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changeset 6:92eee5f31117 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit fe9aabe924f278694d20b82169edacdb3e91eb49
author iuc
date Sun, 11 Feb 2024 00:56:12 +0000
parents 728dacaf08a9
children ba6990f72184
files bakta.xml macro.xml test-data/TEST_1/TEST_1.embl test-data/TEST_1/TEST_1.gbff test-data/TEST_1/TEST_1.gff3 test-data/TEST_1/TEST_1.hypotheticals.tsv test-data/TEST_1/TEST_1.json test-data/TEST_1/TEST_1.tsv test-data/TEST_1/TEST_1.txt test-data/TEST_1/TEST_1_plot.svg test-data/TEST_2/TEST_2.gff3 test-data/TEST_2/TEST_2.tsv test-data/TEST_2/TEST_2_plot.svg test-data/TEST_3/TEST_3.gff3 test-data/TEST_3/TEST_3.tsv test-data/TEST_4/TEST_4.gff3 test-data/TEST_4/TEST_4.tsv test-data/TEST_4/TEST_4_plot.svg test-data/TEST_5/TEST_5.txt test-data/TEST_6/TEST_6.embl test-data/TEST_6/TEST_6.gbff test-data/TEST_6/TEST_6.gff3 test-data/TEST_6/TEST_6.hypotheticals.tsv test-data/TEST_6/TEST_6.json test-data/TEST_6/TEST_6.tsv test-data/TEST_6/TEST_6.txt test-data/TEST_6/TEST_6_plot.svg
diffstat 27 files changed, 69 insertions(+), 65 deletions(-) [+]
line wrap: on
line diff
--- a/bakta.xml	Sat Sep 16 09:01:39 2023 +0000
+++ b/bakta.xml	Sun Feb 11 00:56:12 2024 +0000
@@ -70,6 +70,9 @@
         #if $annotation.proteins
             --proteins '$annotation.proteins'
         #end if
+        #if $annotation.regions
+            --regions '$annotation.regions'
+        #end if
         #*======================================
                     Workflow OPTIONS
          skip some step of the bakta analysis
@@ -132,6 +135,7 @@
             <param argument="--compliant" type="boolean" truevalue="--compliant" falsevalue="" label="Force Genbank/ENA/DDJB compliance"/>
             <param argument="--proteins" type="data" format="fasta" optional="true" label="Protein fasta file" help="Fasta file of trusted protein sequences for CDS annotation"/>
             <param argument="--meta" type="boolean" truevalue="--meta" falsevalue="" label="Metagenome mode" help="Run in metagenome mode. This only affects CDS prediction"/>
+            <param argument="--regions" type="data" format="gff,genbank" optional="true" label="Pre-annotated regions" help="Regions only, no functional annotations."/>
         </section>
         <!-- PARAMETER FOR WORKFLOW ANALYSIS -->
         <section name="workflow" title="Workflow option to skip steps">
--- a/macro.xml	Sat Sep 16 09:01:39 2023 +0000
+++ b/macro.xml	Sun Feb 11 00:56:12 2024 +0000
@@ -1,6 +1,6 @@
 
 <macros>
-    <token name="@TOOL_VERSION@">1.8.2</token>
+    <token name="@TOOL_VERSION@">1.9.2</token>
     <token name="@COMPATIBLE_BAKTA_VERSION@">1.7</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">21.05</token>
--- a/test-data/TEST_1/TEST_1.embl	Sat Sep 16 09:01:39 2023 +0000
+++ b/test-data/TEST_1/TEST_1.embl	Sun Feb 11 00:56:12 2024 +0000
@@ -8,13 +8,13 @@
 OC   .
 XX
 CC   Annotated with Bakta
-CC   Software: v1.8.1
+CC   Software: v1.9.2
 CC   Database: v5.0, full
 CC   DOI: 10.1099/mgen.0.000685
 CC   URL: github.com/oschwengers/bakta
 CC   
 CC   ##Genome Annotation Summary:##
-CC   Annotation Date                :: 06/19/2023, 09:30:06
+CC   Annotation Date                :: 02/11/2024, 00:24:56
 CC   CDSs                           ::     2
 CC   tRNAs                          ::     0
 CC   tmRNAs                         ::     0
--- a/test-data/TEST_1/TEST_1.gbff	Sat Sep 16 09:01:39 2023 +0000
+++ b/test-data/TEST_1/TEST_1.gbff	Sun Feb 11 00:56:12 2024 +0000
@@ -1,4 +1,4 @@
-LOCUS       contig_1                1330 bp    DNA     circular BCT 19-JUN-2023
+LOCUS       contig_1                1330 bp    DNA     circular BCT 11-FEB-2024
 DEFINITION  plasmid unnamed1, complete sequence.
