ruff and remove placeholder

NationalGenomicsInfrastructure · May 28, 2024 · 1fd03e4 · 1fd03e4
1 parent df1662f
commit 1fd03e4
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Showing 4 changed files with 9 additions and 28 deletions.
diff --git a/anglerfish/demux/adaptor.py b/anglerfish/demux/adaptor.py
@@ -139,7 +139,9 @@ def get_mask(self, insert_Ns: bool = True) -> str:
         insert_Ns = True  -> Returns the sequence with index and UMI tokens replaced with Ns of the correct length
         insert_Ns = False -> Returns the sequence without index and UMI tokens
         """
-        index_length = len(self.index_seq) if self.index_seq is not None and insert_Ns else 0
+        index_length = (
+            len(self.index_seq) if self.index_seq is not None and insert_Ns else 0
+        )
         umi_length = (
             max(self.len_umi_after_index, self.len_umi_before_index) if insert_Ns else 0
         )

diff --git a/anglerfish/demux/kladd.py b/anglerfish/demux/kladd.py
diff --git a/anglerfish/demux/samplesheet.py b/anglerfish/demux/samplesheet.py
@@ -125,7 +125,9 @@ def minimum_bc_distance(self) -> int:
             testset[ont_barcode] = []
             for adaptor in adaptors:
                 if adaptor.i5.has_index:
-                    testset[ont_barcode].append(adaptor.i5.index_seq + adaptor.i7.index_seq)
+                    testset[ont_barcode].append(
+                        adaptor.i5.index_seq + adaptor.i7.index_seq
+                    )
                 else:
                     testset[ont_barcode].append(adaptor.i7.index_seq)
 

diff --git a/anglerfish/explore/explore.py b/anglerfish/explore/explore.py
@@ -106,12 +106,8 @@ def run_explore(
         ):
             if adaptor_end.has_index:
                 # Alignment thresholds
-                before_thres = round(
-                    adaptor_end.len_before_index * good_hit_threshold
-                )
-                after_thres = round(
-                    adaptor_end.len_after_index * good_hit_threshold
-                )
+                before_thres = round(adaptor_end.len_before_index * good_hit_threshold)
+                after_thres = round(adaptor_end.len_after_index * good_hit_threshold)
                 insert_thres_low = insert_thres_low
                 insert_thres_high = insert_thres_high
 
@@ -139,10 +135,7 @@ def run_explore(
                 )
 
                 thres = round(
-                    (
-                        adaptor_end.len_before_index
-                        + adaptor_end.len_after_index
-                    )
+                    (adaptor_end.len_before_index + adaptor_end.len_after_index)
                     * good_hit_threshold
                 )
                 df_good_hits = df_good_hits[df_good_hits["match_1_len"] >= thres]