| Previous changeset 3:865ece5ca178 (2023-02-10) Next changeset 5:728dacaf08a9 (2023-09-16) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5 |
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modified:
bakta.xml macro.xml test-data/TEST_1/TEST_1.embl test-data/TEST_1/TEST_1.fna 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.log test-data/TEST_1/TEST_1.tsv test-data/TEST_1/TEST_1.txt test-data/TEST_2/TEST_2.gff3 test-data/TEST_2/TEST_2.tsv 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_5/TEST_5.log test-data/TEST_5/TEST_5.txt test-data/bakta_database.loc test-data/test-db/version.json tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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added:
test-data/TEST_1/TEST_1_plot.svg test-data/TEST_2/TEST_2_plot.svg test-data/TEST_4/TEST_4_plot.svg test-data/TEST_6/TEST_6.embl test-data/TEST_6/TEST_6.faa test-data/TEST_6/TEST_6.ffn test-data/TEST_6/TEST_6.fna test-data/TEST_6/TEST_6.gbff test-data/TEST_6/TEST_6.gff3 test-data/TEST_6/TEST_6.hypotheticals.faa test-data/TEST_6/TEST_6.hypotheticals.tsv test-data/TEST_6/TEST_6.json test-data/TEST_6/TEST_6.log 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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removed:
test-data/TEST_2/TEST_2.embl test-data/TEST_2/TEST_2.gbff test-data/TEST_2/TEST_2.hypotheticals.tsv test-data/TEST_2/TEST_2.json test-data/TEST_2/TEST_2.log test-data/TEST_2/TEST_2.svg test-data/TEST_2/TEST_2.txt test-data/TEST_3/TEST_3.embl test-data/TEST_3/TEST_3.gbff test-data/TEST_3/TEST_3.json test-data/TEST_3/TEST_3.log test-data/TEST_3/TEST_3.svg test-data/TEST_4/TEST_4.embl test-data/TEST_4/TEST_4.gbff test-data/TEST_4/TEST_4.hypotheticals.tsv test-data/TEST_4/TEST_4.json test-data/TEST_4/TEST_4.log test-data/TEST_4/TEST_4.svg test-data/TEST_4/TEST_4.txt |
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| diff -r 865ece5ca178 -r 3f0aa1b3e816 bakta.xml --- a/bakta.xml Fri Feb 10 14:20:09 2023 +0000 +++ b/bakta.xml Mon Jul 24 11:22:16 2023 +0000 |
| [ |
| b'@@ -11,10 +11,12 @@\n <expand macro="version_command"/>\n \n <command detect_errors="aggressive"><![CDATA[\n+\n mkdir -p ./database_path/amrfinderplus-db &&\n ln -s \'$(input_option.bakta_db_select.fields.path)\'/* database_path &&\n ln -s \'$(input_option.amrfinder_db_select.fields.path)/\' database_path/amrfinderplus-db/latest &&\n- bakta\n+ bakta --verbose\n+\n #*======================================\n CPU option\n ======================================*#\n@@ -22,7 +24,8 @@\n #*======================================\n Bakta database\n ======================================*#\n- --db ./database_path\n+ --db \'./database_path\'\n+ --output \'bakta_output\'\n #if $input_option.min_contig_length\n --min-contig-length $input_option.min_contig_length\n #else if $annotation.compliant\n@@ -88,8 +91,8 @@\n <section name="input_option" title="Input/Output options" expanded="true">\n <param name="bakta_db_select" type="select" label="The bakta database">\n <options from_data_table="bakta_database">\n- <filter type="static_value" value="@BAKTA_VERSION@" column="bakta_version"/>\n- <validator message="No bakta database is available" type="no_options"/>\n+ <filter type="static_value" value="@COMPATIBLE_BAKTA_VERSION@" column="bakta_version"/>\n+ <validator message="No bakta database is available" type="no_options"/>\n </options>\n </param>\n <param name="amrfinder_db_select" type="select" label="The amrfinderplus database">\n@@ -128,87 +131,89 @@\n <param argument="--replicons" type="data" format="tabular,csv" optional="true" label="Replicon information table (tsv/csv)" help=""/>\n <param argument="--compliant" type="boolean" truevalue="--compliant" falsevalue="" label="Force Genbank/ENA/DDJB compliance"/>\n <param argument="--proteins" type="data" format="fasta" optional="true" label="Protein fasta file" help="Fasta file of trusted protein sequences for CDS annotation"/>\n+ <param argument="--meta" type="boolean" truevalue="--meta" falsevalue="" label="Metagenome mode" help="Run in metagenome mode. This only affects CDS prediction"/>\n </section>\n <!-- PARAMETER FOR WORKFLOW ANALYSIS -->\n <section name="workflow" title="Workflow option to skip steps">\n <param name="skip_analysis" type="select" display="checkboxes" multiple="true" label="Select steps to skip">\n- <option value="--skip-trna"> Skip tRNA detection and annotation </option>\n- <option value="--skip-tmrna"> Skip tmRNA detection and annotation </option>\n- <option value="--skip-rrna"> Skip rRNA detection and annotation </option>\n- <option value="--skip-ncrna"> Skip ncRNA detection and annotation </option>\n- <option value="--skip-ncrna-region"> Skip ncRNA region detection and annotation </option>\n- <option value="--skip-crispr"> Skip CRISPR array detection and annotation </option>\n- <option value="--skip-cds"> Skip CDS detection and annotation </option>\n- <option value="--skip-pseudo"> Skip pseudogene detection and annotation </option>\n- <option value="--skip-sorf"> Skip sORF detection and annotation </option>\n- <option value="--skip-gap"> Skip gap detection and annotation </option>\n- <option value="--skip-ori"> Skip oriC/oriT detection and annotation </option>\n+ <option value="--skip-trna">Skip tRNA detection and annotation</option>\n+ <option value="--skip-tmrna">Skip tmRNA detection and annotation</option>\n+ <option value="--skip-rrna">Skip rRNA detection and annotation</option>\n+ <option value="--skip-ncrna">Ski'..b'lines_diff="4"/>\n <output name="annotation_gff3" value="TEST_4/TEST_4.gff3" lines_diff="4"/>\n <output name="annotation_ffn" value="TEST_4/TEST_4.ffn"/>\n- <output name="annotation_plot">\n- <assert_contents>\n- <has_size value="418399" delta="1000"/>\n- </assert_contents>\n- </output>\n+ <output name="annotation_plot" value="TEST_4/TEST_4_plot.svg" ftype="svg" compare="sim_size"/>\n </test>\n <test expect_num_outputs="2"> <!-- TEST_5 skip all steps and keep only the logfile and summary -->\n <section name="input_option" >\n- <param name="bakta_db_select" value="V0.1_2022-08-29"/>\n+ <param name="bakta_db_select" value="V5.0_2022-08-19"/>\n <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>\n <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>\n </section>\n@@ -323,14 +311,40 @@\n <param name="translation_table" value="4"/>\n </section>\n <section name="workflow">\n- <param name="skip_analysis" value="--skip-trna,--skip-tmrna,--skip-rrna,--skip-ncrna,--skip-ncrna-region,--skip-crispr,--skip-cds,--skip-sorf,--skip-gap,--skip-ori"/>\n+ <param name="skip_analysis" value="--skip-trna,--skip-tmrna,--skip-rrna,--skip-ncrna,--skip-ncrna-region,--skip-crispr,--skip-cds,--skip-sorf,--skip-gap,--skip-ori,--skip-plot"/>\n </section>\n <section name="output_files">\n <param name="output_selection" value="log_txt,sum_txt"/>\n </section>\n- <output name="logfile" value="TEST_5/TEST_5.log" lines_diff="6"/>\n+ <output name="logfile" value="TEST_5/TEST_5.log" lines_diff="13"/>\n <output name="summary_txt" value="TEST_5/TEST_5.txt" lines_diff="4"/>\n </test>\n+ <test expect_num_outputs="13"> <!-- TEST_6 metagenome option -->\n+ <section name="input_option" >\n+ <param name="bakta_db_select" value="V5.0_2022-08-19"/>\n+ <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>\n+ <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>\n+ </section>\n+ <section name="annotation">\n+ <param name="meta" value="true"/>\n+ </section>\n+ <section name="output_files">\n+ <param name="output_selection" value="file_tsv,file_gff3,file_gbff,file_embl,file_fna,file_ffn,file_faa,hypo_tsv,hypo_fa,sum_txt,file_json,file_plot,log_txt"/>\n+ </section>\n+ <output name="annotation_tsv" value="TEST_6/TEST_6.tsv" lines_diff="2"/>\n+ <output name="annotation_gff3" value="TEST_6/TEST_6.gff3" lines_diff="2"/>\n+ <output name="annotation_gbff" value="TEST_6/TEST_6.gbff" lines_diff="8"/>\n+ <output name="annotation_embl" value="TEST_6/TEST_6.embl" lines_diff="6"/>\n+ <output name="annotation_fna" value="TEST_6/TEST_6.fna"/>\n+ <output name="annotation_ffn" value="TEST_6/TEST_6.ffn"/>\n+ <output name="annotation_faa" value="TEST_6/TEST_6.faa"/>\n+ <output name="hypotheticals_tsv" value="TEST_6/TEST_6.hypotheticals.tsv" lines_diff="4"/>\n+ <output name="hypotheticals_faa" value="TEST_6/TEST_6.hypotheticals.faa"/>\n+ <output name="summary_txt" value="TEST_6/TEST_6.txt" lines_diff="4"/>\n+ <output name="annotation_plot" value="TEST_6/TEST_6_plot.svg" ftype="svg" compare="sim_size"/>\n+ <output name="annotation_json" value="TEST_6/TEST_6.json" lines_diff="6"/>\n+ <output name="logfile" value="TEST_6/TEST_6.log" lines_diff="15"/>\n+ </test>\n </tests>\n <help><![CDATA[**What it does**\n Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.\n' |
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| diff -r 865ece5ca178 -r 3f0aa1b3e816 macro.xml --- a/macro.xml Fri Feb 10 14:20:09 2023 +0000 +++ b/macro.xml Mon Jul 24 11:22:16 2023 +0000 |
| [ |
| @@ -1,8 +1,8 @@ <macros> - <token name="@TOOL_VERSION@">1.6.1</token> - <token name="@BAKTA_VERSION@">1.5</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@TOOL_VERSION@">1.8.1</token> + <token name="@COMPATIBLE_BAKTA_VERSION@">1.7</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">21.05</token> <xml name="version_command"> <version_command><![CDATA[bakta --version]]></version_command> |
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| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/TEST_1/TEST_1.embl --- a/test-data/TEST_1/TEST_1.embl Fri Feb 10 14:20:09 2023 +0000 +++ b/test-data/TEST_1/TEST_1.embl Mon Jul 24 11:22:16 2023 +0000 |
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| @@ -8,16 +8,13 @@ OC . XX CC Annotated with Bakta -CC Software: v1.5.0 -CC Database: v4.0 +CC Software: v1.8.1 +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 :: 09/16/2022, 07:31:59 -CC Annotation Pipeline :: Bakta -CC Annotation Software version :: v1.5.0 -CC Annotation Database version :: v4.0 +CC Annotation Date :: 06/19/2023, 09:30:06 CC CDSs :: 2 CC tRNAs :: 0 CC tmRNAs :: 0 |
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| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/TEST_1/TEST_1.fna --- a/test-data/TEST_1/TEST_1.fna Fri Feb 10 14:20:09 2023 +0000 +++ b/test-data/TEST_1/TEST_1.fna Mon Jul 24 11:22:16 2023 +0000 |
| [ |
| @@ -1,4 +1,4 @@ ->contig_1 [completeness=complete] [topology=circular] [gcode=11] +>contig_1 [gcode=11] [completeness=complete] [topology=circular] [plasmid-name=unnamed1] TTCTTCTGCGAGTTCGTGCAGCTTCTCACACATGGTGGCCTGCTCGTCAGCATCGAGTGC GTCCAGTTTTTCGAGCAGCGTCAGGCTCTGGCTTTTTATGAATCCCGCCATGTTGAGTGC AGTTTGCTGCTGCTTGTTCATCTTTCTGTTTTCTCCGTTCTGTCTGTCATCTGCGTCGTG |
