add support for translation table 25 #323

oschwengers · Sep 24, 2024 · b8c0410 · b8c0410
1 parent c8a93e1
commit b8c0410
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git 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
@@ -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)')