Mercurial > repos > peterjc > get_orfs_or_cdss
changeset 25:9adb26199d9b draft
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss commit 37d5b47ec23e2cbaa453cc660bb1fcbb10dd34ee-dirty
| author | peterjc |
|---|---|
| date | Wed, 17 May 2017 11:18:27 -0400 |
| parents | 84232d9e269c |
| children | bec536fd4640 |
| files | tools/get_orfs_or_cdss/README.rst tools/get_orfs_or_cdss/get_orfs_or_cdss.py tools/get_orfs_or_cdss/get_orfs_or_cdss.xml |
| diffstat | 3 files changed, 8 insertions(+), 5 deletions(-) [+] |
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--- a/tools/get_orfs_or_cdss/README.rst Tue May 16 09:10:25 2017 -0400 +++ b/tools/get_orfs_or_cdss/README.rst Wed May 17 11:18:27 2017 -0400 @@ -82,6 +82,7 @@ Gracilibacteria. v0.2.2 - Use ``<command detect_errors="aggressive">`` (internal change only). - Single quote command line arguments (internal change only). +v0.2.3 - Python 3 compatible print function. ======= ======================================================================
--- a/tools/get_orfs_or_cdss/get_orfs_or_cdss.py Tue May 16 09:10:25 2017 -0400 +++ b/tools/get_orfs_or_cdss/get_orfs_or_cdss.py Wed May 17 11:18:27 2017 -0400 @@ -18,6 +18,8 @@ See accompanying text file for licence details (MIT licence). """ +from __future__ import print_function + import re import sys @@ -79,7 +81,7 @@ options, args = parser.parse_args() if options.version: - print("v0.2.0") + print("v0.2.3") sys.exit(0) if not options.input_file: @@ -102,8 +104,8 @@ else: sys.exit("Unsupported file type %r" % options.seq_format) -print "Genetic code table %i" % options.table -print "Minimum length %i aa" % options.min_len +print("Genetic code table %i" % options.table) +print("Minimum length %i aa" % options.min_len) # print "Taking %s ORF(s) from %s strand(s)" % (mode, strand) starts = sorted(table_obj.start_codons) @@ -283,4 +285,4 @@ if out_bed and out_bed is not sys.stdout: out_bed.close() -print "Found %i %ss in %i sequences" % (out_count, options.ftype, in_count) +print("Found %i %ss in %i sequences" % (out_count, options.ftype, in_count))
--- a/tools/get_orfs_or_cdss/get_orfs_or_cdss.xml Tue May 16 09:10:25 2017 -0400 +++ b/tools/get_orfs_or_cdss/get_orfs_or_cdss.xml Wed May 17 11:18:27 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="get_orfs_or_cdss" name="Get open reading frames (ORFs) or coding sequences (CDSs)" version="0.2.2"> +<tool id="get_orfs_or_cdss" name="Get open reading frames (ORFs) or coding sequences (CDSs)" version="0.2.3"> <description>e.g. to get peptides from ESTs</description> <requirements> <requirement type="package" version="1.67">biopython</requirement>