linting

make_prg/utils/seq_utils.py

@@ -250,7 +250,9 @@ def generate_random_seed(sequences: List[str]) -> bytes:
 def get_consensus_residue(position: int, sequences: List[str]) -> str:
     # Count the residues at this position, ignoring gaps and Ns
     pos_counts = Counter(
-        seq[position] for seq in sequences if seq[position] != GAP and seq[position] != "N"
+        seq[position]
+        for seq in sequences
+        if seq[position] != GAP and seq[position] != "N"
     )
 
     # If there are no residues other than gaps and Ns at this position, use a random base
@@ -283,4 +285,3 @@ def get_majority_consensus_from_MSA(alignment: MSA) -> str:
         consensus += get_consensus_residue(i, all_seqs)
 
     return consensus
-

tests/utils/test_seq_utils.py

@@ -596,9 +596,7 @@ def test___get_majority_consensus_from_MSA___empty_alignment(self):
     def test___get_majority_consensus_from_MSA___all_Ns(self):
         consensus = get_majority_consensus_from_MSA(self.all_N_alignment)
         for char in consensus:
-            self.assertIn(
-                char, "ACGT"
-            )
+            self.assertIn(char, "ACGT")
 
     def test___get_majority_consensus_from_MSA___one_N_one_base(self):
         consensus = get_majority_consensus_from_MSA(self.one_N_one_base_alignment)
@@ -624,7 +622,8 @@ def test___get_majority_consensus_from_MSA___lower_case_sample_alignment(self):
             consensus, "ACGT"
         )  # The consensus should be the most common base at each position
 
-
     def test___get_majority_consensus_from_MSA___equally_likely_bases(self):
         consensus = get_majority_consensus_from_MSA(self.equally_likely_bases)
-        self.assertEqual(set(consensus), {'A', 'C'})  # A and C should be chosen at random
+        self.assertEqual(
+            set(consensus), {"A", "C"}
+        )  # A and C should be chosen at random