core processes

marine.py

@@ -94,7 +94,7 @@ def get_suffix_pairs_from_bam_filepath(bam_filepaths):
     return suffix_pairs, suffix_pair_to_bam_filepath
 
 
-def prepare_combinations_for_split(df, bam_filepaths, output_folder, output_suffix, n_processes=4):
+def prepare_combinations_for_split(df, bam_filepaths, output_folder, output_suffix, processes=4):
     """
     Prepares the chromosome-suffix combinations for multiprocessing.
     For each position in a given barcode, we want to look at the coverage at that
@@ -105,7 +105,7 @@ def prepare_combinations_for_split(df, bam_filepaths, output_folder, output_suff
         bam_filepaths (list): List of processed BAM files to incorporate
         output_folder (str): Path to the output folder for split BED files.
         output_suffix (str): Suffix for output files.
-        n_processes (int): Number of processes for multiprocessing.
+        processes (int): Number of processes for multiprocessing.
 
     Returns:
         list: List of tuples for processing.
@@ -138,8 +138,8 @@ def prepare_combinations_for_split(df, bam_filepaths, output_folder, output_suff
             barcode_finding_tasks.append([chrom, prefix, suffix, bam_filepath, unique_positions, output_folder, output_suffix])
 
     # Get unique barcodes contained in each bam, using a multiprocessing pool for maximal core usage efficiency
-    print(f"Starting multiprocessing to figure out unique barcodes per bam, with {n_processes} processes...")
-    with Pool(n_processes) as pool:
+    print(f"Starting multiprocessing to figure out unique barcodes per bam, with {processes} processes...")
+    with Pool(processes) as pool:
         list_of_unique_barcodes_per_bam = pool.map(get_unique_barcodes_for_reads_in_bamfile, barcode_finding_tasks)
 
     # Make new task list for next step
@@ -261,7 +261,8 @@ def generate_and_split_bed_files_for_all_positions(output_folder, bam_filepaths,
         coverage_calc_sites_bed_df, 
         bam_filepaths, 
         split_bed_folder, 
-        output_suffix
+        output_suffix,
+        processes=processes
     )
 
     print("Pivoting edits dataframe into sparse h5ad files...")
@@ -275,7 +276,7 @@ def generate_and_split_bed_files_for_all_positions(output_folder, bam_filepaths,
             raise  # Properly re-raise the exception
 
     # Run the processing with multiprocessing
-    with Pool(processes=processes) as pool:
+    with Pool(processes=cores) as pool:
         pool.map(process_combination_for_split, combinations)
 
     print(f"\nAll split BED files generated in {output_folder}/combined_{output_suffix}_split_by_suffix\n")
@@ -464,8 +465,8 @@ def run(bam_filepath, annotation_bedfile_path, output_folder, contigs=[], strand
             output_folder,
             bam_filepaths, 
             tabulation_bed=tabulation_bed,
-            processes=cores, 
-            output_suffix=output_suffix
+            output_suffix=output_suffix,
+            processes=cores
         )
 
         make_depth_command_script_single_cell(

tests/integration_tests_auto_check.py

@@ -366,13 +366,6 @@
     print("\n\t ~~~ single cell vs bulk modes on sc dataset equivalency test FAILED! ~~~\n")
     failures += 1
 
-# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-#     Check that the coverage and edit matrices are correct
-# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-print("\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n")
-print("Checking that the position X barcode coverage and edit h5ad sparse matrices are correct and contain the same information as the flat tsv final sites.")
-
-test_folder = 'singlecell_tests/only_5_cells_all_cells_coverage_test/'
 
 def get_all_edited_positions_and_barcodes(test_folder):
     name_to_obs = {}
@@ -422,7 +415,16 @@ def get_all_edited_positions_and_barcodes(test_folder):
 
     return edited_pos, covered_pos, edited_obs, covered_obs, \
     final_filtered_site_info, name_to_pos, name_to_obs, name_to_adata
-
+
+
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+#     Check that the coverage and edit matrices are correct
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+print("\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n")
+print("Checking that the position X barcode coverage and edit h5ad sparse matrices are correct and contain the same information as the flat tsv final sites.")
+
+test_folder = 'singlecell_tests/only_5_cells_all_cells_coverage_test/'
+
 edited_pos, covered_pos, edited_obs, covered_obs, final_filtered_site_info,\
 name_to_pos, name_to_obs, name_to_adata = get_all_edited_positions_and_barcodes(test_folder)