disable multiprocessing for read recruitment

mehrdadbakhtiari · Nov 6, 2019 · 55ee8cd · 55ee8cd
1 parent 2609062
commit 55ee8cd
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Showing 2 changed files with 4 additions and 13 deletions.
diff --git a/advntr/__main__.py b/advntr/__main__.py
@@ -76,7 +76,7 @@ def main():
                                        help='working directory for creating temporary files needed for computation')
     genotype_others_group.add_argument('-m', '--models', type=str, metavar='<file>', default=None,
                                        help='VNTR models file [%s]' % settings.ILLUMINA_DEFAULT_MODELS_FILE)
-    genotype_others_group.add_argument('-t', '--threads', type=int, metavar='<int>', default=4,
+    genotype_others_group.add_argument('-t', '--threads', type=int, metavar='<int>', default=1,
                                        help='number of threads [%(default)s]')
     genotype_others_group.add_argument('-u', '--update', action='store_true', default=False,
                                        help='set this flag to iteratively update the model')

diff --git a/advntr/vntr_finder.py b/advntr/vntr_finder.py
@@ -536,16 +536,12 @@ def iteratively_update_model(self, alignment_file, unmapped_filtered_reads, sele
     @time_usage
     def select_illumina_reads(self, alignment_file, unmapped_filtered_reads, update=False, hmm=None):
         recruitment_score = None
-        sema = Semaphore(settings.CORES)
-        manager = Manager()
-        selected_reads = manager.list()
+        selected_reads = []
         vntr_bp_in_unmapped_reads = Value('d', 0.0)
 
         number_of_reads = 0
         read_length = 150
 
-        process_list = []
-
         for read_segment in unmapped_filtered_reads:
             if number_of_reads == 0:
                 read_length = len(str(read_segment.seq))
@@ -558,13 +554,8 @@ def select_illumina_reads(self, alignment_file, unmapped_filtered_reads, update=
             if len(read_segment.seq) < read_length:
                 continue
 
-            sema.acquire()
-            p = Process(target=self.process_unmapped_read, args=(sema, str(read_segment.seq), hmm, recruitment_score,
-                                                                 vntr_bp_in_unmapped_reads, selected_reads))
-            process_list.append(p)
-            p.start()
-        for p in process_list:
-            p.join()
+            self.process_unmapped_read(None, str(read_segment.seq), hmm, recruitment_score, vntr_bp_in_unmapped_reads,
+                                       selected_reads)
 
         logging.debug('vntr base pairs in unmapped reads: %s' % vntr_bp_in_unmapped_reads.value)