Mercurial > repos > pimarin > bakta
changeset 5:44fb905481f0 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit a7dcdae8bccb5a8d7abdb9c6d058f9bd7c6f6c15
| author | pimarin |
|---|---|
| date | Thu, 12 Jan 2023 11:25:17 +0000 |
| parents | 591cae6ef29d |
| children | f77ebe2e4df0 |
| files | bakta.xml macro.xml test-data/TEST_1/TEST_1.embl test-data/TEST_1/TEST_1.faa test-data/TEST_1/TEST_1.ffn 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.faa 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.ffn test-data/TEST_3/TEST_3.ffn test-data/TEST_4/TEST_4.ffn test-data/TEST_5/TEST_5.log |
| diffstat | 17 files changed, 388 insertions(+), 16 deletions(-) [+] |
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--- a/bakta.xml Thu Dec 22 15:06:32 2022 +0000 +++ b/bakta.xml Thu Jan 12 11:25:17 2023 +0000 @@ -12,8 +12,8 @@ <command detect_errors="aggressive"><![CDATA[ mkdir ./database_path && - ln -s '$(input_option.bakta_db_select.fields.path)/'* database_path && - ln -s '$(input_option.amrfinder_db_select.fields.path)' database_path && + ln -s '$(input_option.bakta_db_select.fields.path)/*' database_path && + ln -rs '$(input_option.amrfinder_db_select.fields.path)' database_path/latest && bakta #*====================================== @@ -92,10 +92,6 @@ <param name="bakta_db_select" type="select" label="The bakta database"> <options from_data_table="bakta_database"> <filter type="static_value" value="@BAKTA_VERSION@" column="bakta_version"/> - <column name="value" index="0"/> - <column name="dbkey" index="1"/> - <column name="bakta_version" index="2"/> - <column name="path" index="3"/> <validator message="No bakta database is available" type="no_options"/> </options> </param>
--- a/macro.xml Thu Dec 22 15:06:32 2022 +0000 +++ b/macro.xml Thu Jan 12 11:25:17 2023 +0000 @@ -2,6 +2,7 @@ <macros> <token name="@TOOL_VERSION@">1.6.1</token> <token name="@BAKTA_VERSION@">1.5</token> + <token name="@DEEPSIG@">1.2.5</token> <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">21.05</token> <xml name="version_command"> @@ -20,6 +21,7 @@ <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">bakta</requirement> + <requirement type="package" version="@DEEPSIG@">deepsig </requirement> </requirements> </xml> <xml name="citations">
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_1/TEST_1.embl Thu Jan 12 11:25:17 2023 +0000 @@ -0,0 +1,88 @@ +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: v1.6.1 +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 :: 01/03/2023, 10:02:08 +CC Annotation Pipeline :: Bakta +CC Annotation Software version :: v1.6.1 +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="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 +//
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_1/TEST_1.faa Thu Jan 12 11:25:17 2023 +0000 @@ -0,0 +1,4 @@ +>IHHALP_00005 hypothetical protein +MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD +>IHHALP_00010 hypothetical protein +MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_1/TEST_1.ffn Thu Jan 12 11:25:17 2023 +0000 @@ -0,0 +1,4 @@ +>IHHALP_00005 hypothetical protein +ATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAG +>IHHALP_00010 hypothetical protein +ATGAACAAGCAGCAGCAAACTGCACTCAACATGGCGGGATTCATAAAAAGCCAGAGCCTGACGCTGCTCGAAAAACTGGACGCACTCGATGCTGACGAGCAGGCCACCATGTGTGAGAAGCTGCACGAACTCGCAGAAGAACAAATAGAAGCAATAAAAAATAAAGATAAAACTTTATTTATTGTCTATGCTACTGATATTTATAGCCCGAGCGAATTTTTCTCAAAAATCGAATCCGACTTGAAGAAAAAGAAAAGCAAGGGTGATGTTTTTTTTGATTTAATAATTCCTAACGGTGGAAAAAAAGATCGTTACGTCTATACGTCATTTAATGGCGAGAAGTTTTCAAGTTACACATTAAACAAAGTTACGAAAACTGATGAATATAATGATTTATCTGAGCTCTCGGCTTCGTTCTTTAAAAAAAACTTTGATAAGATCAACGTAAACCTTCTATCCAAAGCCACATCATTTGCTTTGAAAAAAGGCATTCCAATATAA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_1/TEST_1.fna Thu Jan 12 11:25:17 2023 +0000 @@ -0,0 +1,24 @@ +>contig_1 [completeness=complete] [topology=circular] [gcode=11] +TTCTTCTGCGAGTTCGTGCAGCTTCTCACACATGGTGGCCTGCTCGTCAGCATCGAGTGC +GTCCAGTTTTTCGAGCAGCGTCAGGCTCTGGCTTTTTATGAATCCCGCCATGTTGAGTGC +AGTTTGCTGCTGCTTGTTCATCTTTCTGTTTTCTCCGTTCTGTCTGTCATCTGCGTCGTG +TGATTATATCGCGCACCACTTTTCGACCGTCTTACCGCCGGTATTCTGCCGACGGACATT +TCAGTCAGACAACACTGTCACTGCCAAAAAACAGCAGTGCTTTGTTGGTAATTCGAACTT +GCAGACAGGACAGGATGTGCAATTGTTATACCGCGCATACATGCACGCTATTACAATTAC +CCTGGTCAGGGCTTCGCCCCGACACCCCATGTCAGATACGGAGCCATGTTTTATGACAAA +ACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGA +AGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTT +ACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGA +AGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGA +CAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAG +GCTTATGGCAGATTAGCTTCCCGGAGAGAAACTGTCGAAAACAGACGGTATGAACGCCGT +AAGCCCCCAAACCGATCGCCATTCACTTTCATGCATAGCTATGCAGTGAGCTGAAAGCGA +TCCTGACGCATTTTTCCGGTTTACCCCGGGGAAAACATCTCTTTTTGCGGTGTCTGCGTC +AGAATCGCGTTCAGCGCGTTTTGGCGGTGCGCGTAATGAGACGTTATGGTAAATGTCTTC +TGGCTTGATATTATATTGGAATGCCTTTTTTCAAAGCAAATGATGTGGCTTTGGATAGAA +GGTTTACGTTGATCTTATCAAAGTTTTTTTTAAAGAACGAAGCCGAGAGCTCAGATAAAT +CATTATATTCATCAGTTTTCGTAACTTTGTTTAATGTGTAACTTGAAAACTTCTCGCCAT +TAAATGACGTATAGACGTAACGATCTTTTTTTCCACCGTTAGGAATTATTAAATCAAAAA +AAACATCACCCTTGCTTTTCTTTTTCTTCAAGTCGGATTCGATTTTTGAGAAAAATTCGC +TCGGGCTATAAATATCAGTAGCATAGACAATAAATAAAGTTTTATCTTTATTTTTTATTG +CTTCTATTTG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_1/TEST_1.gbff Thu Jan 12 11:25:17 2023 +0000 @@ -0,0 +1,84 @@ +LOCUS contig_1 1330 bp DNA circular BCT 03-JAN-2023 +DEFINITION plasmid unnamed1, complete sequence. +ACCESSION contig_1 +VERSION contig_1 +KEYWORDS . +SOURCE None + ORGANISM . + . +COMMENT Annotated with Bakta + Software: v1.6.1 + Database: v4.0 + DOI: 10.1099/mgen.0.000685 + URL: github.com/oschwengers/bakta + + ##Genome Annotation Summary:## + Annotation Date :: 01/03/2023, 10:02:08 + Annotation Pipeline :: Bakta + Annotation Software version :: v1.6.1 + 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="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 +//
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_1/TEST_1.gff3 Thu Jan 12 11:25:17 2023 +0000 @@ -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: v1.6.1 +# Database: v4.0 +# 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_1/TEST_1.hypotheticals.faa Thu Jan 12 11:25:17 2023 +0000 @@ -0,0 +1,4 @@ +>IHHALP_00005 hypothetical protein +MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD +>IHHALP_00010 hypothetical protein +MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_1/TEST_1.hypotheticals.tsv Thu Jan 12 11:25:17 2023 +0000 @@ -0,0 +1,5 @@ +#Annotated with Bakta v1.6.1, 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 +contig_1 413 736 + IHHALP_00005 12.1 10.4 +contig_1 971 141 - IHHALP_00010 18.9 7.7
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_1/TEST_1.json Thu Jan 12 11:25:17 2023 +0000 @@ -0,0 +1,90 @@ +{ + "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, + "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, + "seq_stats": { + "molecular_weight": 18866.325799999995, + "isoelectric_point": 7.696590614318848 + }, + "id": "IHHALPPJCH_2", + "locus": "IHHALP_00010" + } + ], + "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": "2023-01-03 10:02:07", + "end": "2023-01-03 10:02:08" + }, + "version": { + "bakta": "1.6.1", + "db": "4.0" + } +} \ No newline at end of file
--- a/test-data/TEST_1/TEST_1.log Thu Dec 22 15:06:32 2022 +0000 +++ b/test-data/TEST_1/TEST_1.log Thu Jan 12 11:25:17 2023 +0000 @@ -79,11 +79,7 @@ oriCs/oriVs: 0 oriTs: 0 -<<<<<<< HEAD -export annotation results to: /tmp/tmptbkng6kx/job_working_directory/000/2/working -======= -export annotation results to: /tmp/tmp4jorszj6/job_working_directory/000/2/working ->>>>>>> 195c8410c (change option for plot) +export annotation results to: /tmp/tmpevwtlk9g/job_working_directory/000/2/working human readable TSV... GFF3... INSDC GenBank & EMBL...