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| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/TEST_1/TEST_1.gbff --- a/test-data/TEST_1/TEST_1.gbff Fri Feb 10 14:20:09 2023 +0000 +++ b/test-data/TEST_1/TEST_1.gbff Mon Jul 24 11:22:16 2023 +0000 |
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| @@ -1,4 +1,4 @@ -LOCUS contig_1 1330 bp DNA circular BCT 16-SEP-2022 +LOCUS contig_1 1330 bp DNA circular BCT 19-JUN-2023 DEFINITION plasmid unnamed1, complete sequence. ACCESSION contig_1 VERSION contig_1 @@ -7,16 +7,13 @@ ORGANISM . . COMMENT Annotated with Bakta - Software: v1.5.0 - Database: v4.0 + Software: v1.8.1 + Database: v5.0, full DOI: 10.1099/mgen.0.000685 URL: github.com/oschwengers/bakta ##Genome Annotation Summary:## - Annotation Date :: 09/16/2022, 07:31:59 - Annotation Pipeline :: Bakta - Annotation Software version :: v1.5.0 - Annotation Database version :: v4.0 + Annotation Date :: 06/19/2023, 09:30:06 CDSs :: 2 tRNAs :: 0 tmRNAs :: 0 |
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| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/TEST_1/TEST_1.gff3 --- a/test-data/TEST_1/TEST_1.gff3 Fri Feb 10 14:20:09 2023 +0000 +++ b/test-data/TEST_1/TEST_1.gff3 Mon Jul 24 11:22:16 2023 +0000 |
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| @@ -1,8 +1,8 @@ ##gff-version 3 ##feature-ontology https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/v3.1/so.obo # Annotated with Bakta -# Software: v1.5.0 -# Database: v4.0 +# Software: v1.8.1 +# Database: v5.0, full # DOI: 10.1099/mgen.0.000685 # URL: github.com/oschwengers/bakta ##sequence-region contig_1 1 1330 |
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| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/TEST_1/TEST_1.hypotheticals.tsv --- a/test-data/TEST_1/TEST_1.hypotheticals.tsv Fri Feb 10 14:20:09 2023 +0000 +++ b/test-data/TEST_1/TEST_1.hypotheticals.tsv Mon Jul 24 11:22:16 2023 +0000 |
| [ |
| @@ -1,5 +1,5 @@ -#Annotated with Bakta v1.5.0, https://github.com/oschwengers/bakta -#Database v4.0, https://doi.org/10.5281/zenodo.4247252 +#Annotated with Bakta v1.8.1, 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 contig_1 971 141 - IHHALP_00010 18.9 7.7 |
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| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/TEST_1/TEST_1.json --- a/test-data/TEST_1/TEST_1.json Fri Feb 10 14:20:09 2023 +0000 +++ b/test-data/TEST_1/TEST_1.json Mon Jul 24 11:22:16 2023 +0000 |
| [ |
| @@ -32,6 +32,7 @@ "aa_hexdigest": "d9bdebc84195542e775c3d22458b507e", "nt": "ATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAG", "hypothetical": true, + "genes": [], "seq_stats": { "molecular_weight": 12072.90819999999, "isoelectric_point": 10.367886161804197 @@ -56,6 +57,7 @@ "edge": true, "nt": "ATGAACAAGCAGCAGCAAACTGCACTCAACATGGCGGGATTCATAAAAAGCCAGAGCCTGACGCTGCTCGAAAAACTGGACGCACTCGATGCTGACGAGCAGGCCACCATGTGTGAGAAGCTGCACGAACTCGCAGAAGAACAAATAGAAGCAATAAAAAATAAAGATAAAACTTTATTTATTGTCTATGCTACTGATATTTATAGCCCGAGCGAATTTTTCTCAAAAATCGAATCCGACTTGAAGAAAAAGAAAAGCAAGGGTGATGTTTTTTTTGATTTAATAATTCCTAACGGTGGAAAAAAAGATCGTTACGTCTATACGTCATTTAATGGCGAGAAGTTTTCAAGTTACACATTAAACAAAGTTACGAAAACTGATGAATATAATGATTTATCTGAGCTCTCGGCTTCGTTCTTTAAAAAAAACTTTGATAAGATCAACGTAAACCTTCTATCCAAAGCCACATCATTTGCTTTGAAAAAAGGCATTCCAATATAA", "hypothetical": true, + "genes": [], "seq_stats": { "molecular_weight": 18866.325799999995, "isoelectric_point": 7.696590614318848 @@ -67,7 +69,7 @@ "sequences": [ { "id": "contig_1", - "description": "[completeness=complete] [topology=circular] [gcode=11]", + "description": "[gcode=11] [completeness=complete] [topology=circular] [plasmid-name=unnamed1]", "sequence": "TTCTTCTGCGAGTTCGTGCAGCTTCTCACACATGGTGGCCTGCTCGTCAGCATCGAGTGCGTCCAGTTTTTCGAGCAGCGTCAGGCTCTGGCTTTTTATGAATCCCGCCATGTTGAGTGCAGTTTGCTGCTGCTTGTTCATCTTTCTGTTTTCTCCGTTCTGTCTGTCATCTGCGTCGTGTGATTATATCGCGCACCACTTTTCGACCGTCTTACCGCCGGTATTCTGCCGACGGACATTTCAGTCAGACAACACTGTCACTGCCAAAAAACAGCAGTGCTTTGTTGGTAATTCGAACTTGCAGACAGGACAGGATGTGCAATTGTTATACCGCGCATACATGCACGCTATTACAATTACCCTGGTCAGGGCTTCGCCCCGACACCCCATGTCAGATACGGAGCCATGTTTTATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAGCTTCCCGGAGAGAAACTGTCGAAAACAGACGGTATGAACGCCGTAAGCCCCCAAACCGATCGCCATTCACTTTCATGCATAGCTATGCAGTGAGCTGAAAGCGATCCTGACGCATTTTTCCGGTTTACCCCGGGGAAAACATCTCTTTTTGCGGTGTCTGCGTCAGAATCGCGTTCAGCGCGTTTTGGCGGTGCGCGTAATGAGACGTTATGGTAAATGTCTTCTGGCTTGATATTATATTGGAATGCCTTTTTTCAAAGCAAATGATGTGGCTTTGGATAGAAGGTTTACGTTGATCTTATCAAAGTTTTTTTTAAAGAACGAAGCCGAGAGCTCAGATAAATCATTATATTCATCAGTTTTCGTAACTTTGTTTAATGTGTAACTTGAAAACTTCTCGCCATTAAATGACGTATAGACGTAACGATCTTTTTTTCCACCGTTAGGAATTATTAAATCAAAAAAAACATCACCCTTGCTTTTCTTTTTCTTCAAGTCGGATTCGATTTTTGAGAAAAATTCGCTCGGGCTATAAATATCAGTAGCATAGACAATAAATAAAGTTTTATCTTTATTTTTTATTGCTTCTATTTG", "length": 1330, "complete": true, @@ -80,11 +82,14 @@ } ], "run": { - "start": "2022-09-16 07:31:58", - "end": "2022-09-16 07:31:59" + "start": "2023-06-19 09:30:05", + "end": "2023-06-19 09:30:06" }, "version": { - "bakta": "1.5.0", - "db": "4.0" + "bakta": "1.8.1", + "db": { + "version": "5.0", + "type": "full" + } } } \ No newline at end of file |
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| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/TEST_1/TEST_1.log --- a/test-data/TEST_1/TEST_1.log Fri Feb 10 14:20:09 2023 +0000 +++ b/test-data/TEST_1/TEST_1.log Mon Jul 24 11:22:16 2023 +0000 |
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| @@ -1,3 +1,13 @@ +Bakta v1.8.1 +Options and arguments: + input: /tmp/tmp6wdeee6u/files/3/2/d/dataset_32d4899b-3214-49f6-a57b-29ff0e04425d.dat + db: /tmp/tmp6wdeee6u/job_working_directory/000/2/working/database_path, version 5.0, full + output: /tmp/tmp6wdeee6u/job_working_directory/000/2/working/bakta_output + tmp directory: /tmp/tmp6wdeee6u/tmp/tmpm3wbu37o + prefix: bakta_output + threads: 1 + translation table: 11 + parse genome sequences... imported: 1 filtered & revised: 1 @@ -53,6 +63,8 @@ apply feature overlap filters... select features and create locus tags... selected: 2 +improve annotations... + revised gene symbols: 0 genome statistics: Genome size: 1,330 bp @@ -70,15 +82,15 @@ ncRNA regions: 0 CRISPR arrays: 0 CDSs: 2 - hypotheticals: 2 - pseudogenes: 0 - signal peptides: 0 + hypotheticals: 2 + pseudogenes: 0 + signal peptides: 0 sORFs: 0 gaps: 0 oriCs/oriVs: 0 oriTs: 0 -export annotation results to: /tmp/tmpmnqj1xog/job_working_directory/000/2/working +export annotation results to: /tmp/tmp6wdeee6u/job_working_directory/000/2/working/bakta_output human readable TSV... GFF3... INSDC GenBank & EMBL... |
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| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/TEST_1/TEST_1.tsv --- a/test-data/TEST_1/TEST_1.tsv Fri Feb 10 14:20:09 2023 +0000 +++ b/test-data/TEST_1/TEST_1.tsv Mon Jul 24 11:22:16 2023 +0000 |
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| @@ -1,5 +1,8 @@ -#Annotated with Bakta (v1.5.0): https://github.com/oschwengers/bakta -#Database (v4.0): https://doi.org/10.5281/zenodo.4247252 +# Annotated with Bakta +# Software: v1.8.1 +# Database: v5.0, full +# DOI: 10.1099/mgen.0.000685 +# URL: github.com/oschwengers/bakta #Sequence Id Type Start Stop Strand Locus Tag Gene Product DbXrefs contig_1 cds 413 736 + IHHALP_00005 hypothetical protein contig_1 cds 971 141 - IHHALP_00010 hypothetical protein |
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| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/TEST_1/TEST_1.txt --- a/test-data/TEST_1/TEST_1.txt Fri Feb 10 14:20:09 2023 +0000 +++ b/test-data/TEST_1/TEST_1.txt Mon Jul 24 11:22:16 2023 +0000 |
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| @@ -24,7 +24,7 @@ oriTs: 0 Bakta: -Software: v1.5.0 -Database: v4.0 +Software: v1.8.1 +Database: v5.0, full DOI: 10.1099/mgen.0.000685 URL: github.com/oschwengers/bakta |
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| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/TEST_1/TEST_1_plot.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_1/TEST_1_plot.svg Mon Jul 24 11:22:16 2023 +0000 |
| b |
| b'@@ -0,0 +1,2400 @@\n+<?xml version="1.0" encoding="utf-8" standalone="no"?>\n+<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">\n+<svg width="3000px" height="3000px" version="1.1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">\n+<g id="bg">\n+<rect x="0" y="0" width="3000px" height="3000px" style="fill:rgb(255,255,255);"/>\n+</g>\n+<g id="ideograms">\n+<path d="M1500.000,230.000 A1270.000,1270.000 40.000 1,1 1499.202,230.000 L1499.199,225.000 A1275.000,1275.000 0.000 1,0 1500.000,225.000 Z" style="stroke-linecap:round;fill:rgb(0,0,0);" />\n+<line x1=\'1500.0\' y1=\'225.0\' x2=\'1500.0\' y2=\'200.0\' style="stroke-width:4.0;stroke:rgb(0,0,0);stroke-linecap:round;fill:none;" />\n+<text x="1522.0" y="190.2" font-size="52.0px" font-family="CMUBright-Roman" style="text-anchor:start;fill:rgb(0,0,0);" transform="rotate(270.0,1522.0,190.2)" >0 bp</text>\n+<line x1=\'1515.1\' y1=\'225.1\' x2=\'1515.1\' 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| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/TEST_2/TEST_2.embl --- a/test-data/TEST_2/TEST_2.embl Fri Feb 10 14:20:09 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,90 +0,0 @@ -ID NC_002127; SV 1; circular; DNA; ; PRO; 1330 BP. -XX -AC NC_002127; -XX -DE Escherichia coli o157:h7 Sakai plasmid pOSAK1, complete sequence -XX -OS Escherichia coli o157:h7 Sakai -OC . -XX -CC Annotated with Bakta -CC Software: v1.5.0 -CC Database: v4.0 -CC DOI: 10.1099/mgen.0.000685 -CC URL: github.com/oschwengers/bakta -CC -CC ##Genome Annotation Summary:## -CC Annotation Date :: 09/16/2022, 07:32:10 -CC Annotation Pipeline :: Bakta -CC Annotation Software version :: v1.5.0 -CC Annotation Database version :: v4.0 -CC CDSs :: 2 -CC tRNAs :: 0 -CC tmRNAs :: 0 -CC rRNAs :: 0 -CC ncRNAs :: 0 -CC regulatory ncRNAs :: 0 -CC CRISPR Arrays :: 0 -CC oriCs/oriVs :: 0 -CC oriTs :: 0 -CC gaps :: 0 -CC pseudogenes :: 0 -XX -FH Key Location/Qualifiers -FH -FT source 1..1330 -FT /mol_type="genomic DNA" -FT /organism="Escherichia coli o157:h7 Sakai" -FT /strain="Sakai" -FT /plasmid="pOSAK1" -FT gene 413..736 -FT /locus_tag="IHHALP_00005" -FT CDS 413..736 -FT /product="hypothetical protein" -FT /locus_tag="IHHALP_00005" -FT /protein_id="gnl|Bakta|IHHALP_00005" -FT /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA -FT AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL -FT MAD" -FT /codon_start=1 -FT /transl_table=11 -FT /inference="ab initio prediction:Prodigal:2.6" -FT gene complement(join(971..1330,1..141)) -FT /locus_tag="IHHALP_00010" -FT CDS complement(join(971..1330,1..141)) -FT /product="hypothetical protein" -FT /locus_tag="IHHALP_00010" -FT /protein_id="gnl|Bakta|IHHALP_00010" -FT /translation="MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELA -FT EEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDR -FT YVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKG -FT IPI" -FT /codon_start=1 -FT /transl_table=11 -FT /inference="ab initio prediction:Prodigal:2.6" -XX -SQ Sequence 1330 BP; 330 A; 291 C; 310 G; 399 T; 0 other; - ttcttctgcg agttcgtgca gcttctcaca catggtggcc tgctcgtcag catcgagtgc 60 - gtccagtttt tcgagcagcg tcaggctctg gctttttatg aatcccgcca tgttgagtgc 120 - agtttgctgc tgcttgttca tctttctgtt ttctccgttc tgtctgtcat ctgcgtcgtg 180 - tgattatatc gcgcaccact tttcgaccgt cttaccgccg gtattctgcc gacggacatt 240 - tcagtcagac aacactgtca ctgccaaaaa acagcagtgc tttgttggta attcgaactt 300 - gcagacagga caggatgtgc aattgttata ccgcgcatac atgcacgcta ttacaattac 360 - cctggtcagg gcttcgcccc gacaccccat gtcagatacg gagccatgtt ttatgacaaa 420 - acgaagtgga agtaatacgc gcaggcgggc tatcagtcgc cctgttcgtc tgacggcaga 480 - agaagaccag gaaatcagaa aaagggctgc tgaatgcggc aagaccgttt ctggtttttt 540 - acgggcggca gctctcggta agaaagttaa ctcactgact gatgaccggg tgctgaaaga 600 - agttatgcga ctgggggcgt tgcagaaaaa actctttatc gacggcaagc gtgtcgggga 660 - cagagagtat gcggaggtgc tgatcgctat tacggagtat caccgtgccc tgttatccag 720 - gcttatggca gattagcttc ccggagagaa actgtcgaaa acagacggta tgaacgccgt 780 - aagcccccaa accgatcgcc attcactttc atgcatagct atgcagtgag ctgaaagcga 840 - tcctgacgca tttttccggt ttaccccggg gaaaacatct ctttttgcgg tgtctgcgtc 900 - agaatcgcgt tcagcgcgtt ttggcggtgc gcgtaatgag acgttatggt aaatgtcttc 960 - tggcttgata ttatattgga atgccttttt tcaaagcaaa tgatgtggct ttggatagaa 1020 - ggtttacgtt gatcttatca aagttttttt taaagaacga agccgagagc tcagataaat 1080 - cattatattc atcagttttc gtaactttgt ttaatgtgta acttgaaaac ttctcgccat 1140 - taaatgacgt atagacgtaa cgatcttttt ttccaccgtt aggaattatt aaatcaaaaa 1200 - aaacatcacc cttgcttttc tttttcttca agtcggattc gatttttgag aaaaattcgc 1260 - tcgggctata aatatcagta gcatagacaa taaataaagt tttatcttta ttttttattg 1320 - cttctatttg 1330 -// |
| b |
| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/TEST_2/TEST_2.gbff --- a/test-data/TEST_2/TEST_2.gbff Fri Feb 10 14:20:09 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,86 +0,0 @@ -LOCUS NC_002127.1 1330 bp DNA circular BCT 16-SEP-2022 -DEFINITION Escherichia coli o157:h7 Sakai plasmid pOSAK1, complete sequence. -ACCESSION NC_002127 -VERSION NC_002127.1 -KEYWORDS . -SOURCE Escherichia coli o157:h7 Sakai - ORGANISM Escherichia coli o157:h7 Sakai - . -COMMENT Annotated with Bakta - Software: v1.5.0 - Database: v4.0 - DOI: 10.1099/mgen.0.000685 - URL: github.com/oschwengers/bakta - - ##Genome Annotation Summary:## - Annotation Date :: 09/16/2022, 07:32:10 - Annotation Pipeline :: Bakta - Annotation Software version :: v1.5.0 - Annotation Database version :: v4.0 - CDSs :: 2 - tRNAs :: 0 - tmRNAs :: 0 - rRNAs :: 0 - ncRNAs :: 0 - regulatory ncRNAs :: 0 - CRISPR Arrays :: 0 - oriCs/oriVs :: 0 - oriTs :: 0 - gaps :: 0 - pseudogenes :: 0 -FEATURES Location/Qualifiers - source 1..1330 - /mol_type="genomic DNA" - /organism="Escherichia coli o157:h7 Sakai" - /strain="Sakai" - /plasmid="pOSAK1" - gene 413..736 - /locus_tag="IHHALP_00005" - CDS 413..736 - /product="hypothetical protein" - /locus_tag="IHHALP_00005" - /protein_id="gnl|Bakta|IHHALP_00005" - /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA - AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL - MAD" - /codon_start=1 - /transl_table=11 - /inference="ab initio prediction:Prodigal:2.6" - gene complement(join(971..1330,1..141)) - /locus_tag="IHHALP_00010" - CDS complement(join(971..1330,1..141)) - /product="hypothetical protein" - /locus_tag="IHHALP_00010" - /protein_id="gnl|Bakta|IHHALP_00010" - /translation="MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELA - EEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDR - YVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKG - IPI" - /codon_start=1 - /transl_table=11 - /inference="ab initio prediction:Prodigal:2.6" -ORIGIN - 1 ttcttctgcg agttcgtgca gcttctcaca catggtggcc tgctcgtcag catcgagtgc - 61 gtccagtttt tcgagcagcg tcaggctctg gctttttatg aatcccgcca tgttgagtgc - 121 agtttgctgc tgcttgttca tctttctgtt ttctccgttc tgtctgtcat ctgcgtcgtg - 181 tgattatatc gcgcaccact tttcgaccgt cttaccgccg gtattctgcc gacggacatt - 241 tcagtcagac aacactgtca ctgccaaaaa acagcagtgc tttgttggta attcgaactt - 301 gcagacagga caggatgtgc aattgttata ccgcgcatac atgcacgcta ttacaattac - 361 cctggtcagg gcttcgcccc gacaccccat gtcagatacg gagccatgtt ttatgacaaa - 421 acgaagtgga agtaatacgc gcaggcgggc tatcagtcgc cctgttcgtc tgacggcaga - 481 agaagaccag gaaatcagaa aaagggctgc tgaatgcggc aagaccgttt ctggtttttt - 541 acgggcggca gctctcggta agaaagttaa ctcactgact gatgaccggg tgctgaaaga - 601 agttatgcga ctgggggcgt tgcagaaaaa actctttatc gacggcaagc gtgtcgggga - 661 cagagagtat gcggaggtgc tgatcgctat tacggagtat caccgtgccc tgttatccag - 721 gcttatggca gattagcttc ccggagagaa actgtcgaaa acagacggta tgaacgccgt - 781 aagcccccaa accgatcgcc attcactttc atgcatagct atgcagtgag ctgaaagcga - 841 tcctgacgca tttttccggt ttaccccggg gaaaacatct ctttttgcgg tgtctgcgtc - 901 agaatcgcgt tcagcgcgtt ttggcggtgc gcgtaatgag acgttatggt aaatgtcttc - 961 tggcttgata ttatattgga atgccttttt tcaaagcaaa tgatgtggct ttggatagaa - 1021 ggtttacgtt gatcttatca aagttttttt taaagaacga agccgagagc tcagataaat - 1081 cattatattc atcagttttc gtaactttgt ttaatgtgta acttgaaaac ttctcgccat - 1141 taaatgacgt atagacgtaa cgatcttttt ttccaccgtt aggaattatt aaatcaaaaa - 1201 aaacatcacc cttgcttttc tttttcttca agtcggattc gatttttgag aaaaattcgc - 1261 tcgggctata aatatcagta gcatagacaa taaataaagt tttatcttta ttttttattg - 1321 cttctatttg -// |
| b |
| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/TEST_2/TEST_2.gff3 --- a/test-data/TEST_2/TEST_2.gff3 Fri Feb 10 14:20:09 2023 +0000 +++ b/test-data/TEST_2/TEST_2.gff3 Mon Jul 24 11:22:16 2023 +0000 |
| b |
| @@ -2,8 +2,8 @@ ##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: v1.5.0 -# Database: v4.0 +# Software: v1.8.1 +# Database: v5.0, full # DOI: 10.1099/mgen.0.000685 # URL: github.com/oschwengers/bakta ##sequence-region NC_002127.1 1 1330 |
| b |
| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/TEST_2/TEST_2.hypotheticals.tsv --- a/test-data/TEST_2/TEST_2.hypotheticals.tsv Fri Feb 10 14:20:09 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,5 +0,0 @@ -#Annotated with Bakta v1.5.0, https://github.com/oschwengers/bakta -#Database v4.0, https://doi.org/10.5281/zenodo.4247252 -#Sequence Id Start Stop Strand Locus Tag Mol Weight [kDa] Iso El. Point Pfam hits Dbxrefs -NC_002127.1 413 736 + IHHALP_00005 12.1 10.4 -NC_002127.1 971 141 - IHHALP_00010 18.9 7.7 |
| b |
| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/TEST_2/TEST_2.json --- a/test-data/TEST_2/TEST_2.json Fri Feb 10 14:20:09 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,89 +0,0 @@ -{ - "genome": { - "genus": "Escherichia", - "species": "coli o157:h7", - "strain": "Sakai", - "plasmid": "pOSAK1", - "complete": true, - "gram": "?", - "translation_table": 11 - }, - "stats": { - "no_sequences": 1, - "size": 1330, - "gc": 0.4518796992481203, - "n_ratio": 0.0, - "n50": 1330, - "coding_ratio": 0.6203007518796992 - }, - "features": [ - { - "type": "cds", - "contig": "NC_002127.1", - "start": 413, - "stop": 736, - "strand": "+", - "gene": null, - "product": "hypothetical protein", - "start_type": "ATG", - "rbs_motif": "GGAG/GAGG", - "db_xrefs": [], - "frame": 2, - "aa": "MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD", - "aa_hexdigest": "d9bdebc84195542e775c3d22458b507e", - "nt": "ATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAG", - "hypothetical": true, - "seq_stats": { - "molecular_weight": 12072.90819999999, - "isoelectric_point": 10.367886161804197 - }, - "id": "IHHALPPJCH_1", - "locus": "IHHALP_00005" - }, - { - "type": "cds", - "contig": "NC_002127.1", - "start": 971, - "stop": 141, - "strand": "-", - "gene": null, - "product": "hypothetical protein", - "start_type": "ATG", - "rbs_motif": "AGGA/GGAG/GAGG", - "db_xrefs": [], - "frame": 1, - "aa": "MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI", - "aa_hexdigest": "1e7027cbe48346e06a83e802a9385584", - "edge": true, - "nt": "ATGAACAAGCAGCAGCAAACTGCACTCAACATGGCGGGATTCATAAAAAGCCAGAGCCTGACGCTGCTCGAAAAACTGGACGCACTCGATGCTGACGAGCAGGCCACCATGTGTGAGAAGCTGCACGAACTCGCAGAAGAACAAATAGAAGCAATAAAAAATAAAGATAAAACTTTATTTATTGTCTATGCTACTGATATTTATAGCCCGAGCGAATTTTTCTCAAAAATCGAATCCGACTTGAAGAAAAAGAAAAGCAAGGGTGATGTTTTTTTTGATTTAATAATTCCTAACGGTGGAAAAAAAGATCGTTACGTCTATACGTCATTTAATGGCGAGAAGTTTTCAAGTTACACATTAAACAAAGTTACGAAAACTGATGAATATAATGATTTATCTGAGCTCTCGGCTTCGTTCTTTAAAAAAAACTTTGATAAGATCAACGTAAACCTTCTATCCAAAGCCACATCATTTGCTTTGAAAAAAGGCATTCCAATATAA", - "hypothetical": true, - "seq_stats": { - "molecular_weight": 18866.325799999995, - "isoelectric_point": 7.696590614318848 - }, - "id": "IHHALPPJCH_2", - "locus": "IHHALP_00010" - } - ], - "sequences": [ - { - "id": "NC_002127.1", - "description": "Escherichia coli O157:H7 str. Sakai plasmid pOSAK1, complete sequence", - "sequence": "TTCTTCTGCGAGTTCGTGCAGCTTCTCACACATGGTGGCCTGCTCGTCAGCATCGAGTGCGTCCAGTTTTTCGAGCAGCGTCAGGCTCTGGCTTTTTATGAATCCCGCCATGTTGAGTGCAGTTTGCTGCTGCTTGTTCATCTTTCTGTTTTCTCCGTTCTGTCTGTCATCTGCGTCGTGTGATTATATCGCGCACCACTTTTCGACCGTCTTACCGCCGGTATTCTGCCGACGGACATTTCAGTCAGACAACACTGTCACTGCCAAAAAACAGCAGTGCTTTGTTGGTAATTCGAACTTGCAGACAGGACAGGATGTGCAATTGTTATACCGCGCATACATGCACGCTATTACAATTACCCTGGTCAGGGCTTCGCCCCGACACCCCATGTCAGATACGGAGCCATGTTTTATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAGCTTCCCGGAGAGAAACTGTCGAAAACAGACGGTATGAACGCCGTAAGCCCCCAAACCGATCGCCATTCACTTTCATGCATAGCTATGCAGTGAGCTGAAAGCGATCCTGACGCATTTTTCCGGTTTACCCCGGGGAAAACATCTCTTTTTGCGGTGTCTGCGTCAGAATCGCGTTCAGCGCGTTTTGGCGGTGCGCGTAATGAGACGTTATGGTAAATGTCTTCTGGCTTGATATTATATTGGAATGCCTTTTTTCAAAGCAAATGATGTGGCTTTGGATAGAAGGTTTACGTTGATCTTATCAAAGTTTTTTTTAAAGAACGAAGCCGAGAGCTCAGATAAATCATTATATTCATCAGTTTTCGTAACTTTGTTTAATGTGTAACTTGAAAACTTCTCGCCATTAAATGACGTATAGACGTAACGATCTTTTTTTCCACCGTTAGGAATTATTAAATCAAAAAAAACATCACCCTTGCTTTTCTTTTTCTTCAAGTCGGATTCGATTTTTGAGAAAAATTCGCTCGGGCTATAAATATCAGTAGCATAGACAATAAATAAAGTTTTATCTTTATTTTTTATTGCTTCTATTTG", - "length": 1330, - "complete": true, - "type": "plasmid", - "topology": "circular", - "simple_id": "contig_1", - "name": "pOSAK1" - } - ], - "run": { - "start": "2022-09-16 07:32:09", - "end": "2022-09-16 07:32:10" - }, - "version": { - "bakta": "1.5.0", - "db": "4.0" - } -} \ No newline at end of file |
