Fix conflicts

BigDataBiology · Feb 26, 2024 · fe52862 · fe52862
1 parent 2f8d572
commit fe52862
Showing 1 changed file with 2 additions and 40 deletions.
diff --git a/SemiBin/main.py b/SemiBin/main.py
@@ -773,43 +773,6 @@ def generate_sequence_features_single(logger, contig_fasta,
         logger.info('We will only calculate k-mer features.')
 
     if not only_kmer:
-        n_sample = len(bams)
-        is_combined = n_sample >= 5
-        bam_list = bams
-
-        logger.info('Calculating coverage for every sample.')
-
-        with Pool(min(num_process, len(bams))) as pool:
-            results = [
-                pool.apply_async(
-                    generate_cov,
-                    args=(
-                        bam_file,
-                        bam_index,
-                        output,
-                        must_link_threshold,
-                        is_combined,
-                        binned_length,
-                        logger,
-                        None
-                    ))
-                for bam_index, bam_file in enumerate(bams)]
-            for r in results:
-                s = r.get()
-                logger.info(f'Processed: {s}')
-
-        for bam_index, bam_file in enumerate(bams):
-            if not os.path.exists(os.path.join(output, '{}_data_cov.csv'.format(
-                    os.path.split(bam_file)[-1] + '_{}'.format(bam_index)))):
-                sys.stderr.write(
-                    f"Error: Generating coverage file fail\n")
-                sys.exit(1)
-            if is_combined:
-                if not os.path.exists(os.path.join(output, '{}_data_split_cov.csv'.format(
-                        os.path.split(bam_file)[-1] + '_{}'.format(bam_index)))):
-                    sys.stderr.write(
-                        f"Error: Generating coverage file fail\n")
-                    sys.exit(1)
 
         logger.debug('Start generating kmer features from fasta file.')
         kmer_whole = generate_kmer_features_from_fasta(
@@ -823,7 +786,7 @@ def generate_sequence_features_single(logger, contig_fasta,
             bam_list = bams
             logger.info('Calculating coverage for every sample.')
 
-            with Pool(num_process if num_process != 0 else None) as pool:
+            with Pool(min(num_process, len(bams))) as pool:
                 results = [
                     pool.apply_async(
                         generate_cov,
@@ -960,9 +923,8 @@ def fasta_sample_iter(fn):
                                         os.path.join(args.output, f'samples/{sample}.fa'),
                                         args.ratio)
 
-
     if args.bams:
-        with Pool(args.num_process if args.num_process != 0 else None) as pool:
+        with Pool(min(args.num_process, len(args.bams))) as pool:
             results = [
                 pool.apply_async(
                             generate_cov,