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_1/TEST_1.tsv Thu Jan 12 11:25:17 2023 +0000 @@ -0,0 +1,5 @@ +#Annotated with Bakta (v1.6.1): https://github.com/oschwengers/bakta +#Database (v4.0): https://doi.org/10.5281/zenodo.4247252 +#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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_1/TEST_1.txt Thu Jan 12 11:25:17 2023 +0000 @@ -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: v1.6.1 +Database: v4.0 +DOI: 10.1099/mgen.0.000685 +URL: github.com/oschwengers/bakta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_2/TEST_2.ffn Thu Jan 12 11:25:17 2023 +0000 @@ -0,0 +1,4 @@ +>IHHALP_00005 hypothetical protein +ATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAG +>IHHALP_00010 hypothetical protein +ATGAACAAGCAGCAGCAAACTGCACTCAACATGGCGGGATTCATAAAAAGCCAGAGCCTGACGCTGCTCGAAAAACTGGACGCACTCGATGCTGACGAGCAGGCCACCATGTGTGAGAAGCTGCACGAACTCGCAGAAGAACAAATAGAAGCAATAAAAAATAAAGATAAAACTTTATTTATTGTCTATGCTACTGATATTTATAGCCCGAGCGAATTTTTCTCAAAAATCGAATCCGACTTGAAGAAAAAGAAAAGCAAGGGTGATGTTTTTTTTGATTTAATAATTCCTAACGGTGGAAAAAAAGATCGTTACGTCTATACGTCATTTAATGGCGAGAAGTTTTCAAGTTACACATTAAACAAAGTTACGAAAACTGATGAATATAATGATTTATCTGAGCTCTCGGCTTCGTTCTTTAAAAAAAACTTTGATAAGATCAACGTAAACCTTCTATCCAAAGCCACATCATTTGCTTTGAAAAAAGGCATTCCAATATAA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_4/TEST_4.ffn Thu Jan 12 11:25:17 2023 +0000 @@ -0,0 +1,4 @@ +>IHHALP_00005 hypothetical protein +ATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAG +>IHHALP_00010 hypothetical protein +ATGAACAAGCAGCAGCAAACTGCACTCAACATGGCGGGATTCATAAAAAGCCAGAGCCTGACGCTGCTCGAAAAACTGGACGCACTCGATGCTGACGAGCAGGCCACCATGTGTGAGAAGCTGCACGAACTCGCAGAAGAACAAATAGAAGCAATAAAAAATAAAGATAAAACTTTATTTATTGTCTATGCTACTGATATTTATAGCCCGAGCGAATTTTTCTCAAAAATCGAATCCGACTTGAAGAAAAAGAAAAGCAAGGGTGATGTTTTTTTTGATTTAATAATTCCTAACGGTGGAAAAAAAGATCGTTACGTCTATACGTCATTTAATGGCGAGAAGTTTTCAAGTTACACATTAAACAAAGTTACGAAAACTGATGAATATAATGATTTATCTGAGCTCTCGGCTTCGTTCTTTAAAAAAAACTTTGATAAGATCAACGTAAACCTTCTATCCAAAGCCACATCATTTGCTTTGAAAAAAGGCATTCCAATATAA
--- a/test-data/TEST_5/TEST_5.log Thu Dec 22 15:06:32 2022 +0000 +++ b/test-data/TEST_5/TEST_5.log Thu Jan 12 11:25:17 2023 +0000 @@ -43,11 +43,7 @@ oriCs/oriVs: 0 oriTs: 0 -<<<<<<< HEAD -export annotation results to: /tmp/tmptbkng6kx/job_working_directory/000/14/working -======= -export annotation results to: /tmp/tmp4jorszj6/job_working_directory/000/14/working ->>>>>>> 195c8410c (change option for plot) +export annotation results to: /tmp/tmpevwtlk9g/job_working_directory/000/14/working human readable TSV... GFF3... INSDC GenBank & EMBL...