b/taranis/seq_cluster.py
@@ -14,7 +14,6 @@
 
 
 class SeqCluster:
-
     @classmethod
     def __init__(cls, res_start, seed, is_verbose=True):
         cls._res_param_start = res_start
@@ -139,9 +138,9 @@ def _convert_cluster_ptrs(src_cluster_ptrs, last_seq_cluster_ptrs):
 
         for cluster_id in range(np.max(src_cluster_ptrs) + 1):
             src_cluster_ids = np.argwhere(src_cluster_ptrs == cluster_id).flatten()
-            output_seq_cluster_ptrs[np.isin(last_seq_cluster_ptrs, src_cluster_ids)] = (
-                cluster_id
-            )
+            output_seq_cluster_ptrs[
+                np.isin(last_seq_cluster_ptrs, src_cluster_ids)
+            ] = cluster_id
 
         return output_seq_cluster_ptrs
 
@@ -240,9 +239,9 @@ def _bin_src_clusters(
         ):
             if len(src_cluster_bins) == 0:
                 src_cluster_bins.append([src_cluster_id])
-                avg_intra_bin_edge_weights[str(src_cluster_id)] = (
-                    global_edge_weight_mtrx[src_cluster_id, src_cluster_id]
-                )
+                avg_intra_bin_edge_weights[
+                    str(src_cluster_id)
+                ] = global_edge_weight_mtrx[src_cluster_id, src_cluster_id]
                 continue
 
             best_bin = None
@@ -268,16 +267,16 @@ def _bin_src_clusters(
 
             if best_bin is None:
                 src_cluster_bins.append([src_cluster_id])
-                avg_intra_bin_edge_weights[str(src_cluster_id)] = (
-                    global_edge_weight_mtrx[src_cluster_id, src_cluster_id]
-                )
+                avg_intra_bin_edge_weights[
+                    str(src_cluster_id)
+                ] = global_edge_weight_mtrx[src_cluster_id, src_cluster_id]
             else:
                 del avg_intra_bin_edge_weights["-".join(map(str, best_bin))]
                 best_bin.append(src_cluster_id)
-                avg_intra_bin_edge_weights["-".join(map(str, best_bin))] = (
-                    cls._cal_cluster_avg_edge_weight(
-                        global_edge_weight_mtrx, src_cluster_edge_counts, best_bin
-                    )
+                avg_intra_bin_edge_weights[
+                    "-".join(map(str, best_bin))
+                ] = cls._cal_cluster_avg_edge_weight(
+                    global_edge_weight_mtrx, src_cluster_edge_counts, best_bin
                 )
 
         return list(map(np.array, src_cluster_bins)), avg_intra_bin_edge_weights
@@ -298,12 +297,12 @@ def _verify_clusters(
 
             for cluster_id in range(np.max(src_cluster_ptrs) + 1):
                 src_cluster_bool_ptrs = src_cluster_ptrs == cluster_id
-                avg_intra_super_cluster_edge_weights[cluster_id] = (
-                    cls._cal_cluster_avg_edge_weight(
-                        global_edge_weight_mtrx,
-                        src_cluster_edge_counts,
-                        src_cluster_bool_ptrs,
-                    )
+                avg_intra_super_cluster_edge_weights[
+                    cluster_id
+                ] = cls._cal_cluster_avg_edge_weight(
+                    global_edge_weight_mtrx,
+                    src_cluster_edge_counts,
+                    src_cluster_bool_ptrs,
                 )
         else:
             src_cluster_ptrs = np.full(candidate_src_cluster_ptrs.size, -1)
@@ -316,17 +315,18 @@ def _verify_clusters(
                 if src_cluster_ids.size == 1:
                     assigned_super_cluster_id = np.max(src_cluster_ptrs) + 1
                     src_cluster_ptrs[src_cluster_ids] = assigned_super_cluster_id
-                    avg_intra_super_cluster_edge_weights[assigned_super_cluster_id] = (
-                        global_edge_weight_mtrx[src_cluster_ids[0], src_cluster_ids[0]]
-                    )
+                    avg_intra_super_cluster_edge_weights[
+                        assigned_super_cluster_id
+                    ] = global_edge_weight_mtrx[src_cluster_ids[0], src_cluster_ids[0]]
                     continue
 
-                qual_src_cluster_bins, avg_intra_bin_edge_weights = (
-                    cls._bin_src_clusters(
-                        src_cluster_ids,
-                        global_edge_weight_mtrx,
-                        src_cluster_edge_counts,
-                    )
+                (
+                    qual_src_cluster_bins,
+                    avg_intra_bin_edge_weights,
+                ) = cls._bin_src_clusters(
+                    src_cluster_ids,
+                    global_edge_weight_mtrx,
+                    src_cluster_edge_counts,
                 )
 
                 assigned_super_cluster_ids = list()