more styling

Author: Yenaled

kb_python/count.py

@@ -1780,7 +1780,9 @@ def update_results_with_suffix(current_results, new_results, suffix):
             if f'bus{suffix}' in unfiltered_results:
                 bus_files_to_delete.append(unfiltered_results[f'bus{suffix}'])
             if f'bus_scs{suffix}' in unfiltered_results:
-                bus_files_to_delete.append(unfiltered_results[f'bus_scs{suffix}'])
+                bus_files_to_delete.append(
+                    unfiltered_results[f'bus_scs{suffix}']
+                )
 
         # Delete filtered bus if exists
         if 'filtered' in results and 'bus_scs' in results['filtered']:
@@ -2189,9 +2191,13 @@ def update_results_with_suffix(current_results, new_results, suffix):
                         elif i == 1:  # unprocessed/unspliced
                             cr_dir = os.path.join(counts_dir, 'unspliced')
                         else:  # ambiguous
-                            cr_dir = os.path.join(counts_dir, f'{CELLRANGER_DIR}_{prefix}{suffix}')
+                            cr_dir = os.path.join(
+                                counts_dir, f'{CELLRANGER_DIR}_{prefix}{suffix}'
+                            )
                     else:
-                        cr_dir = os.path.join(counts_dir, f'{CELLRANGER_DIR}_{prefix}{suffix}')
+                        cr_dir = os.path.join(
+                            counts_dir, f'{CELLRANGER_DIR}_{prefix}{suffix}'
+                        )
 
                     cr_result = matrix_to_cellranger(
                         count_result[i]['mtx'],
@@ -2235,7 +2241,10 @@ def update_results_with_suffix(current_results, new_results, suffix):
                     update_results_with_suffix(prefix_results, res, suffix)
                     if cellranger:
                         cr_result = matrix_to_cellranger(
-                            res['mtx'], res['barcodes'], res['genes'], t2g_path,
+                            res['mtx'],
+                            res['barcodes'],
+                            res['genes'],
+                            t2g_path,
                             os.path.join(
                                 counts_dir, f'{CELLRANGER_DIR}_{prefix}{suffix}'
                             ),
@@ -2376,13 +2385,14 @@ def update_results_with_suffix(current_results, new_results, suffix):
                             )
                     else:
                         cr_dir = os.path.join(
-                            filtered_counts_dir,
-                            f'{CELLRANGER_DIR}_{prefix}'
+                            filtered_counts_dir, f'{CELLRANGER_DIR}_{prefix}'
                         )
 
                     cr_result = matrix_to_cellranger(
-                        count_result[i]['mtx'], count_result[i]['barcodes'],
-                        count_result[i]['genes'], t2g_path,
+                        count_result[i]['mtx'],
+                        count_result[i]['barcodes'],
+                        count_result[i]['genes'],
+                        t2g_path,
                         cr_dir,
                         gzip=gzip
                     )
@@ -2871,10 +2881,8 @@ def count_velocity(
                 if cellranger:
                     if not tcc:
                         cr_result = matrix_to_cellranger(
-                            count_result['mtx'],
-                            count_result['barcodes'],
-                            count_result['genes'],
-                            t2g_path,
+                            count_result['mtx'], count_result['barcodes'],
+                            count_result['genes'], t2g_path,
                             os.path.join(
                                 filtered_counts_dir,
                                 f'{CELLRANGER_DIR}_{prefix}'

kb_python/utils.py

@@ -872,7 +872,11 @@ def do_sum_matrices(
                         "Summing up two matrix files failed: Assertion failed"
                     )
 
-                if to_write and to_write[0] == nums[0] and to_write[1] == nums[1]:
+                if (
+                    to_write
+                    and to_write[0] == nums[0]
+                    and to_write[1] == nums[1]
+                ):
                     to_write[2] += nums[2]
                 else:
                     if to_write:

tests/test_count.py

@@ -2254,7 +2254,7 @@ def test_count_kite_filter(self):
                 counts_prefix=os.path.join(
                     out_dir, FILTERED_COUNTS_DIR, FEATURE_PREFIX
                 ),
-                kite=False,
+                kite=True,
                 tcc=False,
                 temp_dir=temp_dir,
                 threads=threads,