 ACCESSION   contig_1
 VERSION     contig_1
@@ -7,13 +7,13 @@
   ORGANISM  .
             .
 COMMENT     Annotated with Bakta
-            Software: v1.8.1
+            Software: v1.9.2
             Database: v5.0, full
             DOI: 10.1099/mgen.0.000685
             URL: github.com/oschwengers/bakta
             
             ##Genome Annotation Summary:##
-            Annotation Date                :: 06/19/2023, 09:30:06
+            Annotation Date                :: 02/11/2024, 00:24:56
             CDSs                           ::     2
             tRNAs                          ::     0
             tmRNAs                         ::     0
--- a/test-data/TEST_1/TEST_1.gff3	Sat Sep 16 09:01:39 2023 +0000
+++ b/test-data/TEST_1/TEST_1.gff3	Sun Feb 11 00:56:12 2024 +0000
@@ -1,7 +1,7 @@
 ##gff-version 3
 ##feature-ontology https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/v3.1/so.obo
 # Annotated with Bakta
-# Software: v1.8.2
+# Software: v1.9.2
 # Database: v5.0, full
 # DOI: 10.1099/mgen.0.000685
 # URL: github.com/oschwengers/bakta
--- a/test-data/TEST_1/TEST_1.hypotheticals.tsv	Sat Sep 16 09:01:39 2023 +0000
+++ b/test-data/TEST_1/TEST_1.hypotheticals.tsv	Sun Feb 11 00:56:12 2024 +0000
@@ -1,4 +1,4 @@
-#Annotated with Bakta v1.8.2, https://github.com/oschwengers/bakta
+#Annotated with Bakta v1.9.2, https://github.com/oschwengers/bakta
 #Database v5.0, https://doi.org/10.5281/zenodo.4247252
 #Sequence Id	Start	Stop	Strand	Locus Tag	Mol Weight [kDa]	Iso El. Point	Pfam hits	Dbxrefs
 contig_1	413	736	+	IHHALP_00005	12.1	10.4		
--- a/test-data/TEST_1/TEST_1.json	Sat Sep 16 09:01:39 2023 +0000
+++ b/test-data/TEST_1/TEST_1.json	Sun Feb 11 00:56:12 2024 +0000
@@ -22,15 +22,15 @@
             "start": 413,
             "stop": 736,
             "strand": "+",
+            "frame": 2,
             "gene": null,
             "product": "hypothetical protein",
+            "db_xrefs": [],
+            "nt": "ATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAG",
+            "aa": "MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD",
+            "aa_hexdigest": "d9bdebc84195542e775c3d22458b507e",
             "start_type": "ATG",
             "rbs_motif": "GGAG/GAGG",
-            "db_xrefs": [],
-            "frame": 2,
-            "aa": "MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD",
-            "aa_hexdigest": "d9bdebc84195542e775c3d22458b507e",
-            "nt": "ATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAG",
             "hypothetical": true,
             "genes": [],
             "seq_stats": {
@@ -46,16 +46,16 @@
             "start": 971,
             "stop": 141,
             "strand": "-",
+            "frame": 1,
             "gene": null,
             "product": "hypothetical protein",
+            "db_xrefs": [],