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| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/TEST_2/TEST_2.log --- a/test-data/TEST_2/TEST_2.log Fri Feb 10 14:20:09 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,93 +0,0 @@ -parse genome sequences... - imported: 1 - filtered & revised: 1 - plasmids: 1 - -start annotation... -skip tRNA prediction... -skip tmRNA prediction... -predict rRNAs... - found: 0 -predict ncRNAs... - found: 0 -predict ncRNA regions... - found: 0 -predict CRISPR arrays... - found: 0 -predict & annotate CDSs... - predicted: 2 - discarded spurious: 0 - revised translational exceptions: 0 - detected IPSs: 0 - found PSCs: 0 - found PSCCs: 0 - lookup annotations... - conduct expert systems... - amrfinder: 0 - protein sequences: 0 - combine annotations and mark hypotheticals... - detect pseudogenes... - pseudogene candidates: 0 - found pseudogenes: 0 -analyze hypothetical proteins: 2 - detected Pfam hits: 0 - calculated proteins statistics - revise special cases... -extract sORF... - potential: 22 - discarded due to overlaps: 2 - discarded spurious: 0 - detected IPSs: 0 - found PSCs: 0 - lookup annotations... - filter and combine annotations... - filtered sORFs: 0 -detect gaps... - found: 0 -detect oriCs/oriVs... - found: 0 -detect oriTs... - found: 0 -apply feature overlap filters... -select features and create locus tags... -selected: 2 - -genome statistics: - Genome size: 1,330 bp - Contigs/replicons: 1 - GC: 45.2 % - N50: 1,330 - N ratio: 0.0 % - coding density: 62.0 % - -annotation summary: - tRNAs: 0 - tmRNAs: 0 - rRNAs: 0 - ncRNAs: 0 - ncRNA regions: 0 - CRISPR arrays: 0 - CDSs: 2 - hypotheticals: 2 - pseudogenes: 0 - signal peptides: 0 - sORFs: 0 - gaps: 0 - oriCs/oriVs: 0 - oriTs: 0 - -export annotation results to: /tmp/tmpmnqj1xog/job_working_directory/000/4/working - human readable TSV... - GFF3... - INSDC GenBank & EMBL... - genome sequences... - feature nucleotide sequences... - translated CDS sequences... - circular genome plot... - hypothetical TSV... - translated hypothetical CDS sequences... - machine readable JSON... - genome and annotation summary... - -If you use these results please cite Bakta: https://doi.org/10.1099/mgen.0.000685 -Annotation successfully finished in 0:00 [mm:ss]. |
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| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/TEST_2/TEST_2.tsv --- a/test-data/TEST_2/TEST_2.tsv Fri Feb 10 14:20:09 2023 +0000 +++ b/test-data/TEST_2/TEST_2.tsv Mon Jul 24 11:22:16 2023 +0000 |
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| @@ -1,5 +1,8 @@ -#Annotated with Bakta (v1.5.0): https://github.com/oschwengers/bakta -#Database (v4.0): https://doi.org/10.5281/zenodo.4247252 +# Annotated with Bakta +# Software: v1.8.1 +# Database: v5.0, full +# DOI: 10.1099/mgen.0.000685 +# URL: github.com/oschwengers/bakta #Sequence Id Type Start Stop Strand Locus Tag Gene Product DbXrefs NC_002127.1 cds 413 736 + IHHALP_00005 hypothetical protein NC_002127.1 cds 971 141 - IHHALP_00010 hypothetical protein |
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| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/TEST_2/TEST_2.txt --- a/test-data/TEST_2/TEST_2.txt Fri Feb 10 14:20:09 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,30 +0,0 @@ -Sequence(s): -Length: 1330 -Count: 1 -GC: 45.2 -N50: 1330 -N ratio: 0.0 -coding density: 62.0 - -Annotation: -tRNAs: 0 -tmRNAs: 0 -rRNAs: 0 -ncRNAs: 0 -ncRNA regions: 0 -CRISPR arrays: 0 -CDSs: 2 -pseudogenes: 0 -hypotheticals: 2 -signal peptides: 0 -sORFs: 0 -gaps: 0 -oriCs: 0 -oriVs: 0 -oriTs: 0 - -Bakta: -Software: v1.5.0 -Database: v4.0 -DOI: 10.1099/mgen.0.000685 -URL: github.com/oschwengers/bakta |
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| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/TEST_3/TEST_3.embl --- a/test-data/TEST_3/TEST_3.embl Fri Feb 10 14:20:09 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,63 +0,0 @@ -ID contig_1; ; circular; DNA; ; PRO; 1330 BP. -XX -AC contig_1; -XX -DE plasmid unnamed1, complete sequence -XX -OS . -OC . -XX -CC Annotated with Bakta -CC Software: v1.5.0 -CC Database: v4.0 -CC DOI: 10.1099/mgen.0.000685 -CC URL: github.com/oschwengers/bakta -CC -CC ##Genome Annotation Summary:## -CC Annotation Date :: 09/16/2022, 07:32:21 -CC Annotation Pipeline :: Bakta -CC Annotation Software version :: v1.5.0 -CC Annotation Database version :: v4.0 -CC CDSs :: 0 -CC tRNAs :: 0 -CC tmRNAs :: 0 -CC rRNAs :: 0 -CC ncRNAs :: 0 -CC regulatory ncRNAs :: 0 -CC CRISPR Arrays :: 0 -CC oriCs/oriVs :: 0 -CC oriTs :: 0 -CC gaps :: 0 -CC pseudogenes :: 0 -XX -FH Key Location/Qualifiers -FH -FT source 1..1330 -FT /mol_type="genomic DNA" -FT /plasmid="unnamed1" -XX -SQ Sequence 1330 BP; 330 A; 291 C; 310 G; 399 T; 0 other; - ttcttctgcg agttcgtgca gcttctcaca catggtggcc tgctcgtcag catcgagtgc 60 - gtccagtttt tcgagcagcg tcaggctctg gctttttatg aatcccgcca tgttgagtgc 120 - agtttgctgc tgcttgttca tctttctgtt ttctccgttc tgtctgtcat ctgcgtcgtg 180 - tgattatatc gcgcaccact tttcgaccgt cttaccgccg gtattctgcc gacggacatt 240 - tcagtcagac aacactgtca ctgccaaaaa acagcagtgc tttgttggta attcgaactt 300 - gcagacagga caggatgtgc aattgttata ccgcgcatac atgcacgcta ttacaattac 360 - cctggtcagg gcttcgcccc gacaccccat gtcagatacg gagccatgtt ttatgacaaa 420 - acgaagtgga agtaatacgc gcaggcgggc tatcagtcgc cctgttcgtc tgacggcaga 480 - agaagaccag gaaatcagaa aaagggctgc tgaatgcggc aagaccgttt ctggtttttt 540 - acgggcggca gctctcggta agaaagttaa ctcactgact gatgaccggg tgctgaaaga 600 - agttatgcga ctgggggcgt tgcagaaaaa actctttatc gacggcaagc gtgtcgggga 660 - cagagagtat gcggaggtgc tgatcgctat tacggagtat caccgtgccc tgttatccag 720 - gcttatggca gattagcttc ccggagagaa actgtcgaaa acagacggta tgaacgccgt 780 - aagcccccaa accgatcgcc attcactttc atgcatagct atgcagtgag ctgaaagcga 840 - tcctgacgca tttttccggt ttaccccggg gaaaacatct ctttttgcgg tgtctgcgtc 900 - agaatcgcgt tcagcgcgtt ttggcggtgc gcgtaatgag acgttatggt aaatgtcttc 960 - tggcttgata ttatattgga atgccttttt tcaaagcaaa tgatgtggct ttggatagaa 1020 - ggtttacgtt gatcttatca aagttttttt taaagaacga agccgagagc tcagataaat 1080 - cattatattc atcagttttc gtaactttgt ttaatgtgta acttgaaaac ttctcgccat 1140 - taaatgacgt atagacgtaa cgatcttttt ttccaccgtt aggaattatt aaatcaaaaa 1200 - aaacatcacc cttgcttttc tttttcttca agtcggattc gatttttgag aaaaattcgc 1260 - tcgggctata aatatcagta gcatagacaa taaataaagt tttatcttta ttttttattg 1320 - cttctatttg 1330 -// |
| b |
| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/TEST_3/TEST_3.gbff --- a/test-data/TEST_3/TEST_3.gbff Fri Feb 10 14:20:09 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,59 +0,0 @@ -LOCUS contig_1 1330 bp DNA circular BCT 16-SEP-2022 -DEFINITION plasmid unnamed1, complete sequence. -ACCESSION contig_1 -VERSION contig_1 -KEYWORDS . -SOURCE None - ORGANISM . - . -COMMENT Annotated with Bakta - Software: v1.5.0 - Database: v4.0 - DOI: 10.1099/mgen.0.000685 - URL: github.com/oschwengers/bakta - - ##Genome Annotation Summary:## - Annotation Date :: 09/16/2022, 07:32:21 - Annotation Pipeline :: Bakta - Annotation Software version :: v1.5.0 - Annotation Database version :: v4.0 - CDSs :: 0 - tRNAs :: 0 - tmRNAs :: 0 - rRNAs :: 0 - ncRNAs :: 0 - regulatory ncRNAs :: 0 - CRISPR Arrays :: 0 - oriCs/oriVs :: 0 - oriTs :: 0 - gaps :: 0 - pseudogenes :: 0 -FEATURES Location/Qualifiers - source 1..1330 - /mol_type="genomic DNA" - /plasmid="unnamed1" -ORIGIN - 1 ttcttctgcg agttcgtgca gcttctcaca catggtggcc tgctcgtcag catcgagtgc - 61 gtccagtttt tcgagcagcg tcaggctctg gctttttatg aatcccgcca tgttgagtgc - 121 agtttgctgc tgcttgttca tctttctgtt ttctccgttc tgtctgtcat ctgcgtcgtg - 181 tgattatatc gcgcaccact tttcgaccgt cttaccgccg gtattctgcc gacggacatt - 241 tcagtcagac aacactgtca ctgccaaaaa acagcagtgc tttgttggta attcgaactt - 301 gcagacagga caggatgtgc aattgttata ccgcgcatac atgcacgcta ttacaattac - 361 cctggtcagg gcttcgcccc gacaccccat gtcagatacg gagccatgtt ttatgacaaa - 421 acgaagtgga agtaatacgc gcaggcgggc tatcagtcgc cctgttcgtc tgacggcaga - 481 agaagaccag gaaatcagaa aaagggctgc tgaatgcggc aagaccgttt ctggtttttt - 541 acgggcggca gctctcggta agaaagttaa ctcactgact gatgaccggg tgctgaaaga - 601 agttatgcga ctgggggcgt tgcagaaaaa actctttatc gacggcaagc gtgtcgggga - 661 cagagagtat gcggaggtgc tgatcgctat tacggagtat caccgtgccc tgttatccag - 721 gcttatggca gattagcttc ccggagagaa actgtcgaaa acagacggta tgaacgccgt - 781 aagcccccaa accgatcgcc attcactttc atgcatagct atgcagtgag ctgaaagcga - 841 tcctgacgca tttttccggt ttaccccggg gaaaacatct ctttttgcgg tgtctgcgtc - 901 agaatcgcgt tcagcgcgtt ttggcggtgc gcgtaatgag acgttatggt aaatgtcttc - 961 tggcttgata ttatattgga atgccttttt tcaaagcaaa tgatgtggct ttggatagaa - 1021 ggtttacgtt gatcttatca aagttttttt taaagaacga agccgagagc tcagataaat - 1081 cattatattc atcagttttc gtaactttgt ttaatgtgta acttgaaaac ttctcgccat - 1141 taaatgacgt atagacgtaa cgatcttttt ttccaccgtt aggaattatt aaatcaaaaa - 1201 aaacatcacc cttgcttttc tttttcttca agtcggattc gatttttgag aaaaattcgc - 1261 tcgggctata aatatcagta gcatagacaa taaataaagt tttatcttta ttttttattg - 1321 cttctatttg -// |
| b |
| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/TEST_3/TEST_3.gff3 --- a/test-data/TEST_3/TEST_3.gff3 Fri Feb 10 14:20:09 2023 +0000 +++ b/test-data/TEST_3/TEST_3.gff3 Mon Jul 24 11:22:16 2023 +0000 |
| b |
| @@ -1,8 +1,8 @@ ##gff-version 3 ##feature-ontology https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/v3.1/so.obo # Annotated with Bakta -# Software: v1.5.0 -# Database: v4.0 +# Software: v1.8.1 +# Database: v5.0, full # DOI: 10.1099/mgen.0.000685 # URL: github.com/oschwengers/bakta ##sequence-region contig_1 1 1330 |
| b |
| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/TEST_3/TEST_3.json --- a/test-data/TEST_3/TEST_3.json Fri Feb 10 14:20:09 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,42 +0,0 @@ -{ - "genome": { - "genus": null, - "species": null, - "strain": null, - "complete": true, - "gram": "?", - "translation_table": 11 - }, - "stats": { - "no_sequences": 1, - "size": 1330, - "gc": 0.4518796992481203, - "n_ratio": 0.0, - "n50": 1330, - "coding_ratio": 0.0 - }, - "features": [], - "sequences": [ - { - "id": "contig_1", - "description": "[completeness=complete] [topology=circular] [gcode=11]", - "sequence": "TTCTTCTGCGAGTTCGTGCAGCTTCTCACACATGGTGGCCTGCTCGTCAGCATCGAGTGCGTCCAGTTTTTCGAGCAGCGTCAGGCTCTGGCTTTTTATGAATCCCGCCATGTTGAGTGCAGTTTGCTGCTGCTTGTTCATCTTTCTGTTTTCTCCGTTCTGTCTGTCATCTGCGTCGTGTGATTATATCGCGCACCACTTTTCGACCGTCTTACCGCCGGTATTCTGCCGACGGACATTTCAGTCAGACAACACTGTCACTGCCAAAAAACAGCAGTGCTTTGTTGGTAATTCGAACTTGCAGACAGGACAGGATGTGCAATTGTTATACCGCGCATACATGCACGCTATTACAATTACCCTGGTCAGGGCTTCGCCCCGACACCCCATGTCAGATACGGAGCCATGTTTTATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAGCTTCCCGGAGAGAAACTGTCGAAAACAGACGGTATGAACGCCGTAAGCCCCCAAACCGATCGCCATTCACTTTCATGCATAGCTATGCAGTGAGCTGAAAGCGATCCTGACGCATTTTTCCGGTTTACCCCGGGGAAAACATCTCTTTTTGCGGTGTCTGCGTCAGAATCGCGTTCAGCGCGTTTTGGCGGTGCGCGTAATGAGACGTTATGGTAAATGTCTTCTGGCTTGATATTATATTGGAATGCCTTTTTTCAAAGCAAATGATGTGGCTTTGGATAGAAGGTTTACGTTGATCTTATCAAAGTTTTTTTTAAAGAACGAAGCCGAGAGCTCAGATAAATCATTATATTCATCAGTTTTCGTAACTTTGTTTAATGTGTAACTTGAAAACTTCTCGCCATTAAATGACGTATAGACGTAACGATCTTTTTTTCCACCGTTAGGAATTATTAAATCAAAAAAAACATCACCCTTGCTTTTCTTTTTCTTCAAGTCGGATTCGATTTTTGAGAAAAATTCGCTCGGGCTATAAATATCAGTAGCATAGACAATAAATAAAGTTTTATCTTTATTTTTTATTGCTTCTATTTG", - "length": 1330, - "complete": true, - "type": "plasmid", - "topology": "circular", - "simple_id": "contig_1", - "orig_id": "NC_002127.1", - "orig_description": "Escherichia coli O157:H7 str. Sakai plasmid pOSAK1, complete sequence", - "name": "unnamed1" - } - ], - "run": { - "start": "2022-09-16 07:32:20", - "end": "2022-09-16 07:32:21" - }, - "version": { - "bakta": "1.5.0", - "db": "4.0" - } -} \ No newline at end of file |
