From b8c0410b88ca152469b75a9e37ca984d59b59a63 Mon Sep 17 00:00:00 2001 From: Oliver Schwengers Date: Tue, 24 Sep 2024 18:15:50 +0200 Subject: [PATCH] add support for translation table 25 #323 --- README.md | 6 +++--- bakta/utils.py | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index ea38870d..e5762b33 100644 --- a/README.md +++ b/README.md @@ -344,7 +344,7 @@ Exemplary annotation result files for several genomes (mostly ESKAPE species) ar ```bash usage: bakta [--db DB] [--min-contig-length MIN_CONTIG_LENGTH] [--prefix PREFIX] [--output OUTPUT] [--genus GENUS] [--species SPECIES] [--strain STRAIN] [--plasmid PLASMID] - [--complete] [--prodigal-tf PRODIGAL_TF] [--translation-table {11,4}] [--gram {+,-,?}] [--locus LOCUS] + [--complete] [--prodigal-tf PRODIGAL_TF] [--translation-table {11,4,25}] [--gram {+,-,?}] [--locus LOCUS] [--locus-tag LOCUS_TAG] [--keep-contig-headers] [--replicons REPLICONS] [--compliant] [--replicons REPLICONS] [--regions REGIONS] [--proteins PROTEINS] [--meta] [--skip-trna] [--skip-tmrna] [--skip-rrna] [--skip-ncrna] [--skip-ncrna-region] [--skip-crispr] [--skip-cds] [--skip-pseudo] [--skip-sorf] [--skip-gap] [--skip-ori] [--skip-plot] @@ -376,8 +376,8 @@ Annotation: --complete All sequences are complete replicons (chromosome/plasmid[s]) --prodigal-tf PRODIGAL_TF Path to existing Prodigal training file to use for CDS prediction - --translation-table {11,4} - Translation table: 11/4 (default = 11) + --translation-table {11,4,25} + Translation table: 11/4/25 (default = 11) --gram {+,-,?} Gram type for signal peptide predictions: +/-/? (default = ?) --locus LOCUS Locus prefix (default = 'contig') --locus-tag LOCUS_TAG diff --git a/bakta/utils.py b/bakta/utils.py index 7be14693..8760d0f3 100644 --- a/bakta/utils.py +++ b/bakta/utils.py @@ -82,7 +82,7 @@ def parse_arguments(): arg_group_annotation = parser.add_argument_group('Annotation') arg_group_annotation.add_argument('--complete', action='store_true', help='All sequences are complete replicons (chromosome/plasmid[s])') arg_group_annotation.add_argument('--prodigal-tf', action='store', default=None, dest='prodigal_tf', help='Path to existing Prodigal training file to use for CDS prediction') - arg_group_annotation.add_argument('--translation-table', action='store', type=int, default=11, choices=[11, 4], dest='translation_table', help='Translation table: 11/4 (default = 11)') + arg_group_annotation.add_argument('--translation-table', action='store', type=int, default=11, choices=[11, 4, 25], dest='translation_table', help='Translation table: 11/4/25 (default = 11)') arg_group_annotation.add_argument('--gram', action='store', default=bc.GRAM_UNKNOWN, choices=[bc.GRAM_POSITIVE, bc.GRAM_NEGATIVE, bc.GRAM_UNKNOWN], help=f'Gram type for signal peptide predictions: {bc.GRAM_POSITIVE}/{bc.GRAM_NEGATIVE}/{bc.GRAM_UNKNOWN} (default = {bc.GRAM_UNKNOWN})') arg_group_annotation.add_argument('--locus', action='store', default=None, help="Locus prefix (default = 'contig')") arg_group_annotation.add_argument('--locus-tag', action='store', default=None, dest='locus_tag', help='Locus tag prefix (default = autogenerated)')