+            "nt": "ATGAACAAGCAGCAGCAAACTGCACTCAACATGGCGGGATTCATAAAAAGCCAGAGCCTGACGCTGCTCGAAAAACTGGACGCACTCGATGCTGACGAGCAGGCCACCATGTGTGAGAAGCTGCACGAACTCGCAGAAGAACAAATAGAAGCAATAAAAAATAAAGATAAAACTTTATTTATTGTCTATGCTACTGATATTTATAGCCCGAGCGAATTTTTCTCAAAAATCGAATCCGACTTGAAGAAAAAGAAAAGCAAGGGTGATGTTTTTTTTGATTTAATAATTCCTAACGGTGGAAAAAAAGATCGTTACGTCTATACGTCATTTAATGGCGAGAAGTTTTCAAGTTACACATTAAACAAAGTTACGAAAACTGATGAATATAATGATTTATCTGAGCTCTCGGCTTCGTTCTTTAAAAAAAACTTTGATAAGATCAACGTAAACCTTCTATCCAAAGCCACATCATTTGCTTTGAAAAAAGGCATTCCAATATAA",
+            "aa": "MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI",
+            "aa_hexdigest": "1e7027cbe48346e06a83e802a9385584",
             "start_type": "ATG",
             "rbs_motif": "AGGA/GGAG/GAGG",
-            "db_xrefs": [],
-            "frame": 1,
-            "aa": "MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI",
-            "aa_hexdigest": "1e7027cbe48346e06a83e802a9385584",
             "edge": true,
-            "nt": "ATGAACAAGCAGCAGCAAACTGCACTCAACATGGCGGGATTCATAAAAAGCCAGAGCCTGACGCTGCTCGAAAAACTGGACGCACTCGATGCTGACGAGCAGGCCACCATGTGTGAGAAGCTGCACGAACTCGCAGAAGAACAAATAGAAGCAATAAAAAATAAAGATAAAACTTTATTTATTGTCTATGCTACTGATATTTATAGCCCGAGCGAATTTTTCTCAAAAATCGAATCCGACTTGAAGAAAAAGAAAAGCAAGGGTGATGTTTTTTTTGATTTAATAATTCCTAACGGTGGAAAAAAAGATCGTTACGTCTATACGTCATTTAATGGCGAGAAGTTTTCAAGTTACACATTAAACAAAGTTACGAAAACTGATGAATATAATGATTTATCTGAGCTCTCGGCTTCGTTCTTTAAAAAAAACTTTGATAAGATCAACGTAAACCTTCTATCCAAAGCCACATCATTTGCTTTGAAAAAAGGCATTCCAATATAA",
             "hypothetical": true,
             "genes": [],
             "seq_stats": {
@@ -82,11 +82,11 @@
         }
     ],
     "run": {
-        "start": "2023-06-19 09:30:05",
-        "end": "2023-06-19 09:30:06"
+        "start": "2024-02-11 00:24:53",
+        "end": "2024-02-11 00:25:06"
     },
     "version": {
-        "bakta": "1.8.1",
+        "bakta": "1.9.2",
         "db": {
             "version": "5.0",
             "type": "full"
--- a/test-data/TEST_1/TEST_1.tsv	Sat Sep 16 09:01:39 2023 +0000
+++ b/test-data/TEST_1/TEST_1.tsv	Sun Feb 11 00:56:12 2024 +0000
@@ -1,5 +1,5 @@
 # Annotated with Bakta
-# Software: v1.8.2
+# Software: v1.9.2
 # Database: v5.0, full
 # DOI: 10.1099/mgen.0.000685
 # URL: github.com/oschwengers/bakta
--- a/test-data/TEST_1/TEST_1.txt	Sat Sep 16 09:01:39 2023 +0000
+++ b/test-data/TEST_1/TEST_1.txt	Sun Feb 11 00:56:12 2024 +0000
@@ -24,7 +24,7 @@
 oriTs: 0
 
 Bakta:
-Software: v1.8.2
+Software: v1.9.2
 Database: v5.0, full
 DOI: 10.1099/mgen.0.000685
 URL: github.com/oschwengers/bakta
--- a/test-data/TEST_1/TEST_1_plot.svg	Sat Sep 16 09:01:39 2023 +0000
+++ b/test-data/TEST_1/TEST_1_plot.svg	Sun Feb 11 00:56:12 2024 +0000
@@ -2390,11 +2390,11 @@
 <path d="M 1496.73,889.46 L 1496.60,865.01 " style="stroke-linecap:round;fill:none;" />
 </g>
 <defs>
+<pattern id="hline" width="10" height="10" patternTransform="rotate(0 0 0)" patternUnits="userSpaceOnUse"><line x1="0" y1="0" x2="10" y2="0" style="stroke:black;stroke-width:5" /></pattern>
