added trace to have a n idea of the time needed to retrieve the number of...

added trace to have a n idea of the time needed to retrieve the number of reacors in the input fastq file

phagetermvirome/IData_handling.py

@@ -6,7 +6,8 @@ from __future__ import print_function
 import gzip
 from utilities import reverseComplement,changeCase
 from time import gmtime, strftime
-import datetime
+import io
+import time # temporary : just to make an idea of the time we spend getting a chunk of reads or getting the number of lines in the file.
 
 try:
     import cPickle as pickle
@@ -284,7 +285,9 @@ class ReadGetter:
 ### READS Functions
 def totReads(filin):
     """Verify and retrieve the number of reads in the fastq file before alignment"""
+    start_t=time.perf_counter_ns()
     if filin.endswith('.gz'):
+        print(io.DEFAULT_BUFFER_SIZE)
         filein = gzip.open(filin, 'rb')
     else:
         filein = open(filin, 'r')
@@ -294,6 +297,11 @@ def totReads(filin):
         line += 1
     seq = float(round(line / 4))
     filein.close()
+    end_t = time.perf_counter_ns()
+    d=end_t-start_t
+    d=d/1000000000
+    d=d//60
+    print("spent ", d," minutes to get the number of reads from input file")
     return seq
 
 ### SEQUENCE parsing function