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| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/TEST_3/TEST_3.log --- a/test-data/TEST_3/TEST_3.log Fri Feb 10 14:20:09 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,57 +0,0 @@ -parse genome sequences... - imported: 1 - filtered & revised: 1 - plasmids: 1 - -start annotation... -skip tRNA prediction... -skip tmRNA prediction... -skip rRNA prediction... -skip ncRNA prediction... -skip ncRNA region prediction... -skip CRISPR array prediction... -skip CDS prediction... -skip sORF prediction... -skip gap annotation... -skip oriC/T annotation... -apply feature overlap filters... -select features and create locus tags... -selected: 0 - -genome statistics: - Genome size: 1,330 bp - Contigs/replicons: 1 - GC: 45.2 % - N50: 1,330 - N ratio: 0.0 % - coding density: 0.0 % - -annotation summary: - tRNAs: 0 - tmRNAs: 0 - rRNAs: 0 - ncRNAs: 0 - ncRNA regions: 0 - CRISPR arrays: 0 - CDSs: 0 - hypotheticals: 0 - pseudogenes: 0 - signal peptides: 0 - sORFs: 0 - gaps: 0 - oriCs/oriVs: 0 - oriTs: 0 - -export annotation results to: /tmp/tmpmnqj1xog/job_working_directory/000/6/working - human readable TSV... - GFF3... - INSDC GenBank & EMBL... - genome sequences... - feature nucleotide sequences... - translated CDS sequences... - circular genome plot... - machine readable JSON... - genome and annotation summary... - -If you use these results please cite Bakta: https://doi.org/10.1099/mgen.0.000685 -Annotation successfully finished in 0:00 [mm:ss]. |
| b |
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| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/TEST_3/TEST_3.tsv --- a/test-data/TEST_3/TEST_3.tsv Fri Feb 10 14:20:09 2023 +0000 +++ b/test-data/TEST_3/TEST_3.tsv Mon Jul 24 11:22:16 2023 +0000 |
| b |
| @@ -1,3 +1,6 @@ -#Annotated with Bakta (v1.5.0): https://github.com/oschwengers/bakta -#Database (v4.0): https://doi.org/10.5281/zenodo.4247252 +# Annotated with Bakta +# Software: v1.8.1 +# Database: v5.0, full +# DOI: 10.1099/mgen.0.000685 +# URL: github.com/oschwengers/bakta #Sequence Id Type Start Stop Strand Locus Tag Gene Product DbXrefs |
| b |
| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/TEST_4/TEST_4.embl --- a/test-data/TEST_4/TEST_4.embl Fri Feb 10 14:20:09 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,88 +0,0 @@ -ID p2; ; circular; DNA; ; PRO; 1330 BP. -XX -AC p2; -XX -DE plasmid pOSAK1, complete sequence -XX -OS . -OC . -XX -CC Annotated with Bakta -CC Software: v1.5.0 -CC Database: v4.0 -CC DOI: 10.1099/mgen.0.000685 -CC URL: github.com/oschwengers/bakta -CC -CC ##Genome Annotation Summary:## -CC Annotation Date :: 09/16/2022, 07:32:50 -CC Annotation Pipeline :: Bakta -CC Annotation Software version :: v1.5.0 -CC Annotation Database version :: v4.0 -CC CDSs :: 2 -CC tRNAs :: 0 -CC tmRNAs :: 0 -CC rRNAs :: 0 -CC ncRNAs :: 0 -CC regulatory ncRNAs :: 0 -CC CRISPR Arrays :: 0 -CC oriCs/oriVs :: 0 -CC oriTs :: 0 -CC gaps :: 0 -CC pseudogenes :: 0 -XX -FH Key Location/Qualifiers -FH -FT source 1..1330 -FT /mol_type="genomic DNA" -FT /plasmid="pOSAK1" -FT gene 413..736 -FT /locus_tag="IHHALP_00005" -FT CDS 413..736 -FT /product="hypothetical protein" -FT /locus_tag="IHHALP_00005" -FT /protein_id="gnl|Bakta|IHHALP_00005" -FT /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA -FT AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL -FT MAD" -FT /codon_start=1 -FT /transl_table=4 -FT /inference="ab initio prediction:Prodigal:2.6" -FT gene complement(join(971..1330,1..141)) -FT /locus_tag="IHHALP_00010" -FT CDS complement(join(971..1330,1..141)) -FT /product="hypothetical protein" -FT /locus_tag="IHHALP_00010" -FT /protein_id="gnl|Bakta|IHHALP_00010" -FT /translation="MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELA -FT EEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDR -FT YVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKG -FT IPI" -FT /codon_start=1 -FT /transl_table=4 -FT /inference="ab initio prediction:Prodigal:2.6" -XX -SQ Sequence 1330 BP; 330 A; 291 C; 310 G; 399 T; 0 other; - ttcttctgcg agttcgtgca gcttctcaca catggtggcc tgctcgtcag catcgagtgc 60 - gtccagtttt tcgagcagcg tcaggctctg gctttttatg aatcccgcca tgttgagtgc 120 - agtttgctgc tgcttgttca tctttctgtt ttctccgttc tgtctgtcat ctgcgtcgtg 180 - tgattatatc gcgcaccact tttcgaccgt cttaccgccg gtattctgcc gacggacatt 240 - tcagtcagac aacactgtca ctgccaaaaa acagcagtgc tttgttggta attcgaactt 300 - gcagacagga caggatgtgc aattgttata ccgcgcatac atgcacgcta ttacaattac 360 - cctggtcagg gcttcgcccc gacaccccat gtcagatacg gagccatgtt ttatgacaaa 420 - acgaagtgga agtaatacgc gcaggcgggc tatcagtcgc cctgttcgtc tgacggcaga 480 - agaagaccag gaaatcagaa aaagggctgc tgaatgcggc aagaccgttt ctggtttttt 540 - acgggcggca gctctcggta agaaagttaa ctcactgact gatgaccggg tgctgaaaga 600 - agttatgcga ctgggggcgt tgcagaaaaa actctttatc gacggcaagc gtgtcgggga 660 - cagagagtat gcggaggtgc tgatcgctat tacggagtat caccgtgccc tgttatccag 720 - gcttatggca gattagcttc ccggagagaa actgtcgaaa acagacggta tgaacgccgt 780 - aagcccccaa accgatcgcc attcactttc atgcatagct atgcagtgag ctgaaagcga 840 - tcctgacgca tttttccggt ttaccccggg gaaaacatct ctttttgcgg tgtctgcgtc 900 - agaatcgcgt tcagcgcgtt ttggcggtgc gcgtaatgag acgttatggt aaatgtcttc 960 - tggcttgata ttatattgga atgccttttt tcaaagcaaa tgatgtggct ttggatagaa 1020 - ggtttacgtt gatcttatca aagttttttt taaagaacga agccgagagc tcagataaat 1080 - cattatattc atcagttttc gtaactttgt ttaatgtgta acttgaaaac ttctcgccat 1140 - taaatgacgt atagacgtaa cgatcttttt ttccaccgtt aggaattatt aaatcaaaaa 1200 - aaacatcacc cttgcttttc tttttcttca agtcggattc gatttttgag aaaaattcgc 1260 - tcgggctata aatatcagta gcatagacaa taaataaagt tttatcttta ttttttattg 1320 - cttctatttg 1330 -// |
| b |
| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/TEST_4/TEST_4.gbff --- a/test-data/TEST_4/TEST_4.gbff Fri Feb 10 14:20:09 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,84 +0,0 @@ -LOCUS p2 1330 bp DNA circular BCT 16-SEP-2022 -DEFINITION plasmid pOSAK1, complete sequence. -ACCESSION p2 -VERSION p2 -KEYWORDS . -SOURCE None - ORGANISM . - . -COMMENT Annotated with Bakta - Software: v1.5.0 - Database: v4.0 - DOI: 10.1099/mgen.0.000685 - URL: github.com/oschwengers/bakta - - ##Genome Annotation Summary:## - Annotation Date :: 09/16/2022, 07:32:50 - Annotation Pipeline :: Bakta - Annotation Software version :: v1.5.0 - Annotation Database version :: v4.0 - CDSs :: 2 - tRNAs :: 0 - tmRNAs :: 0 - rRNAs :: 0 - ncRNAs :: 0 - regulatory ncRNAs :: 0 - CRISPR Arrays :: 0 - oriCs/oriVs :: 0 - oriTs :: 0 - gaps :: 0 - pseudogenes :: 0 -FEATURES Location/Qualifiers - source 1..1330 - /mol_type="genomic DNA" - /plasmid="pOSAK1" - gene 413..736 - /locus_tag="IHHALP_00005" - CDS 413..736 - /product="hypothetical protein" - /locus_tag="IHHALP_00005" - /protein_id="gnl|Bakta|IHHALP_00005" - /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA - AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL - MAD" - /codon_start=1 - /transl_table=4 - /inference="ab initio prediction:Prodigal:2.6" - gene complement(join(971..1330,1..141)) - /locus_tag="IHHALP_00010" - CDS complement(join(971..1330,1..141)) - /product="hypothetical protein" - /locus_tag="IHHALP_00010" - /protein_id="gnl|Bakta|IHHALP_00010" - /translation="MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELA - EEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDR - YVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKG - IPI" - /codon_start=1 - /transl_table=4 - /inference="ab initio prediction:Prodigal:2.6" -ORIGIN - 1 ttcttctgcg agttcgtgca gcttctcaca catggtggcc tgctcgtcag catcgagtgc - 61 gtccagtttt tcgagcagcg tcaggctctg gctttttatg aatcccgcca tgttgagtgc - 121 agtttgctgc tgcttgttca tctttctgtt ttctccgttc tgtctgtcat ctgcgtcgtg - 181 tgattatatc gcgcaccact tttcgaccgt cttaccgccg gtattctgcc gacggacatt - 241 tcagtcagac aacactgtca ctgccaaaaa acagcagtgc tttgttggta attcgaactt - 301 gcagacagga caggatgtgc aattgttata ccgcgcatac atgcacgcta ttacaattac - 361 cctggtcagg gcttcgcccc gacaccccat gtcagatacg gagccatgtt ttatgacaaa - 421 acgaagtgga agtaatacgc gcaggcgggc tatcagtcgc cctgttcgtc tgacggcaga - 481 agaagaccag gaaatcagaa aaagggctgc tgaatgcggc aagaccgttt ctggtttttt - 541 acgggcggca gctctcggta agaaagttaa ctcactgact gatgaccggg tgctgaaaga - 601 agttatgcga ctgggggcgt tgcagaaaaa actctttatc gacggcaagc gtgtcgggga - 661 cagagagtat gcggaggtgc tgatcgctat tacggagtat caccgtgccc tgttatccag - 721 gcttatggca gattagcttc ccggagagaa actgtcgaaa acagacggta tgaacgccgt - 781 aagcccccaa accgatcgcc attcactttc atgcatagct atgcagtgag ctgaaagcga - 841 tcctgacgca tttttccggt ttaccccggg gaaaacatct ctttttgcgg tgtctgcgtc - 901 agaatcgcgt tcagcgcgtt ttggcggtgc gcgtaatgag acgttatggt aaatgtcttc - 961 tggcttgata ttatattgga atgccttttt tcaaagcaaa tgatgtggct ttggatagaa - 1021 ggtttacgtt gatcttatca aagttttttt taaagaacga agccgagagc tcagataaat - 1081 cattatattc atcagttttc gtaactttgt ttaatgtgta acttgaaaac ttctcgccat - 1141 taaatgacgt atagacgtaa cgatcttttt ttccaccgtt aggaattatt aaatcaaaaa - 1201 aaacatcacc cttgcttttc tttttcttca agtcggattc gatttttgag aaaaattcgc - 1261 tcgggctata aatatcagta gcatagacaa taaataaagt tttatcttta ttttttattg - 1321 cttctatttg -// |
| b |
| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/TEST_4/TEST_4.gff3 --- a/test-data/TEST_4/TEST_4.gff3 Fri Feb 10 14:20:09 2023 +0000 +++ b/test-data/TEST_4/TEST_4.gff3 Mon Jul 24 11:22:16 2023 +0000 |
| b |
| @@ -1,8 +1,8 @@ ##gff-version 3 ##feature-ontology https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/v3.1/so.obo # Annotated with Bakta -# Software: v1.5.0 -# Database: v4.0 +# Software: v1.8.1 +# Database: v5.0, full # DOI: 10.1099/mgen.0.000685 # URL: github.com/oschwengers/bakta ##sequence-region p2 1 1330 |
| b |
| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/TEST_4/TEST_4.hypotheticals.tsv --- a/test-data/TEST_4/TEST_4.hypotheticals.tsv Fri Feb 10 14:20:09 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,5 +0,0 @@ -#Annotated with Bakta v1.5.0, https://github.com/oschwengers/bakta -#Database v4.0, https://doi.org/10.5281/zenodo.4247252 -#Sequence Id Start Stop Strand Locus Tag Mol Weight [kDa] Iso El. Point Pfam hits Dbxrefs -p2 413 736 + IHHALP_00005 12.1 10.4 -p2 971 141 - IHHALP_00010 18.9 7.7 |
| b |
| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/TEST_4/TEST_4.json --- a/test-data/TEST_4/TEST_4.json Fri Feb 10 14:20:09 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,89 +0,0 @@ -{ - "genome": { - "genus": null, - "species": null, - "strain": null, - "complete": true, - "gram": "?", - "translation_table": 4 - }, - "stats": { - "no_sequences": 1, - "size": 1330, - "gc": 0.4518796992481203, - "n_ratio": 0.0, - "n50": 1330, - "coding_ratio": 0.6203007518796992 - }, - "features": [ - { - "type": "cds", - "contig": "p2", - "start": 413, - "stop": 736, - "strand": "+", - "gene": null, - "product": "hypothetical protein", - "start_type": "ATG", - "rbs_motif": "GGAG/GAGG", - "db_xrefs": [], - "frame": 2, - "aa": "MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD", - "aa_hexdigest": "d9bdebc84195542e775c3d22458b507e", - "nt": "ATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAG", - "hypothetical": true, - "seq_stats": { - "molecular_weight": 12072.90819999999, - "isoelectric_point": 10.367886161804197 - }, - "id": "IHHALPPJCH_1", - "locus": "IHHALP_00005" - }, - { - "type": "cds", - "contig": "p2", - "start": 971, - "stop": 141, - "strand": "-", - "gene": null, - "product": "hypothetical protein", - "start_type": "ATG", - "rbs_motif": "AGGA/GGAG/GAGG", - "db_xrefs": [], - "frame": 1, - "aa": "MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI", - "aa_hexdigest": "1e7027cbe48346e06a83e802a9385584", - "edge": true, - "nt": "ATGAACAAGCAGCAGCAAACTGCACTCAACATGGCGGGATTCATAAAAAGCCAGAGCCTGACGCTGCTCGAAAAACTGGACGCACTCGATGCTGACGAGCAGGCCACCATGTGTGAGAAGCTGCACGAACTCGCAGAAGAACAAATAGAAGCAATAAAAAATAAAGATAAAACTTTATTTATTGTCTATGCTACTGATATTTATAGCCCGAGCGAATTTTTCTCAAAAATCGAATCCGACTTGAAGAAAAAGAAAAGCAAGGGTGATGTTTTTTTTGATTTAATAATTCCTAACGGTGGAAAAAAAGATCGTTACGTCTATACGTCATTTAATGGCGAGAAGTTTTCAAGTTACACATTAAACAAAGTTACGAAAACTGATGAATATAATGATTTATCTGAGCTCTCGGCTTCGTTCTTTAAAAAAAACTTTGATAAGATCAACGTAAACCTTCTATCCAAAGCCACATCATTTGCTTTGAAAAAAGGCATTCCAATATAA", - "hypothetical": true, - "seq_stats": { - "molecular_weight": 18866.325799999995, - "isoelectric_point": 7.696590614318848 - }, - "id": "IHHALPPJCH_2", - "locus": "IHHALP_00010" - } - ], - "sequences": [ - { - "id": "p2", - "description": "[completeness=complete] [topology=circular] [gcode=4] [plasmid-name=pOSAK1]", - "sequence": "TTCTTCTGCGAGTTCGTGCAGCTTCTCACACATGGTGGCCTGCTCGTCAGCATCGAGTGCGTCCAGTTTTTCGAGCAGCGTCAGGCTCTGGCTTTTTATGAATCCCGCCATGTTGAGTGCAGTTTGCTGCTGCTTGTTCATCTTTCTGTTTTCTCCGTTCTGTCTGTCATCTGCGTCGTGTGATTATATCGCGCACCACTTTTCGACCGTCTTACCGCCGGTATTCTGCCGACGGACATTTCAGTCAGACAACACTGTCACTGCCAAAAAACAGCAGTGCTTTGTTGGTAATTCGAACTTGCAGACAGGACAGGATGTGCAATTGTTATACCGCGCATACATGCACGCTATTACAATTACCCTGGTCAGGGCTTCGCCCCGACACCCCATGTCAGATACGGAGCCATGTTTTATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAGCTTCCCGGAGAGAAACTGTCGAAAACAGACGGTATGAACGCCGTAAGCCCCCAAACCGATCGCCATTCACTTTCATGCATAGCTATGCAGTGAGCTGAAAGCGATCCTGACGCATTTTTCCGGTTTACCCCGGGGAAAACATCTCTTTTTGCGGTGTCTGCGTCAGAATCGCGTTCAGCGCGTTTTGGCGGTGCGCGTAATGAGACGTTATGGTAAATGTCTTCTGGCTTGATATTATATTGGAATGCCTTTTTTCAAAGCAAATGATGTGGCTTTGGATAGAAGGTTTACGTTGATCTTATCAAAGTTTTTTTTAAAGAACGAAGCCGAGAGCTCAGATAAATCATTATATTCATCAGTTTTCGTAACTTTGTTTAATGTGTAACTTGAAAACTTCTCGCCATTAAATGACGTATAGACGTAACGATCTTTTTTTCCACCGTTAGGAATTATTAAATCAAAAAAAACATCACCCTTGCTTTTCTTTTTCTTCAAGTCGGATTCGATTTTTGAGAAAAATTCGCTCGGGCTATAAATATCAGTAGCATAGACAATAAATAAAGTTTTATCTTTATTTTTTATTGCTTCTATTTG", - "length": 1330, - "complete": true, - "type": "plasmid", - "topology": "circular", - "orig_id": "NC_002127.1", - "orig_description": "Escherichia coli O157:H7 str. Sakai plasmid pOSAK1, complete sequence", - "name": "pOSAK1" - } - ], - "run": { - "start": "2022-09-16 07:32:48", - "end": "2022-09-16 07:32:50" - }, - "version": { - "bakta": "1.5.0", - "db": "4.0" - } -} \ No newline at end of file |
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| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/TEST_4/TEST_4.log --- a/test-data/TEST_4/TEST_4.log Fri Feb 10 14:20:09 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,96 +0,0 @@ -parse genome sequences... - imported: 1 - filtered & revised: 1 - plasmids: 1 - -start annotation... -predict tRNAs... - found: 0 -predict tmRNAs... - found: 0 -predict rRNAs... - found: 0 -predict ncRNAs... - found: 0 -predict ncRNA regions... - found: 0 -predict CRISPR arrays... - found: 0 -predict & annotate CDSs... - predicted: 2 - discarded spurious: 0 - revised translational exceptions: 0 - detected IPSs: 0 - found PSCs: 0 - found PSCCs: 0 - lookup annotations... - conduct expert systems... - amrfinder: 0 - protein sequences: 0 - user protein sequences: 0 - combine annotations and mark hypotheticals... - detect pseudogenes... - pseudogene candidates: 0 - found pseudogenes: 0 -analyze hypothetical proteins: 2 - detected Pfam hits: 0 - calculated proteins statistics - revise special cases... -extract sORF... - potential: 16 - discarded due to overlaps: 2 - discarded spurious: 0 - detected IPSs: 0 - found PSCs: 0 - lookup annotations... - filter and combine annotations... - filtered sORFs: 0 -detect gaps... - found: 0 -detect oriCs/oriVs... - found: 0 -detect oriTs... - found: 0 -apply feature overlap filters... -select features and create locus tags... -selected: 2 - -genome statistics: - Genome size: 1,330 bp - Contigs/replicons: 1 - GC: 45.2 % - N50: 1,330 - N ratio: 0.0 % - coding density: 62.0 % - -annotation summary: - tRNAs: 0 - tmRNAs: 0 - rRNAs: 0 - ncRNAs: 0 - ncRNA regions: 0 - CRISPR arrays: 0 - CDSs: 2 - hypotheticals: 2 - pseudogenes: 0 - signal peptides: 0 - sORFs: 0 - gaps: 0 - oriCs/oriVs: 0 - oriTs: 0 - -export annotation results to: /tmp/tmpmnqj1xog/job_working_directory/000/12/working - human readable TSV... - GFF3... - INSDC GenBank & EMBL... - genome sequences... - feature nucleotide sequences... - translated CDS sequences... - circular genome plot... - hypothetical TSV... - translated hypothetical CDS sequences... - machine readable JSON... - genome and annotation summary... - -If you use these results please cite Bakta: https://doi.org/10.1099/mgen.0.000685 -Annotation successfully finished in 0:01 [mm:ss]. |
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| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/TEST_4/TEST_4.tsv --- a/test-data/TEST_4/TEST_4.tsv Fri Feb 10 14:20:09 2023 +0000 +++ b/test-data/TEST_4/TEST_4.tsv Mon Jul 24 11:22:16 2023 +0000 |
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| @@ -1,5 +1,8 @@ -#Annotated with Bakta (v1.5.0): https://github.com/oschwengers/bakta -#Database (v4.0): https://doi.org/10.5281/zenodo.4247252 +# Annotated with Bakta +# Software: v1.8.1 +# Database: v5.0, full +# DOI: 10.1099/mgen.0.000685 +# URL: github.com/oschwengers/bakta #Sequence Id Type Start Stop Strand Locus Tag Gene Product DbXrefs p2 cds 413 736 + IHHALP_00005 hypothetical protein p2 cds 971 141 - IHHALP_00010 hypothetical protein |
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| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/TEST_4/TEST_4.txt --- a/test-data/TEST_4/TEST_4.txt Fri Feb 10 14:20:09 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,30 +0,0 @@ -Sequence(s): -Length: 1330 -Count: 1 -GC: 45.2 -N50: 1330 -N ratio: 0.0 -coding density: 62.0 - -Annotation: -tRNAs: 0 -tmRNAs: 0 -rRNAs: 0 -ncRNAs: 0 -ncRNA regions: 0 -CRISPR arrays: 0 -CDSs: 2 -pseudogenes: 0 -hypotheticals: 2 -signal peptides: 0 -sORFs: 0 -gaps: 0 -oriCs: 0 -oriVs: 0 -oriTs: 0 - -Bakta: -Software: v1.5.0 -Database: v4.0 -DOI: 10.1099/mgen.0.000685 -URL: github.com/oschwengers/bakta |
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| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/TEST_4/TEST_4_plot.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_4/TEST_4_plot.svg Mon Jul 24 11:22:16 2023 +0000 |
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| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/TEST_5/TEST_5.log --- a/test-data/TEST_5/TEST_5.log Fri Feb 10 14:20:09 2023 +0000 +++ b/test-data/TEST_5/TEST_5.log Mon Jul 24 11:22:16 2023 +0000 |
| b |
| @@ -1,3 +1,25 @@ +Bakta v1.8.1 +Options and arguments: + input: /tmp/tmp6wdeee6u/files/0/2/9/dataset_0293aae0-943d-4d1b-af6c-e5ed41b419da.dat + db: /tmp/tmp6wdeee6u/job_working_directory/000/13/working/database_path, version 5.0, full + output: /tmp/tmp6wdeee6u/job_working_directory/000/13/working/bakta_output + tmp directory: /tmp/tmp6wdeee6u/tmp/tmpigp60rnb + prefix: bakta_output + threads: 1 + translation table: 4 + complete replicons: True + skip tRNA: True + skip tmRNA: True + skip rRNA: True + skip ncRNA: True + skip ncRNA region: True + skip CRISPR: True + skip CDS: True + skip sORF: True + skip gap: True + skip oriC/V/T: True + skip plot: True + parse genome sequences... imported: 1 filtered & revised: 1 @@ -17,6 +39,8 @@ apply feature overlap filters... select features and create locus tags... selected: 0 +improve annotations... + revised gene symbols: 0 genome statistics: Genome size: 1,330 bp @@ -34,22 +58,22 @@ ncRNA regions: 0 CRISPR arrays: 0 CDSs: 0 - hypotheticals: 0 - pseudogenes: 0 - signal peptides: 0 + hypotheticals: 0 + pseudogenes: 0 + signal peptides: 0 sORFs: 0 gaps: 0 oriCs/oriVs: 0 oriTs: 0 -export annotation results to: /tmp/tmpmnqj1xog/job_working_directory/000/14/working +export annotation results to: /tmp/tmp6wdeee6u/job_working_directory/000/13/working/bakta_output human readable TSV... GFF3... INSDC GenBank & EMBL... genome sequences... feature nucleotide sequences... translated CDS sequences... - circular genome plot... + skip generation of circular genome plot... machine readable JSON... genome and annotation summary... |
| b |
| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/TEST_5/TEST_5.txt --- a/test-data/TEST_5/TEST_5.txt Fri Feb 10 14:20:09 2023 +0000 +++ b/test-data/TEST_5/TEST_5.txt Mon Jul 24 11:22:16 2023 +0000 |
| b |
| @@ -24,7 +24,7 @@ oriTs: 0 Bakta: -Software: v1.5.0 -Database: v4.0 +Software: v1.8.1 +Database: v5.0, full DOI: 10.1099/mgen.0.000685 URL: github.com/oschwengers/bakta |
| b |
| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/TEST_6/TEST_6.embl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_6/TEST_6.embl Mon Jul 24 11:22:16 2023 +0000 |
| b |