+<pattern id="checker" width="10" height="10" patternTransform="rotate(45 0 0)" patternUnits="userSpaceOnUse"><line x1="0" y1="0" x2="10" y2="0" style="stroke:black;stroke-width:5" /><line x1="0" y1="0" x2="0" y2="10" style="stroke:black;stroke-width:4" /></pattern>
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-<pattern id="hline" width="10" height="10" patternTransform="rotate(0 0 0)" patternUnits="userSpaceOnUse"><line x1="0" y1="0" x2="10" y2="0" style="stroke:black;stroke-width:5" /></pattern>
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-<pattern id="checker" width="10" height="10" patternTransform="rotate(45 0 0)" patternUnits="userSpaceOnUse"><line x1="0" y1="0" x2="10" y2="0" style="stroke:black;stroke-width:5" /><line x1="0" y1="0" x2="0" y2="10" style="stroke:black;stroke-width:4" /></pattern>
 </defs>
 </svg>
--- a/test-data/TEST_2/TEST_2.gff3	Sat Sep 16 09:01:39 2023 +0000
+++ b/test-data/TEST_2/TEST_2.gff3	Sun Feb 11 00:56:12 2024 +0000
@@ -2,7 +2,7 @@
 ##feature-ontology https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/v3.1/so.obo
 # organism Escherichia coli o157:h7 Sakai
 # Annotated with Bakta
-# Software: v1.8.2
+# Software: v1.9.2
 # Database: v5.0, full
 # DOI: 10.1099/mgen.0.000685
 # URL: github.com/oschwengers/bakta
--- a/test-data/TEST_2/TEST_2.tsv	Sat Sep 16 09:01:39 2023 +0000
+++ b/test-data/TEST_2/TEST_2.tsv	Sun Feb 11 00:56:12 2024 +0000
@@ -1,5 +1,5 @@
 # Annotated with Bakta
-# Software: v1.8.2
+# Software: v1.9.2
 # Database: v5.0, full
 # DOI: 10.1099/mgen.0.000685
 # URL: github.com/oschwengers/bakta
--- a/test-data/TEST_2/TEST_2_plot.svg	Sat Sep 16 09:01:39 2023 +0000
+++ b/test-data/TEST_2/TEST_2_plot.svg	Sun Feb 11 00:56:12 2024 +0000
@@ -2390,11 +2390,11 @@
 <path d="M 1496.73,889.46 L 1496.60,865.01 " style="stroke-linecap:round;fill:none;" />
 </g>
 <defs>
+<pattern id="checker" width="10" height="10" patternTransform="rotate(45 0 0)" patternUnits="userSpaceOnUse"><line x1="0" y1="0" x2="10" y2="0" style="stroke:black;stroke-width:2" /><line x1="0" y1="0" x2="0" y2="10" style="stroke:black;stroke-width:2" /></pattern>
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-<pattern id="hline" width="10" height="10" patternTransform="rotate(0 0 0)" patternUnits="userSpaceOnUse"><line x1="0" y1="0" x2="10" y2="0" style="stroke:black;stroke-width:5" /></pattern>
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+<pattern id="checker" width="10" height="10" patternTransform="rotate(45 0 0)" patternUnits="userSpaceOnUse"><line x1="0" y1="0" x2="10" y2="0" style="stroke:black;stroke-width:5" /><line x1="0" y1="0" x2="0" y2="10" style="stroke:black;stroke-width:4" /></pattern>
+<pattern id="hline" width="10" height="10" patternTransform="rotate(0 0 0)" patternUnits="userSpaceOnUse"><line x1="0" y1="0" x2="10" y2="0" style="stroke:black;stroke-width:5" /></pattern>
