diff FilterUncorrectabledPEfastq.py @ 1:6703b98884a2 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit 65ada0f9589f3ffebad1db6636ccb50d58082606"
author iuc
date Thu, 26 Dec 2019 05:21:50 -0500
parents 9a0b65ad3c84
children
line wrap: on
line diff
--- a/FilterUncorrectabledPEfastq.py	Thu Sep 13 07:00:00 2018 -0400
+++ b/FilterUncorrectabledPEfastq.py	Thu Dec 26 05:21:50 2019 -0500
@@ -16,11 +16,9 @@
 or gzipped files on the fly, so long as the gzipped files end with 'gz'.
 """
 
-# import sys
 import argparse
 import gzip
-from itertools import izip_longest
-# izip
+from itertools import zip_longest
 from os.path import basename
 
 
@@ -38,7 +36,7 @@
     "Collect data into fixed-length chunks or blocks"
     # grouper('ABCDEFG', 3, 'x') --> ABC DEF Gxx
     args = [iter(iterable)] * n
-    return izip_longest(fillvalue=fillvalue, * args)
+    return zip_longest(fillvalue=fillvalue, * args)
 
 
 if __name__ == "__main__":
@@ -61,9 +59,9 @@
         for entry in R1:
             counter += 1
             if counter % 100000 == 0:
-                print "%s reads processed" % counter
+                print("%s reads processed" % counter)
             head1, seq1, placeholder1, qual1 = [i.strip() for i in entry]
-            head2, seq2, placeholder2, qual2 = [j.strip() for j in R2.next()]
+            head2, seq2, placeholder2, qual2 = [j.strip() for j in next(R2)]
             if 'unfixable' in head1 or 'unfixable' in head2:
                 unfix_count += 1
             else: