final code to find CNV with multithreading

CNV/test_final_multithreading.py

@@ -2,10 +2,13 @@ import pysam
 import concurrent.futures
 import sys
 import getopt
+import logging
+
 
 #Options
+output_file = ""
 try:
-    opts, args = getopt.getopt(sys.argv[1:], 'b:w:s:t:o:e')
+    opts, args = getopt.getopt(sys.argv[1:], 'b:w:s:t:o:e:')
     for opt, arg in opts:
         if opt in ("-b"):
             bamfile = arg
@@ -16,15 +19,18 @@ try:
         if opt in ("-t"):
             num_threads = int(arg)
         if opt in ("-o"):
-            output_file = open(arg, "w")
-        if opt in ("-e") :
-            logfile = open(arg, "w")
+            output_file = open(arg, "a")
+        if opt in ("-e"):
+            logfile = arg
 except getopt.GetoptError:
     print('Invalid argument')
     sys.exit(1)
     
-def calcul_depth_seq(bamfile, seq, window_size, step_size):
+logging.basicConfig(filename =  '%s' % (logfile), filemode = 'a', level = logging.INFO, format = '%(asctime)s %(levelname)s - %(message)s')
+logging.info('start')
 
+def calcul_depth_seq(bamfile, seq, window_size, step_size, numero_de_thread):
+    sys.stderr.write("\t entering calcul_depth_seq : thread numero %s\n" % numero_de_thread)
     samfile = pysam.AlignmentFile(bamfile, "rb")
     seq_length = samfile.lengths[samfile.references.index(seq)] #Permet d'obtenir la longueur de la sequence
 
@@ -36,30 +42,31 @@ def calcul_depth_seq(bamfile, seq, window_size, step_size):
             window_depths.append(pileupcolumn.n)#ajoute le nb de lecture couvrant cette position à la liste window_depths
 
         if window_depths:#calcul la profondeur moyenne pour chaque sequence
+            sys.stderr.write("\t\t entering wd thread numero %s\n" % numero_de_thread)
             avg_depth = sum(window_depths) / len(window_depths)
-            print(f"{seq}:{pos_start}-{pos_end}: {avg_depth}")
+            sys.stdout.write(f"{seq}:{pos_start}-{pos_end}: {avg_depth}\n")            
+            output_file.write(f"{seq}:{pos_start}-{pos_end}: {avg_depth}\n")
            
-    samfile.close()
+    sys.stderr.write("\t leaving calcul_depth_seq thread numero %s\n" % numero_de_thread)
     
 def calcul_depth_all(bamfile, window_size, step_size, num_threads):
+    sys.stderr.write("entering calcul_depth_all \n")
     samfile=pysam.AlignmentFile(bamfile, "rb")
     
     with concurrent.futures.ThreadPoolExecutor(max_workers = num_threads) as executor:
         futures = [] #liste pour stocker les futures
-    
+        n=0
         for seq in samfile.references:
-            future = executor.submit(calcul_depth_seq, bamfile, seq, window_size, step_size)
+            n+=1
+            future = executor.submit(calcul_depth_seq, bamfile, seq, window_size, step_size, n)
             futures.append(future)
             
         concurrent.futures.wait(futures)
         
         samfile.close()
 
-if output_file != sys.stdout:
-    output_file.close()
-
-if logfile:
-    logfile.close()
+#if output_file != sys.stdout:
+ #   output_file.close()
 
 #Programme principal
 if len(sys.argv) <2 or bamfile is None:
@@ -68,3 +75,5 @@ if len(sys.argv) <2 or bamfile is None:
 
 bamfile_path = bamfile
 calcul_depth_all(bamfile_path, window_size, step_size, num_threads)
+logging.info('end')
+samfile.close()