Mercurial > repos > iuc > kraken_taxonomy_report
changeset 3:b11b3ac48bb9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
| author | iuc |
|---|---|
| date | Tue, 30 Oct 2018 18:58:54 -0400 |
| parents | 528a1d91b066 |
| children | 27d65c78863c |
| files | kraken_taxonomy_report.py |
| diffstat | 1 files changed, 2 insertions(+), 2 deletions(-) [+] |
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--- a/kraken_taxonomy_report.py Thu Nov 09 14:06:54 2017 -0500 +++ b/kraken_taxonomy_report.py Tue Oct 30 18:58:54 2018 -0400 @@ -68,7 +68,7 @@ PRIMARY_RANK_NAMES.append( 'superkingdom' ) NAME_STUB = "%s__%s" -NAME_RE = re.compile( "(\t| |\||\.;)" ) +NAME_RE = re.compile(r"(\t| |\||\.;)") NAME_REPL = "_" @@ -218,7 +218,7 @@ parser.add_option( '', '--taxonomy', dest='taxonomy', action='store_true', default=False, help='Output taxonomy in last column' ) parser.add_option( '', '--cluster', dest='cluster', action='store', type="string", default=None, help='Cluster counts to specified rank' ) parser.add_option( '', '--summation', dest='summation', action='store_true', default=False, help='Add summation of child counts to each taxa' ) - parser.add_option( '', '--sanitize-names', dest='sanitize_names', action='store_true', default=False, help='Replace special chars (\t| |\||\.;) with underscore (_)' ) + parser.add_option('', '--sanitize-names', dest='sanitize_names', action='store_true', default=False, help=r'Replace special chars (\t| |\||\.;) with underscore (_)') parser.add_option( '', '--show-rank', dest='show_rank', action='store_true', default=False, help='Output column with Rank name' ) parser.add_option( '', '--db', dest='db', action='store', type="string", default=None, help='Name of Kraken database' ) parser.add_option( '', '--output', dest='output', action='store', type="string", default=None, help='Name of output file' )