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-<pattern id="checker" width="10" height="10" patternTransform="rotate(45 0 0)" patternUnits="userSpaceOnUse"><line x1="0" y1="0" x2="10" y2="0" style="stroke:black;stroke-width:2" /><line x1="0" y1="0" x2="0" y2="10" style="stroke:black;stroke-width:2" /></pattern>
-<pattern id="checker" width="10" height="10" patternTransform="rotate(45 0 0)" patternUnits="userSpaceOnUse"><line x1="0" y1="0" x2="10" y2="0" style="stroke:black;stroke-width:5" /><line x1="0" y1="0" x2="0" y2="10" style="stroke:black;stroke-width:4" /></pattern>
 </defs>
 </svg>
--- a/test-data/TEST_3/TEST_3.gff3	Sat Sep 16 09:01:39 2023 +0000
+++ b/test-data/TEST_3/TEST_3.gff3	Sun Feb 11 00:56:12 2024 +0000
@@ -1,7 +1,7 @@
 ##gff-version 3
 ##feature-ontology https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/v3.1/so.obo
 # Annotated with Bakta
-# Software: v1.8.2
+# Software: v1.9.2
 # Database: v5.0, full
 # DOI: 10.1099/mgen.0.000685
 # URL: github.com/oschwengers/bakta
--- a/test-data/TEST_3/TEST_3.tsv	Sat Sep 16 09:01:39 2023 +0000
+++ b/test-data/TEST_3/TEST_3.tsv	Sun Feb 11 00:56:12 2024 +0000
@@ -1,5 +1,5 @@
 # Annotated with Bakta
-# Software: v1.8.2
+# Software: v1.9.2
 # Database: v5.0, full
 # DOI: 10.1099/mgen.0.000685
 # URL: github.com/oschwengers/bakta
--- a/test-data/TEST_4/TEST_4.gff3	Sat Sep 16 09:01:39 2023 +0000
+++ b/test-data/TEST_4/TEST_4.gff3	Sun Feb 11 00:56:12 2024 +0000
@@ -1,7 +1,7 @@
 ##gff-version 3
 ##feature-ontology https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/v3.1/so.obo
 # Annotated with Bakta
-# Software: v1.8.2
+# Software: v1.9.2
 # Database: v5.0, full
 # DOI: 10.1099/mgen.0.000685
 # URL: github.com/oschwengers/bakta
--- a/test-data/TEST_4/TEST_4.tsv	Sat Sep 16 09:01:39 2023 +0000
+++ b/test-data/TEST_4/TEST_4.tsv	Sun Feb 11 00:56:12 2024 +0000
@@ -1,5 +1,5 @@
 # Annotated with Bakta
-# Software: v1.8.2
+# Software: v1.9.2
 # Database: v5.0, full
 # DOI: 10.1099/mgen.0.000685
 # URL: github.com/oschwengers/bakta
--- a/test-data/TEST_4/TEST_4_plot.svg	Sat Sep 16 09:01:39 2023 +0000
+++ b/test-data/TEST_4/TEST_4_plot.svg	Sun Feb 11 00:56:12 2024 +0000
@@ -2390,11 +2390,11 @@
 <path d="M 1496.73,889.46 L 1496.60,865.01 " style="stroke-linecap:round;fill:none;" />
 </g>
 <defs>
-<pattern id="vline-sparse" width="10" height="10" patternTransform="rotate(0 0 0)" patternUnits="userSpaceOnUse"><line x1="0" y1="0" x2="0" y2="10" style="stroke:black;stroke-width:2" /></pattern>
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--- a/test-data/TEST_5/TEST_5.txt	Sat Sep 16 09:01:39 2023 +0000
+++ b/test-data/TEST_5/TEST_5.txt	Sun Feb 11 00:56:12 2024 +0000
@@ -24,7 +24,7 @@
 oriTs: 0
 
 Bakta:
-Software: v1.8.2
+Software: v1.9.2
 Database: v5.0, full
 DOI: 10.1099/mgen.0.000685
 URL: github.com/oschwengers/bakta
--- a/test-data/TEST_6/TEST_6.embl	Sat Sep 16 09:01:39 2023 +0000
+++ b/test-data/TEST_6/TEST_6.embl	Sun Feb 11 00:56:12 2024 +0000
@@ -8,13 +8,13 @@
 OC   .
