Mercurial > repos > peterjc > get_orfs_or_cdss
changeset 11:d51db443aaa4 draft
v0.2.3 Python 3 compatible print function.
| author | peterjc |
|---|---|
| date | Wed, 30 May 2018 08:33:20 -0400 |
| parents | 01b0488d9cfb |
| children | 71905a6d52a7 |
| 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 tools/get_orfs_or_cdss/tool_dependencies.xml |
| diffstat | 4 files changed, 14 insertions(+), 9 deletions(-) [+] |
line wrap: on
line diff
--- a/tools/get_orfs_or_cdss/README.rst Tue May 16 09:11:27 2017 -0400 +++ b/tools/get_orfs_or_cdss/README.rst Wed May 30 08:33:20 2018 -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 09:11:27 2017 -0400 +++ b/tools/get_orfs_or_cdss/get_orfs_or_cdss.py Wed May 30 08:33:20 2018 -0400 @@ -18,14 +18,18 @@ See accompanying text file for licence details (MIT licence). """ +from __future__ import print_function + import re import sys from optparse import OptionParser -usage = """Use as follows: +usage = r"""Use as follows: -$ python get_orfs_or_cdss.py -i genome.fa -f fasta --table 11 -t CDS -e open -m all -s both --on cds.nuc.fa --op cds.protein.fa --ob cds.bed --og cds.gff3 +$ python get_orfs_or_cdss.py -i genome.fa -f fasta --table 11 \ +-t CDS -e open -m all -s both --on cds.nuc.fa --op cds.protein.fa \ +--ob cds.bed --og cds.gff3 """ try: @@ -79,7 +83,7 @@ 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 +106,8 @@ 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 +287,4 @@ 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 09:11:27 2017 -0400 +++ b/tools/get_orfs_or_cdss/get_orfs_or_cdss.xml Wed May 30 08:33:20 2018 -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> @@ -52,7 +52,7 @@ <option value="26">31. Blastocrithidia Nuclear</option> --> </param> - <param name="ftype" type="select" value="True" label="Look for ORFs or CDSs"> + <param name="ftype" type="select" value="true" label="Look for ORFs or CDSs"> <option value="ORF">Look for ORFs (check for stop codons only, ignore start codons)</option> <option value="CDS">Look for CDSs (with start and stop codons)</option> </param>
--- a/tools/get_orfs_or_cdss/tool_dependencies.xml Tue May 16 09:11:27 2017 -0400 +++ b/tools/get_orfs_or_cdss/tool_dependencies.xml Wed May 30 08:33:20 2018 -0400 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> <package name="biopython" version="1.67"> - <repository changeset_revision="a42f244cce44" name="package_biopython_1_67" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="a12f73c3b116" name="package_biopython_1_67" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency>