update

Bio/GenBank/__init__.py

@@ -233,13 +233,12 @@ class _BaseGenBankConsumer:
         else:
             tax_info = taxonomy_string
         tax_list = tax_info.split(";")
-        new_tax_list = []
-        for tax_item in tax_list:
-            new_items = tax_item.split("\n")
-            new_tax_list.extend(new_items)
-        while "" in new_tax_list:
-            new_tax_list.remove("")
-        return [x.strip() for x in new_tax_list]
+        return [
+            item.strip()
+            for tax_item in tax_list
+            for item in tax_item.split("\n")
+            if item
+        ]
 
     @staticmethod
     def _clean_location(location_string):

Bio/Graphics/BasicChromosome.py

@@ -324,11 +324,11 @@ class Chromosome(_ChromosomeComponent):
             self.end_x_position - self.start_x_position - segment_width
         )
 
-        y_limits = []
-        for sub_component in self._sub_components:
-            y_limits.extend(
-                (sub_component.start_y_position, sub_component.end_y_position)
-            )
+        y_limits = [
+            limit
+            for sub_component in self._sub_components
+            for limit in (sub_component.start_y_position, sub_component.end_y_position)
+        ]
         y_min = min(y_limits)
         y_max = max(y_limits)
         del y_limits

Bio/Nexus/Nexus.py

@@ -593,9 +593,7 @@ class Commandline:
                         for n in range(len(options))
                         if options[n] == "=" and n != 0 and n != len(options)
                     ]
-                    indices = []
-                    for sl in valued_indices:
-                        indices.extend(sl)
+                    indices = [index for sl in valued_indices for index in sl]
                     token_indices = [n for n in range(len(options)) if n not in indices]
                     for opt in valued_indices:
                         # self.options[options[opt[0]].lower()] = options[opt[2]].lower()

Bio/PDB/internal_coords.py

@@ -1034,11 +1034,8 @@ class IC_Chain:
                 self.initNCaCs.append(tuple(initNCaC))
 
             # next residue NCaCKeys so can do per-residue assemble()
-            ric.NCaCKey = []
-            ric.NCaCKey.extend(
-                ric.split_akl(
-                    (AtomKey(ric, "N"), AtomKey(ric, "CA"), AtomKey(ric, "C"))
-                )
+            ric.NCaCKey = ric.split_akl(
+                (AtomKey(ric, "N"), AtomKey(ric, "CA"), AtomKey(ric, "C"))
             )
             ric._link_dihedra()
 
@@ -2709,11 +2706,8 @@ class IC_Residue:
             self._build_rak_cache()
 
         # initialise NCaCKey here:
-        self.NCaCKey = []
-        self.NCaCKey.extend(
-            self.split_akl(
-                (AtomKey(self, "N"), AtomKey(self, "CA"), AtomKey(self, "C"))
-            )
+        self.NCaCKey = self.split_akl(
+            (AtomKey(self, "N"), AtomKey(self, "CA"), AtomKey(self, "C"))
         )
 
     def set_flexible(self) -> None:

Bio/Phylo/Consensus.py

@@ -274,7 +274,7 @@ def strict_consensus(trees):
 def majority_consensus(trees, cutoff=0):
     """Search majority rule consensus tree from multiple trees.
 
-    This is a extend majority rule method, which means the you can set any
+    This is an extend majority rule method, which means the you can set any
     cutoff between 0 ~ 1 instead of 0.5. The default value of cutoff is 0 to
     create a relaxed binary consensus tree in any condition (as long as one of
     the provided trees is a binary tree). The branch length of each consensus