 XX
 CC   Annotated with Bakta
-CC   Software: v1.8.1
+CC   Software: v1.9.2
 CC   Database: v5.0, full
 CC   DOI: 10.1099/mgen.0.000685
 CC   URL: github.com/oschwengers/bakta
 CC   
 CC   ##Genome Annotation Summary:##
-CC   Annotation Date                :: 06/19/2023, 09:31:33
+CC   Annotation Date                :: 02/11/2024, 00:27:34
 CC   CDSs                           ::     2
 CC   tRNAs                          ::     0
 CC   tmRNAs                         ::     0
--- a/test-data/TEST_6/TEST_6.gbff	Sat Sep 16 09:01:39 2023 +0000
+++ b/test-data/TEST_6/TEST_6.gbff	Sun Feb 11 00:56:12 2024 +0000
@@ -1,4 +1,4 @@
-LOCUS       contig_1                1330 bp    DNA     circular BCT 19-JUN-2023
+LOCUS       contig_1                1330 bp    DNA     circular BCT 11-FEB-2024
 DEFINITION  plasmid unnamed1, complete sequence.
 ACCESSION   contig_1
 VERSION     contig_1
@@ -7,13 +7,13 @@
   ORGANISM  .
             .
 COMMENT     Annotated with Bakta
-            Software: v1.8.1
+            Software: v1.9.2
             Database: v5.0, full
             DOI: 10.1099/mgen.0.000685
             URL: github.com/oschwengers/bakta
             
             ##Genome Annotation Summary:##
-            Annotation Date                :: 06/19/2023, 09:31:33
+            Annotation Date                :: 02/11/2024, 00:27:34
             CDSs                           ::     2
             tRNAs                          ::     0
             tmRNAs                         ::     0
--- a/test-data/TEST_6/TEST_6.gff3	Sat Sep 16 09:01:39 2023 +0000
+++ b/test-data/TEST_6/TEST_6.gff3	Sun Feb 11 00:56:12 2024 +0000
@@ -1,7 +1,7 @@
 ##gff-version 3
 ##feature-ontology https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/v3.1/so.obo
 # Annotated with Bakta
-# Software: v1.8.1
+# Software: v1.9.2
 # Database: v5.0, full
 # DOI: 10.1099/mgen.0.000685
 # URL: github.com/oschwengers/bakta
--- a/test-data/TEST_6/TEST_6.hypotheticals.tsv	Sat Sep 16 09:01:39 2023 +0000
+++ b/test-data/TEST_6/TEST_6.hypotheticals.tsv	Sun Feb 11 00:56:12 2024 +0000
@@ -1,4 +1,4 @@
-#Annotated with Bakta v1.8.1, https://github.com/oschwengers/bakta
+#Annotated with Bakta v1.9.2, https://github.com/oschwengers/bakta
 #Database v5.0, https://doi.org/10.5281/zenodo.4247252
 #Sequence Id	Start	Stop	Strand	Locus Tag	Mol Weight [kDa]	Iso El. Point	Pfam hits	Dbxrefs
 contig_1	413	736	+	IHHALP_00005	12.1	10.4		
--- a/test-data/TEST_6/TEST_6.json	Sat Sep 16 09:01:39 2023 +0000
+++ b/test-data/TEST_6/TEST_6.json	Sun Feb 11 00:56:12 2024 +0000
@@ -22,15 +22,15 @@
             "start": 413,
             "stop": 736,
             "strand": "+",
+            "frame": 2,
             "gene": null,
             "product": "hypothetical protein",
+            "db_xrefs": [],
+            "nt": "ATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAG",
+            "aa": "MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD",
+            "aa_hexdigest": "d9bdebc84195542e775c3d22458b507e",
             "start_type": "ATG",
             "rbs_motif": "GGAG/GAGG",
-            "db_xrefs": [],
-            "frame": 2,
-            "aa": "MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD",
