# HG changeset patch
# User iuc
# Date 1577355710 18000
# Node ID 6703b98884a22dbef573e7a9acc73bbe4d4c3a59
# Parent 9a0b65ad3c84e55a6fe62e04081c817f6deab702
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit 65ada0f9589f3ffebad1db6636ccb50d58082606"
diff -r 9a0b65ad3c84 -r 6703b98884a2 FilterUncorrectabledPEfastq.py
--- 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:
diff -r 9a0b65ad3c84 -r 6703b98884a2 rcorrector.xml
--- a/rcorrector.xml Thu Sep 13 07:00:00 2018 -0400
+++ b/rcorrector.xml Thu Dec 26 05:21:50 2019 -0500
@@ -1,136 +1,137 @@
-
- a kmer-based error correction method for RNA-seq data
-
- rcorrector
-
- &1 > rmunfixable.log && cat rmunfixable.log
- #end if
- #end if
- ]]>
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- library['lib'] == 'single'
-
-
- library['lib'] == 'paired' and library['filter'] is False
-
-
- library['lib'] == 'paired' and library['filter'] is False
-
-
- library['lib'] == 'paired' and library['filter']
-
-
- library['lib'] == 'paired' and library['filter']
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- 10.1186/s13742-015-0089-y
-
- @misc{githubFilterUncorrectabledPEfastq,
- author = {Adam H. Freedman},
- year = {2016},
- title = {FilterUncorrectabledPEfastq},
- publisher = {GitHub},
- journal = {GitHub repository},
- url = {https://github.com/harvardinformatics/TranscriptomeAssemblyTools/blob/master/FilterUncorrectabledPEfastq.py}
- }
-
-
-
+
+ a kmer-based error correction method for RNA-seq data
+
+ rcorrector
+ python
+
+ &1 > rmunfixable.log && cat rmunfixable.log
+ #end if
+ #end if
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ library['lib'] == 'single'
+
+
+ library['lib'] == 'paired' and library['filter'] is False
+
+
+ library['lib'] == 'paired' and library['filter'] is False
+
+
+ library['lib'] == 'paired' and library['filter']
+
+
+ library['lib'] == 'paired' and library['filter']
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 10.1186/s13742-015-0089-y
+
+ @misc{githubFilterUncorrectabledPEfastq,
+ author = {Adam H. Freedman},
+ year = {2016},
+ title = {FilterUncorrectabledPEfastq},
+ publisher = {GitHub},
+ journal = {GitHub repository},
+ url = {https://github.com/harvardinformatics/TranscriptomeAssemblyTools/blob/master/FilterUncorrectabledPEfastq.py}
+ }
+
+
+