| @@ -0,0 +1,85 @@ +ID contig_1; ; circular; DNA; ; PRO; 1330 BP. +XX +AC contig_1; +XX +DE plasmid unnamed1, complete sequence +XX +OS . +OC . +XX +CC Annotated with Bakta +CC Software: v1.8.1 +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 CDSs :: 2 +CC tRNAs :: 0 +CC tmRNAs :: 0 +CC rRNAs :: 0 +CC ncRNAs :: 0 +CC regulatory ncRNAs :: 0 +CC CRISPR Arrays :: 0 +CC oriCs/oriVs :: 0 +CC oriTs :: 0 +CC gaps :: 0 +CC pseudogenes :: 0 +XX +FH Key Location/Qualifiers +FH +FT source 1..1330 +FT /mol_type="genomic DNA" +FT /plasmid="unnamed1" +FT gene 413..736 +FT /locus_tag="IHHALP_00005" +FT CDS 413..736 +FT /product="hypothetical protein" +FT /locus_tag="IHHALP_00005" +FT /protein_id="gnl|Bakta|IHHALP_00005" +FT /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA +FT AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL +FT MAD" +FT /codon_start=1 +FT /transl_table=11 +FT /inference="ab initio prediction:Prodigal:2.6" +FT gene complement(join(971..1330,1..141)) +FT /locus_tag="IHHALP_00010" +FT CDS complement(join(971..1330,1..141)) +FT /product="hypothetical protein" +FT /locus_tag="IHHALP_00010" +FT /protein_id="gnl|Bakta|IHHALP_00010" +FT /translation="MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELA +FT EEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDR +FT YVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKG +FT IPI" +FT /codon_start=1 +FT /transl_table=11 +FT /inference="ab initio prediction:Prodigal:2.6" +XX +SQ Sequence 1330 BP; 330 A; 291 C; 310 G; 399 T; 0 other; + ttcttctgcg agttcgtgca gcttctcaca catggtggcc tgctcgtcag catcgagtgc 60 + gtccagtttt tcgagcagcg tcaggctctg gctttttatg aatcccgcca tgttgagtgc 120 + agtttgctgc tgcttgttca tctttctgtt ttctccgttc tgtctgtcat ctgcgtcgtg 180 + tgattatatc gcgcaccact tttcgaccgt cttaccgccg gtattctgcc gacggacatt 240 + tcagtcagac aacactgtca ctgccaaaaa acagcagtgc tttgttggta attcgaactt 300 + gcagacagga caggatgtgc aattgttata ccgcgcatac atgcacgcta ttacaattac 360 + cctggtcagg gcttcgcccc gacaccccat gtcagatacg gagccatgtt ttatgacaaa 420 + acgaagtgga agtaatacgc gcaggcgggc tatcagtcgc cctgttcgtc tgacggcaga 480 + agaagaccag gaaatcagaa aaagggctgc tgaatgcggc aagaccgttt ctggtttttt 540 + acgggcggca gctctcggta agaaagttaa ctcactgact gatgaccggg tgctgaaaga 600 + agttatgcga ctgggggcgt tgcagaaaaa actctttatc gacggcaagc gtgtcgggga 660 + cagagagtat gcggaggtgc tgatcgctat tacggagtat caccgtgccc tgttatccag 720 + gcttatggca gattagcttc ccggagagaa actgtcgaaa acagacggta tgaacgccgt 780 + aagcccccaa accgatcgcc attcactttc atgcatagct atgcagtgag ctgaaagcga 840 + tcctgacgca tttttccggt ttaccccggg gaaaacatct ctttttgcgg tgtctgcgtc 900 + agaatcgcgt tcagcgcgtt ttggcggtgc gcgtaatgag acgttatggt aaatgtcttc 960 + tggcttgata ttatattgga atgccttttt tcaaagcaaa tgatgtggct ttggatagaa 1020 + ggtttacgtt gatcttatca aagttttttt taaagaacga agccgagagc tcagataaat 1080 + cattatattc atcagttttc gtaactttgt ttaatgtgta acttgaaaac ttctcgccat 1140 + taaatgacgt atagacgtaa cgatcttttt ttccaccgtt aggaattatt aaatcaaaaa 1200 + aaacatcacc cttgcttttc tttttcttca agtcggattc gatttttgag aaaaattcgc 1260 + tcgggctata aatatcagta gcatagacaa taaataaagt tttatcttta ttttttattg 1320 + cttctatttg 1330 +// |
| b |
| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/TEST_6/TEST_6.faa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_6/TEST_6.faa Mon Jul 24 11:22:16 2023 +0000 |
| b |
| @@ -0,0 +1,4 @@ +>IHHALP_00005 hypothetical protein +MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD +>IHHALP_00010 hypothetical protein +MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI |
| b |
| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/TEST_6/TEST_6.ffn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_6/TEST_6.ffn Mon Jul 24 11:22:16 2023 +0000 |
| b |
| @@ -0,0 +1,4 @@ +>IHHALP_00005 hypothetical protein +ATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAG +>IHHALP_00010 hypothetical protein +ATGAACAAGCAGCAGCAAACTGCACTCAACATGGCGGGATTCATAAAAAGCCAGAGCCTGACGCTGCTCGAAAAACTGGACGCACTCGATGCTGACGAGCAGGCCACCATGTGTGAGAAGCTGCACGAACTCGCAGAAGAACAAATAGAAGCAATAAAAAATAAAGATAAAACTTTATTTATTGTCTATGCTACTGATATTTATAGCCCGAGCGAATTTTTCTCAAAAATCGAATCCGACTTGAAGAAAAAGAAAAGCAAGGGTGATGTTTTTTTTGATTTAATAATTCCTAACGGTGGAAAAAAAGATCGTTACGTCTATACGTCATTTAATGGCGAGAAGTTTTCAAGTTACACATTAAACAAAGTTACGAAAACTGATGAATATAATGATTTATCTGAGCTCTCGGCTTCGTTCTTTAAAAAAAACTTTGATAAGATCAACGTAAACCTTCTATCCAAAGCCACATCATTTGCTTTGAAAAAAGGCATTCCAATATAA |
| b |
| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/TEST_6/TEST_6.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_6/TEST_6.fna Mon Jul 24 11:22:16 2023 +0000 |
| [ |
| @@ -0,0 +1,24 @@ +>contig_1 [gcode=11] [completeness=complete] [topology=circular] [plasmid-name=unnamed1] +TTCTTCTGCGAGTTCGTGCAGCTTCTCACACATGGTGGCCTGCTCGTCAGCATCGAGTGC +GTCCAGTTTTTCGAGCAGCGTCAGGCTCTGGCTTTTTATGAATCCCGCCATGTTGAGTGC +AGTTTGCTGCTGCTTGTTCATCTTTCTGTTTTCTCCGTTCTGTCTGTCATCTGCGTCGTG +TGATTATATCGCGCACCACTTTTCGACCGTCTTACCGCCGGTATTCTGCCGACGGACATT +TCAGTCAGACAACACTGTCACTGCCAAAAAACAGCAGTGCTTTGTTGGTAATTCGAACTT +GCAGACAGGACAGGATGTGCAATTGTTATACCGCGCATACATGCACGCTATTACAATTAC +CCTGGTCAGGGCTTCGCCCCGACACCCCATGTCAGATACGGAGCCATGTTTTATGACAAA +ACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGA +AGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTT +ACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGA +AGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGA +CAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAG +GCTTATGGCAGATTAGCTTCCCGGAGAGAAACTGTCGAAAACAGACGGTATGAACGCCGT +AAGCCCCCAAACCGATCGCCATTCACTTTCATGCATAGCTATGCAGTGAGCTGAAAGCGA +TCCTGACGCATTTTTCCGGTTTACCCCGGGGAAAACATCTCTTTTTGCGGTGTCTGCGTC +AGAATCGCGTTCAGCGCGTTTTGGCGGTGCGCGTAATGAGACGTTATGGTAAATGTCTTC +TGGCTTGATATTATATTGGAATGCCTTTTTTCAAAGCAAATGATGTGGCTTTGGATAGAA +GGTTTACGTTGATCTTATCAAAGTTTTTTTTAAAGAACGAAGCCGAGAGCTCAGATAAAT +CATTATATTCATCAGTTTTCGTAACTTTGTTTAATGTGTAACTTGAAAACTTCTCGCCAT +TAAATGACGTATAGACGTAACGATCTTTTTTTCCACCGTTAGGAATTATTAAATCAAAAA +AAACATCACCCTTGCTTTTCTTTTTCTTCAAGTCGGATTCGATTTTTGAGAAAAATTCGC +TCGGGCTATAAATATCAGTAGCATAGACAATAAATAAAGTTTTATCTTTATTTTTTATTG +CTTCTATTTG |
| b |
| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/TEST_6/TEST_6.gbff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_6/TEST_6.gbff Mon Jul 24 11:22:16 2023 +0000 |
| b |
| @@ -0,0 +1,81 @@ +LOCUS contig_1 1330 bp DNA circular BCT 19-JUN-2023 +DEFINITION plasmid unnamed1, complete sequence. +ACCESSION contig_1 +VERSION contig_1 +KEYWORDS . +SOURCE None + ORGANISM . + . +COMMENT Annotated with Bakta + Software: v1.8.1 + 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 + CDSs :: 2 + tRNAs :: 0 + tmRNAs :: 0 + rRNAs :: 0 + ncRNAs :: 0 + regulatory ncRNAs :: 0 + CRISPR Arrays :: 0 + oriCs/oriVs :: 0 + oriTs :: 0 + gaps :: 0 + pseudogenes :: 0 +FEATURES Location/Qualifiers + source 1..1330 + /mol_type="genomic DNA" + /plasmid="unnamed1" + gene 413..736 + /locus_tag="IHHALP_00005" + CDS 413..736 + /product="hypothetical protein" + /locus_tag="IHHALP_00005" + /protein_id="gnl|Bakta|IHHALP_00005" + /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA + AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL + MAD" + /codon_start=1 + /transl_table=11 + /inference="ab initio prediction:Prodigal:2.6" + gene complement(join(971..1330,1..141)) + /locus_tag="IHHALP_00010" + CDS complement(join(971..1330,1..141)) + /product="hypothetical protein" + /locus_tag="IHHALP_00010" + /protein_id="gnl|Bakta|IHHALP_00010" + /translation="MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELA + EEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDR + YVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKG + IPI" + /codon_start=1 + /transl_table=11 + /inference="ab initio prediction:Prodigal:2.6" +ORIGIN + 1 ttcttctgcg agttcgtgca gcttctcaca catggtggcc tgctcgtcag catcgagtgc + 61 gtccagtttt tcgagcagcg tcaggctctg gctttttatg aatcccgcca tgttgagtgc + 121 agtttgctgc tgcttgttca tctttctgtt ttctccgttc tgtctgtcat ctgcgtcgtg + 181 tgattatatc gcgcaccact tttcgaccgt cttaccgccg gtattctgcc gacggacatt + 241 tcagtcagac aacactgtca ctgccaaaaa acagcagtgc tttgttggta attcgaactt + 301 gcagacagga caggatgtgc aattgttata ccgcgcatac atgcacgcta ttacaattac + 361 cctggtcagg gcttcgcccc gacaccccat gtcagatacg gagccatgtt ttatgacaaa + 421 acgaagtgga agtaatacgc gcaggcgggc tatcagtcgc cctgttcgtc tgacggcaga + 481 agaagaccag gaaatcagaa aaagggctgc tgaatgcggc aagaccgttt ctggtttttt + 541 acgggcggca gctctcggta agaaagttaa ctcactgact gatgaccggg tgctgaaaga + 601 agttatgcga ctgggggcgt tgcagaaaaa actctttatc gacggcaagc gtgtcgggga + 661 cagagagtat gcggaggtgc tgatcgctat tacggagtat caccgtgccc tgttatccag + 721 gcttatggca gattagcttc ccggagagaa actgtcgaaa acagacggta tgaacgccgt + 781 aagcccccaa accgatcgcc attcactttc atgcatagct atgcagtgag ctgaaagcga + 841 tcctgacgca tttttccggt ttaccccggg gaaaacatct ctttttgcgg tgtctgcgtc + 901 agaatcgcgt tcagcgcgtt ttggcggtgc gcgtaatgag acgttatggt aaatgtcttc + 961 tggcttgata ttatattgga atgccttttt tcaaagcaaa tgatgtggct ttggatagaa + 1021 ggtttacgtt gatcttatca aagttttttt taaagaacga agccgagagc tcagataaat + 1081 cattatattc atcagttttc gtaactttgt ttaatgtgta acttgaaaac ttctcgccat + 1141 taaatgacgt atagacgtaa cgatcttttt ttccaccgtt aggaattatt aaatcaaaaa + 1201 aaacatcacc cttgcttttc tttttcttca agtcggattc gatttttgag aaaaattcgc + 1261 tcgggctata aatatcagta gcatagacaa taaataaagt tttatcttta ttttttattg + 1321 cttctatttg +// |
| b |
| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/TEST_6/TEST_6.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_6/TEST_6.gff3 Mon Jul 24 11:22:16 2023 +0000 |
| b |
| @@ -0,0 +1,36 @@ +##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 +# Database: v5.0, full +# DOI: 10.1099/mgen.0.000685 +# URL: github.com/oschwengers/bakta +##sequence-region contig_1 1 1330 +contig_1 Bakta region 1 1330 . + . ID=contig_1;Name=contig_1;Is_circular=true +contig_1 Prodigal CDS 413 736 . + 0 ID=IHHALP_00005;Name=hypothetical protein;locus_tag=IHHALP_00005;product=hypothetical protein +contig_1 Prodigal CDS 971 1471 . - 0 ID=IHHALP_00010;Name=hypothetical protein;locus_tag=IHHALP_00010;product=hypothetical protein +##FASTA +>contig_1 +TTCTTCTGCGAGTTCGTGCAGCTTCTCACACATGGTGGCCTGCTCGTCAGCATCGAGTGC +GTCCAGTTTTTCGAGCAGCGTCAGGCTCTGGCTTTTTATGAATCCCGCCATGTTGAGTGC +AGTTTGCTGCTGCTTGTTCATCTTTCTGTTTTCTCCGTTCTGTCTGTCATCTGCGTCGTG +TGATTATATCGCGCACCACTTTTCGACCGTCTTACCGCCGGTATTCTGCCGACGGACATT +TCAGTCAGACAACACTGTCACTGCCAAAAAACAGCAGTGCTTTGTTGGTAATTCGAACTT +GCAGACAGGACAGGATGTGCAATTGTTATACCGCGCATACATGCACGCTATTACAATTAC +CCTGGTCAGGGCTTCGCCCCGACACCCCATGTCAGATACGGAGCCATGTTTTATGACAAA +ACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGA +AGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTT +ACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGA +AGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGA +CAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAG +GCTTATGGCAGATTAGCTTCCCGGAGAGAAACTGTCGAAAACAGACGGTATGAACGCCGT +AAGCCCCCAAACCGATCGCCATTCACTTTCATGCATAGCTATGCAGTGAGCTGAAAGCGA +TCCTGACGCATTTTTCCGGTTTACCCCGGGGAAAACATCTCTTTTTGCGGTGTCTGCGTC +AGAATCGCGTTCAGCGCGTTTTGGCGGTGCGCGTAATGAGACGTTATGGTAAATGTCTTC +TGGCTTGATATTATATTGGAATGCCTTTTTTCAAAGCAAATGATGTGGCTTTGGATAGAA +GGTTTACGTTGATCTTATCAAAGTTTTTTTTAAAGAACGAAGCCGAGAGCTCAGATAAAT +CATTATATTCATCAGTTTTCGTAACTTTGTTTAATGTGTAACTTGAAAACTTCTCGCCAT +TAAATGACGTATAGACGTAACGATCTTTTTTTCCACCGTTAGGAATTATTAAATCAAAAA +AAACATCACCCTTGCTTTTCTTTTTCTTCAAGTCGGATTCGATTTTTGAGAAAAATTCGC +TCGGGCTATAAATATCAGTAGCATAGACAATAAATAAAGTTTTATCTTTATTTTTTATTG +CTTCTATTTG |
| b |
| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/TEST_6/TEST_6.hypotheticals.faa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_6/TEST_6.hypotheticals.faa Mon Jul 24 11:22:16 2023 +0000 |
| b |
