Mercurial > repos > iuc > rcorrector
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 |
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--- 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: