| Previous changeset 5:728dacaf08a9 (2023-09-16) Next changeset 7:ba6990f72184 (2024-06-05) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit fe9aabe924f278694d20b82169edacdb3e91eb49 |
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modified:
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 |
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| diff -r 728dacaf08a9 -r 92eee5f31117 bakta.xml --- a/bakta.xml Sat Sep 16 09:01:39 2023 +0000 +++ b/bakta.xml Sun Feb 11 00:56:12 2024 +0000 |
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| @@ -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"> |
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| diff -r 728dacaf08a9 -r 92eee5f31117 macro.xml --- a/macro.xml Sat Sep 16 09:01:39 2023 +0000 +++ b/macro.xml Sun Feb 11 00:56:12 2024 +0000 |
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| @@ -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> |
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| diff -r 728dacaf08a9 -r 92eee5f31117 test-data/TEST_1/TEST_1.embl --- 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 |
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| @@ -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 |
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| diff -r 728dacaf08a9 -r 92eee5f31117 test-data/TEST_1/TEST_1.gbff --- 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 |
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| @@ -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 |
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| diff -r 728dacaf08a9 -r 92eee5f31117 test-data/TEST_1/TEST_1.gff3 --- 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 |
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| @@ -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 |
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| diff -r 728dacaf08a9 -r 92eee5f31117 test-data/TEST_1/TEST_1.hypotheticals.tsv --- 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 |
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| @@ -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 |
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| diff -r 728dacaf08a9 -r 92eee5f31117 test-data/TEST_1/TEST_1.json --- 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 |
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| @@ -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" |
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| diff -r 728dacaf08a9 -r 92eee5f31117 test-data/TEST_1/TEST_1.tsv --- 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 |
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| @@ -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 |
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| diff -r 728dacaf08a9 -r 92eee5f31117 test-data/TEST_1/TEST_1.txt --- 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 |
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| @@ -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 |
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| diff -r 728dacaf08a9 -r 92eee5f31117 test-data/TEST_1/TEST_1_plot.svg --- 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 |
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| @@ -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> +<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> <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="hline-sparse" 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:2" /></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> -<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> <pattern id="vline" 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: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> </defs> </svg> |
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| diff -r 728dacaf08a9 -r 92eee5f31117 test-data/TEST_2/TEST_2.gff3 --- 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 |
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| @@ -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 |
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| diff -r 728dacaf08a9 -r 92eee5f31117 test-data/TEST_2/TEST_2.tsv --- 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 |
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| @@ -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 |
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| diff -r 728dacaf08a9 -r 92eee5f31117 test-data/TEST_2/TEST_2_plot.svg --- 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 |
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| @@ -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> <pattern id="vline" 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:5" /></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> <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> +<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> <pattern id="hline-sparse" 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: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: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> |
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| diff -r 728dacaf08a9 -r 92eee5f31117 test-data/TEST_3/TEST_3.gff3 --- 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 |
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| @@ -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 |
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| diff -r 728dacaf08a9 -r 92eee5f31117 test-data/TEST_3/TEST_3.tsv --- 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 |
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| @@ -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 |
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| diff -r 728dacaf08a9 -r 92eee5f31117 test-data/TEST_4/TEST_4.gff3 --- 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 |
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| @@ -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 |
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| diff -r 728dacaf08a9 -r 92eee5f31117 test-data/TEST_4/TEST_4.tsv --- 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 |
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| @@ -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 |
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| diff -r 728dacaf08a9 -r 92eee5f31117 test-data/TEST_4/TEST_4_plot.svg --- 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 |
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| @@ -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> <pattern id="hline-sparse" 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: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> <pattern id="vline" 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: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> +<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:2" /><line x1="0" y1="0" x2="0" y2="10" style="stroke:black;stroke-width:2" /></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> +<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> </defs> </svg> |
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| diff -r 728dacaf08a9 -r 92eee5f31117 test-data/TEST_5/TEST_5.txt --- 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 |
| b |
| @@ -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 |
| b |
| diff -r 728dacaf08a9 -r 92eee5f31117 test-data/TEST_6/TEST_6.embl --- 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 |
| b |
| @@ -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 |
| b |
| diff -r 728dacaf08a9 -r 92eee5f31117 test-data/TEST_6/TEST_6.gbff --- 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 |
| b |
| @@ -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 |
| b |
| diff -r 728dacaf08a9 -r 92eee5f31117 test-data/TEST_6/TEST_6.gff3 --- 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 |
| b |
| @@ -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 |
| b |
| diff -r 728dacaf08a9 -r 92eee5f31117 test-data/TEST_6/TEST_6.hypotheticals.tsv --- 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 |
| b |
| diff -r 728dacaf08a9 -r 92eee5f31117 test-data/TEST_6/TEST_6.json --- 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" |
| b |
| diff -r 728dacaf08a9 -r 92eee5f31117 test-data/TEST_6/TEST_6.tsv --- 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 |
| b |
| @@ -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 |
| b |
| diff -r 728dacaf08a9 -r 92eee5f31117 test-data/TEST_6/TEST_6.txt --- 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 |
| b |
| @@ -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 |
| b |
| diff -r 728dacaf08a9 -r 92eee5f31117 test-data/TEST_6/TEST_6_plot.svg --- 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 |
| b |
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