-            "aa_hexdigest": "d9bdebc84195542e775c3d22458b507e",
-            "nt": "ATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAG",
             "hypothetical": true,
             "genes": [],
             "seq_stats": {
@@ -46,16 +46,16 @@
             "start": 971,
             "stop": 141,
             "strand": "-",
+            "frame": 1,
             "gene": null,
             "product": "hypothetical protein",
+            "db_xrefs": [],
+            "nt": "ATGAACAAGCAGCAGCAAACTGCACTCAACATGGCGGGATTCATAAAAAGCCAGAGCCTGACGCTGCTCGAAAAACTGGACGCACTCGATGCTGACGAGCAGGCCACCATGTGTGAGAAGCTGCACGAACTCGCAGAAGAACAAATAGAAGCAATAAAAAATAAAGATAAAACTTTATTTATTGTCTATGCTACTGATATTTATAGCCCGAGCGAATTTTTCTCAAAAATCGAATCCGACTTGAAGAAAAAGAAAAGCAAGGGTGATGTTTTTTTTGATTTAATAATTCCTAACGGTGGAAAAAAAGATCGTTACGTCTATACGTCATTTAATGGCGAGAAGTTTTCAAGTTACACATTAAACAAAGTTACGAAAACTGATGAATATAATGATTTATCTGAGCTCTCGGCTTCGTTCTTTAAAAAAAACTTTGATAAGATCAACGTAAACCTTCTATCCAAAGCCACATCATTTGCTTTGAAAAAAGGCATTCCAATATAA",
+            "aa": "MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI",
+            "aa_hexdigest": "1e7027cbe48346e06a83e802a9385584",
             "start_type": "ATG",
             "rbs_motif": "AGGA/GGAG/GAGG",
-            "db_xrefs": [],
-            "frame": 1,
-            "aa": "MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI",
-            "aa_hexdigest": "1e7027cbe48346e06a83e802a9385584",
             "edge": true,
-            "nt": "ATGAACAAGCAGCAGCAAACTGCACTCAACATGGCGGGATTCATAAAAAGCCAGAGCCTGACGCTGCTCGAAAAACTGGACGCACTCGATGCTGACGAGCAGGCCACCATGTGTGAGAAGCTGCACGAACTCGCAGAAGAACAAATAGAAGCAATAAAAAATAAAGATAAAACTTTATTTATTGTCTATGCTACTGATATTTATAGCCCGAGCGAATTTTTCTCAAAAATCGAATCCGACTTGAAGAAAAAGAAAAGCAAGGGTGATGTTTTTTTTGATTTAATAATTCCTAACGGTGGAAAAAAAGATCGTTACGTCTATACGTCATTTAATGGCGAGAAGTTTTCAAGTTACACATTAAACAAAGTTACGAAAACTGATGAATATAATGATTTATCTGAGCTCTCGGCTTCGTTCTTTAAAAAAAACTTTGATAAGATCAACGTAAACCTTCTATCCAAAGCCACATCATTTGCTTTGAAAAAAGGCATTCCAATATAA",
             "hypothetical": true,
             "genes": [],
             "seq_stats": {
@@ -82,11 +82,11 @@
         }
     ],
     "run": {
-        "start": "2023-06-19 09:31:32",
-        "end": "2023-06-19 09:31:33"
+        "start": "2024-02-11 00:27:31",
+        "end": "2024-02-11 00:27:43"
     },
     "version": {
-        "bakta": "1.8.1",
+        "bakta": "1.9.2",
         "db": {
             "version": "5.0",
             "type": "full"
--- a/test-data/TEST_6/TEST_6.tsv	Sat Sep 16 09:01:39 2023 +0000
+++ b/test-data/TEST_6/TEST_6.tsv	Sun Feb 11 00:56:12 2024 +0000
@@ -1,5 +1,5 @@
 # Annotated with Bakta
-# Software: v1.8.1
+# Software: v1.9.2
 # Database: v5.0, full
 # DOI: 10.1099/mgen.0.000685
 # URL: github.com/oschwengers/bakta
--- a/test-data/TEST_6/TEST_6.txt	Sat Sep 16 09:01:39 2023 +0000
+++ b/test-data/TEST_6/TEST_6.txt	Sun Feb 11 00:56:12 2024 +0000
@@ -24,7 +24,7 @@
 oriTs: 0
 
 Bakta:
-Software: v1.8.1
+Software: v1.9.2
 Database: v5.0, full
 DOI: 10.1099/mgen.0.000685
 URL: github.com/oschwengers/bakta
--- a/test-data/TEST_6/TEST_6_plot.svg	Sat Sep 16 09:01:39 2023 +0000
+++ b/test-data/TEST_6/TEST_6_plot.svg	Sun Feb 11 00:56:12 2024 +0000
@@ -2390,11 +2390,11 @@
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