| @@ -0,0 +1,4 @@ +>IHHALP_00005 hypothetical protein +MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD +>IHHALP_00010 hypothetical protein +MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI |
| b |
| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/TEST_6/TEST_6.hypotheticals.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_6/TEST_6.hypotheticals.tsv Mon Jul 24 11:22:16 2023 +0000 |
| [ |
| @@ -0,0 +1,5 @@ +#Annotated with Bakta v1.8.1, 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 +contig_1 971 141 - IHHALP_00010 18.9 7.7 |
| b |
| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/TEST_6/TEST_6.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_6/TEST_6.json Mon Jul 24 11:22:16 2023 +0000 |
| [ |
| @@ -0,0 +1,95 @@ +{ + "genome": { + "genus": null, + "species": null, + "strain": null, + "complete": true, + "gram": "?", + "translation_table": 11 + }, + "stats": { + "no_sequences": 1, + "size": 1330, + "gc": 0.4518796992481203, + "n_ratio": 0.0, + "n50": 1330, + "coding_ratio": 0.6203007518796992 + }, + "features": [ + { + "type": "cds", + "contig": "contig_1", + "start": 413, + "stop": 736, + "strand": "+", + "gene": null, + "product": "hypothetical protein", + "start_type": "ATG", + "rbs_motif": "GGAG/GAGG", + "db_xrefs": [], + "frame": 2, + "aa": "MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD", + "aa_hexdigest": "d9bdebc84195542e775c3d22458b507e", + "nt": "ATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAG", + "hypothetical": true, + "genes": [], + "seq_stats": { + "molecular_weight": 12072.90819999999, + "isoelectric_point": 10.367886161804197 + }, + "id": "IHHALPPJCH_1", + "locus": "IHHALP_00005" + }, + { + "type": "cds", + "contig": "contig_1", + "start": 971, + "stop": 141, + "strand": "-", + "gene": null, + "product": "hypothetical protein", + "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": { + "molecular_weight": 18866.325799999995, + "isoelectric_point": 7.696590614318848 + }, + "id": "IHHALPPJCH_2", + "locus": "IHHALP_00010" + } + ], + "sequences": [ + { + "id": "contig_1", + "description": "[gcode=11] [completeness=complete] [topology=circular] [plasmid-name=unnamed1]", + "sequence": "TTCTTCTGCGAGTTCGTGCAGCTTCTCACACATGGTGGCCTGCTCGTCAGCATCGAGTGCGTCCAGTTTTTCGAGCAGCGTCAGGCTCTGGCTTTTTATGAATCCCGCCATGTTGAGTGCAGTTTGCTGCTGCTTGTTCATCTTTCTGTTTTCTCCGTTCTGTCTGTCATCTGCGTCGTGTGATTATATCGCGCACCACTTTTCGACCGTCTTACCGCCGGTATTCTGCCGACGGACATTTCAGTCAGACAACACTGTCACTGCCAAAAAACAGCAGTGCTTTGTTGGTAATTCGAACTTGCAGACAGGACAGGATGTGCAATTGTTATACCGCGCATACATGCACGCTATTACAATTACCCTGGTCAGGGCTTCGCCCCGACACCCCATGTCAGATACGGAGCCATGTTTTATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAGCTTCCCGGAGAGAAACTGTCGAAAACAGACGGTATGAACGCCGTAAGCCCCCAAACCGATCGCCATTCACTTTCATGCATAGCTATGCAGTGAGCTGAAAGCGATCCTGACGCATTTTTCCGGTTTACCCCGGGGAAAACATCTCTTTTTGCGGTGTCTGCGTCAGAATCGCGTTCAGCGCGTTTTGGCGGTGCGCGTAATGAGACGTTATGGTAAATGTCTTCTGGCTTGATATTATATTGGAATGCCTTTTTTCAAAGCAAATGATGTGGCTTTGGATAGAAGGTTTACGTTGATCTTATCAAAGTTTTTTTTAAAGAACGAAGCCGAGAGCTCAGATAAATCATTATATTCATCAGTTTTCGTAACTTTGTTTAATGTGTAACTTGAAAACTTCTCGCCATTAAATGACGTATAGACGTAACGATCTTTTTTTCCACCGTTAGGAATTATTAAATCAAAAAAAACATCACCCTTGCTTTTCTTTTTCTTCAAGTCGGATTCGATTTTTGAGAAAAATTCGCTCGGGCTATAAATATCAGTAGCATAGACAATAAATAAAGTTTTATCTTTATTTTTTATTGCTTCTATTTG", + "length": 1330, + "complete": true, + "type": "plasmid", + "topology": "circular", + "simple_id": "contig_1", + "orig_id": "NC_002127.1", + "orig_description": "Escherichia coli O157:H7 str. Sakai plasmid pOSAK1, complete sequence", + "name": "unnamed1" + } + ], + "run": { + "start": "2023-06-19 09:31:32", + "end": "2023-06-19 09:31:33" + }, + "version": { + "bakta": "1.8.1", + "db": { + "version": "5.0", + "type": "full" + } + } +} \ No newline at end of file |
| b |
| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/TEST_6/TEST_6.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_6/TEST_6.log Mon Jul 24 11:22:16 2023 +0000 |
| [ |
| @@ -0,0 +1,107 @@ +Bakta v1.8.1 +Options and arguments: + input: /tmp/tmp6wdeee6u/files/4/2/7/dataset_4276a0b6-bcea-42e6-a1e2-9f880300f5a1.dat + db: /tmp/tmp6wdeee6u/job_working_directory/000/15/working/database_path, version 5.0, full + output: /tmp/tmp6wdeee6u/job_working_directory/000/15/working/bakta_output + tmp directory: /tmp/tmp6wdeee6u/tmp/tmpkzvj8z8k + prefix: bakta_output + threads: 1 + translation table: 11 + +parse genome sequences... + imported: 1 + filtered & revised: 1 + plasmids: 1 + +start annotation... +predict tRNAs... + found: 0 +predict tmRNAs... + found: 0 +predict rRNAs... + found: 0 +predict ncRNAs... + found: 0 +predict ncRNA regions... + found: 0 +predict CRISPR arrays... + found: 0 +predict & annotate CDSs... + predicted: 2 + discarded spurious: 0 + revised translational exceptions: 0 + detected IPSs: 0 + found PSCs: 0 + found PSCCs: 0 + lookup annotations... + conduct expert systems... + amrfinder: 0 + protein sequences: 0 + combine annotations and mark hypotheticals... + detect pseudogenes... + pseudogene candidates: 0 + found pseudogenes: 0 +analyze hypothetical proteins: 2 + detected Pfam hits: 0 + calculated proteins statistics + revise special cases... +extract sORF... + potential: 22 + discarded due to overlaps: 2 + discarded spurious: 0 + detected IPSs: 0 + found PSCs: 0 + lookup annotations... + filter and combine annotations... + filtered sORFs: 0 +detect gaps... + found: 0 +detect oriCs/oriVs... + found: 0 +detect oriTs... + found: 0 +apply feature overlap filters... +select features and create locus tags... +selected: 2 +improve annotations... + revised gene symbols: 0 + +genome statistics: + Genome size: 1,330 bp + Contigs/replicons: 1 + GC: 45.2 % + N50: 1,330 + N ratio: 0.0 % + coding density: 62.0 % + +annotation summary: + tRNAs: 0 + tmRNAs: 0 + rRNAs: 0 + ncRNAs: 0 + ncRNA regions: 0 + CRISPR arrays: 0 + CDSs: 2 + hypotheticals: 2 + pseudogenes: 0 + signal peptides: 0 + sORFs: 0 + gaps: 0 + oriCs/oriVs: 0 + oriTs: 0 + +export annotation results to: /tmp/tmp6wdeee6u/job_working_directory/000/15/working/bakta_output + human readable TSV... + GFF3... + INSDC GenBank & EMBL... + genome sequences... + feature nucleotide sequences... + translated CDS sequences... + circular genome plot... + hypothetical TSV... + translated hypothetical CDS sequences... + machine readable JSON... + genome and annotation summary... + +If you use these results please cite Bakta: https://doi.org/10.1099/mgen.0.000685 +Annotation successfully finished in 0:01 [mm:ss]. |
| b |
| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/TEST_6/TEST_6.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_6/TEST_6.tsv Mon Jul 24 11:22:16 2023 +0000 |
| b |
| @@ -0,0 +1,8 @@ +# Annotated with Bakta +# Software: v1.8.1 +# Database: v5.0, full +# DOI: 10.1099/mgen.0.000685 +# URL: github.com/oschwengers/bakta +#Sequence Id Type Start Stop Strand Locus Tag Gene Product DbXrefs +contig_1 cds 413 736 + IHHALP_00005 hypothetical protein +contig_1 cds 971 141 - IHHALP_00010 hypothetical protein |
| b |
| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/TEST_6/TEST_6.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_6/TEST_6.txt Mon Jul 24 11:22:16 2023 +0000 |
| b |
| @@ -0,0 +1,30 @@ +Sequence(s): +Length: 1330 +Count: 1 +GC: 45.2 +N50: 1330 +N ratio: 0.0 +coding density: 62.0 + +Annotation: +tRNAs: 0 +tmRNAs: 0 +rRNAs: 0 +ncRNAs: 0 +ncRNA regions: 0 +CRISPR arrays: 0 +CDSs: 2 +pseudogenes: 0 +hypotheticals: 2 +signal peptides: 0 +sORFs: 0 +gaps: 0 +oriCs: 0 +oriVs: 0 +oriTs: 0 + +Bakta: +Software: v1.8.1 +Database: v5.0, full +DOI: 10.1099/mgen.0.000685 +URL: github.com/oschwengers/bakta |
| b |
| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/TEST_6/TEST_6_plot.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_6/TEST_6_plot.svg Mon Jul 24 11:22:16 2023 +0000 |
| b |
| b'@@ -0,0 +1,2400 @@\n+<?xml version="1.0" encoding="utf-8" standalone="no"?>\n+<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">\n+<svg width="3000px" height="3000px" version="1.1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">\n+<g id="bg">\n+<rect x="0" y="0" width="3000px" height="3000px" style="fill:rgb(255,255,255);"/>\n+</g>\n+<g id="ideograms">\n+<path d="M1500.000,230.000 A1270.000,1270.000 40.000 1,1 1499.202,230.000 L1499.199,225.000 A1275.000,1275.000 0.000 1,0 1500.000,225.000 Z" style="stroke-linecap:round;fill:rgb(0,0,0);" />\n+<line x1=\'1500.0\' y1=\'225.0\' x2=\'1500.0\' y2=\'200.0\' style="stroke-width:4.0;stroke:rgb(0,0,0);stroke-linecap:round;fill:none;" />\n+<text x="1522.0" y="190.2" font-size="52.0px" font-family="CMUBright-Roman" style="text-anchor:start;fill:rgb(0,0,0);" transform="rotate(270.0,1522.0,190.2)" >0 bp</text>\n+<line x1=\'1515.1\' y1=\'225.1\' x2=\'1515.1\' 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| b |
| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/bakta_database.loc --- a/test-data/bakta_database.loc Fri Feb 10 14:20:09 2023 +0000 +++ b/test-data/bakta_database.loc Mon Jul 24 11:22:16 2023 +0000 |
| b |
| @@ -5,7 +5,6 @@ # path : final oath to bakta database on galaxy # value, dbkey, bakta_version, path # eg. -# 7025248 V4.0_2022-08-29 1.5 path/to/db V0.0_date_test 7190015 1.5 ${__HERE__}/test-db -V0.1_2022-08-29 7197216 1.5 ${__HERE__}/test-db -V0.2_2022-08-19 7197217 1.7 ${__HERE__}/test-db +V4.0_2022-08-29 7197216 1.5 ${__HERE__}/test-db +V5.0_2022-08-19 7197217 1.7 ${__HERE__}/test-db |
| b |
| diff -r 865ece5ca178 -r 3f0aa1b3e816 test-data/test-db/version.json --- a/test-data/test-db/version.json Fri Feb 10 14:20:09 2023 +0000 +++ b/test-data/test-db/version.json Mon Jul 24 11:22:16 2023 +0000 |
| [ |
| @@ -1,7 +1,8 @@ { - "date": "2022-08-25", - "major": 4, + "date": "2023-02-20", + "major": 5, "minor": 0, + "type": "full", "dependencies": [ { "name": "AMRFinderPlus", |
| b |
| diff -r 865ece5ca178 -r 3f0aa1b3e816 tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Fri Feb 10 14:20:09 2023 +0000 +++ b/tool_data_table_conf.xml.sample Mon Jul 24 11:22:16 2023 +0000 |
| b |
| @@ -2,6 +2,10 @@ <tables> <table name="bakta_database" comment_char="#"> <columns>value, dbkey, bakta_version, path</columns> - <file path="tool-data/bakta_database.loc.sample" /> + <file path="tool-data/bakta_database.loc.sample"/> + </table> + <table name="amrfinderplus_database" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/amrfinderplus_database.loc.sample"/> </table> </tables> |
| b |
| diff -r 865ece5ca178 -r 3f0aa1b3e816 tool_data_table_conf.xml.test --- a/tool_data_table_conf.xml.test Fri Feb 10 14:20:09 2023 +0000 +++ b/tool_data_table_conf.xml.test Mon Jul 24 11:22:16 2023 +0000 |
| b |
| @@ -7,6 +7,5 @@ <table name="amrfinderplus_database" comment_char="#"> <columns>value, name, path</columns> <file path="${__HERE__}/test-data/amrfinderplus_database.loc" /> - </table> </tables> |
