Mercurial > repos > peterjc > fastq_pair_names
changeset 6:7df3a874f232 draft
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names commit 37d5b47ec23e2cbaa453cc660bb1fcbb10dd34ee-dirty
| author | peterjc |
|---|---|
| date | Wed, 17 May 2017 11:17:25 -0400 |
| parents | 73b6d81cda48 |
| children | 1b064e96cb50 |
| files | tools/fastq_pair_names/README.rst tools/fastq_pair_names/fastq_pair_names.py tools/fastq_pair_names/fastq_pair_names.xml |
| diffstat | 3 files changed, 10 insertions(+), 7 deletions(-) [+] |
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--- a/tools/fastq_pair_names/README.rst Thu May 11 18:34:08 2017 -0400 +++ b/tools/fastq_pair_names/README.rst Wed May 17 11:17:25 2017 -0400 @@ -59,6 +59,7 @@ - Minor internal changes to Python script for error reporting & style. v0.0.5 - Use ``<command detect_errors="aggressive">`` (internal change only). - Single quote command line arguments (internal change only). + - Python 3 compatible print function. ======= ======================================================================
--- a/tools/fastq_pair_names/fastq_pair_names.py Thu May 11 18:34:08 2017 -0400 +++ b/tools/fastq_pair_names/fastq_pair_names.py Wed May 17 11:17:25 2017 -0400 @@ -8,21 +8,23 @@ Note that the FASTQ variant is unimportant (Sanger, Solexa, Illumina, or even Color Space should all work equally well). -This script is copyright 2014 by Peter Cock, The James Hutton Institute +This script is copyright 2014-2017 by Peter Cock, The James Hutton Institute (formerly SCRI), Scotland, UK. All rights reserved. See accompanying text file for licence details (MIT license). """ +from __future__ import print_function + import os import re import sys -from galaxy_utils.sequence.fastq import fastqReader +if "-v" in sys.argv or "--version" in sys.argv: + print("0.0.5") + sys.exit(0) -if "-v" in sys.argv or "--version" in sys.argv: - print "Version 0.0.1" - sys.exit(0) +from galaxy_utils.sequence.fastq import fastqReader msg = """Expects at least 3 arguments: @@ -134,4 +136,4 @@ out_pairs.close() out_nonpairs.close() -print "%i reads (%i forward, %i reverse, %i neither), %i pairs" % (count, forward, reverse, neither, len(pairs)) +print("%i reads (%i forward, %i reverse, %i neither), %i pairs" % (count, forward, reverse, neither, len(pairs)))
--- a/tools/fastq_pair_names/fastq_pair_names.xml Thu May 11 18:34:08 2017 -0400 +++ b/tools/fastq_pair_names/fastq_pair_names.xml Wed May 17 11:17:25 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="fastq_pair_names" name="Identify paired reads in FASTQ files" version="0.0.4"> +<tool id="fastq_pair_names" name="Identify paired reads in FASTQ files" version="0.0.5"> <description>using the read name suffices</description> <requirements> <requirement type="package" version="1.0.1">galaxy_sequence_utils</requirement>