# HG changeset patch # User pimarin # Date 1673614953 0 # Node ID f77ebe2e4df06a9a4a696ced2eb3383aa136f7d9 # Parent 44fb905481f097faf39199211f67ac2a1fadf39c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit bd3e03930af39dc50e6640430256555851e7b096 diff -r 44fb905481f0 -r f77ebe2e4df0 bakta.xml --- a/bakta.xml Thu Jan 12 11:25:17 2023 +0000 +++ b/bakta.xml Fri Jan 13 13:02:33 2023 +0000 @@ -1,6 +1,6 @@ - genome annotation via alignment-free sequence identification + Genome annotation via alignment-free sequence identification macro.xml @@ -11,10 +11,9 @@ -
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1.6.1 1.5 - 1.2.5 + 0 21.05 @@ -21,7 +21,7 @@ bakta - deepsig + diff -r 44fb905481f0 -r f77ebe2e4df0 test-data/amrfinderplus_database.loc --- a/test-data/amrfinderplus_database.loc Thu Jan 12 11:25:17 2023 +0000 +++ b/test-data/amrfinderplus_database.loc Fri Jan 13 13:02:33 2023 +0000 @@ -4,5 +4,5 @@ # value, name, path # # for example -amrfinderplus_V3.10_2022-10-11.2 V3.10-2022-10-11.2 ${__HERE__}/amrfinderplus-db -amrfinderplus_V3.6_2020-03-20.1 V3.6-2020-03-20.1 ${__HERE__}/amrfinderplus-db +amrfinderplus_V3.10_2022-10-11.2 V3.10-2022-10-11.2 ${__HERE__}/amrfinderplus-db/2021-09-30.1 +amrfinderplus_V3.6_2020-03-20.1 V3.6-2020-03-20.1 ${__HERE__}/amrfinderplus-db/2021-09-30.1 diff -r 44fb905481f0 -r f77ebe2e4df0 test-data/tmp/TEST_1.embl --- a/test-data/tmp/TEST_1.embl Thu Jan 12 11:25:17 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,100 +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: v1.6.1 -CC Database: v4.0 -CC DOI: 10.1099/mgen.0.000685 -CC URL: github.com/oschwengers/bakta -CC -CC ##Genome Annotation Summary:## -<<<<<<< HEAD:tools/bakta/test-data/tmp/TEST_1.embl -<<<<<<< HEAD:tools/bakta/test-data/TEST_1/TEST_1.embl -CC Annotation Date :: 12/19/2022, 10:20:25 -======= -<<<<<<< HEAD:tools/bakta/test-data/TEST_4/TEST_4.embl -CC Annotation Date :: 09/16/2022, 07:32:50 -======= -CC Annotation Date :: 12/21/2022, 14:34:39 ->>>>>>> f1bb03fb2 (update bakta for plot output and to reduce number of output files):tools/bakta/test-data/tmp/TEST_1.embl ->>>>>>> 17d4de2b8 (update bakta for plot output and to reduce number of output files):tools/bakta/test-data/tmp/TEST_1.embl -======= -CC Annotation Date :: 12/21/2022, 19:53:31 ->>>>>>> 195c8410c (change option for plot):tools/bakta/test-data/TEST_1/TEST_1.embl -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 -// diff -r 44fb905481f0 -r f77ebe2e4df0 test-data/tmp/TEST_1.faa --- a/test-data/tmp/TEST_1.faa Thu Jan 12 11:25:17 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ ->IHHALP_00005 hypothetical protein -MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD ->IHHALP_00010 hypothetical protein -MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI diff -r 44fb905481f0 -r f77ebe2e4df0 test-data/tmp/TEST_1.ffn --- a/test-data/tmp/TEST_1.ffn Thu Jan 12 11:25:17 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ ->IHHALP_00005 hypothetical protein -ATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAG ->IHHALP_00010 hypothetical protein -ATGAACAAGCAGCAGCAAACTGCACTCAACATGGCGGGATTCATAAAAAGCCAGAGCCTGACGCTGCTCGAAAAACTGGACGCACTCGATGCTGACGAGCAGGCCACCATGTGTGAGAAGCTGCACGAACTCGCAGAAGAACAAATAGAAGCAATAAAAAATAAAGATAAAACTTTATTTATTGTCTATGCTACTGATATTTATAGCCCGAGCGAATTTTTCTCAAAAATCGAATCCGACTTGAAGAAAAAGAAAAGCAAGGGTGATGTTTTTTTTGATTTAATAATTCCTAACGGTGGAAAAAAAGATCGTTACGTCTATACGTCATTTAATGGCGAGAAGTTTTCAAGTTACACATTAAACAAAGTTACGAAAACTGATGAATATAATGATTTATCTGAGCTCTCGGCTTCGTTCTTTAAAAAAAACTTTGATAAGATCAACGTAAACCTTCTATCCAAAGCCACATCATTTGCTTTGAAAAAAGGCATTCCAATATAA diff -r 44fb905481f0 -r f77ebe2e4df0 test-data/tmp/TEST_1.fna --- a/test-data/tmp/TEST_1.fna Thu Jan 12 11:25:17 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,24 +0,0 @@ ->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 diff -r 44fb905481f0 -r f77ebe2e4df0 test-data/tmp/TEST_1.gbff --- a/test-data/tmp/TEST_1.gbff Thu Jan 12 11:25:17 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,107 +0,0 @@ -<<<<<<< HEAD:tools/bakta/test-data/TEST_1/TEST_1.gbff -LOCUS contig_1 1330 bp DNA circular BCT 19-DEC-2022 -======= -<<<<<<< HEAD:tools/bakta/test-data/TEST_4/TEST_4.gbff -LOCUS p2 1330 bp DNA circular BCT 16-SEP-2022 -DEFINITION plasmid pOSAK1, complete sequence. -ACCESSION p2 -VERSION p2 -======= -LOCUS contig_1 1330 bp DNA circular BCT 21-DEC-2022 ->>>>>>> 17d4de2b8 (update bakta for plot output and to reduce number of output files):tools/bakta/test-data/tmp/TEST_1.gbff -DEFINITION plasmid unnamed1, complete sequence. -ACCESSION contig_1 -VERSION contig_1 ->>>>>>> f1bb03fb2 (update bakta for plot output and to reduce number of output files):tools/bakta/test-data/tmp/TEST_1.gbff -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:## -<<<<<<< HEAD:tools/bakta/test-data/tmp/TEST_1.gbff -<<<<<<< HEAD:tools/bakta/test-data/TEST_1/TEST_1.gbff - Annotation Date :: 12/19/2022, 10:20:25 -======= -<<<<<<< HEAD:tools/bakta/test-data/TEST_4/TEST_4.gbff - Annotation Date :: 09/16/2022, 07:32:50 -======= - Annotation Date :: 12/21/2022, 14:34:39 ->>>>>>> f1bb03fb2 (update bakta for plot output and to reduce number of output files):tools/bakta/test-data/tmp/TEST_1.gbff ->>>>>>> 17d4de2b8 (update bakta for plot output and to reduce number of output files):tools/bakta/test-data/tmp/TEST_1.gbff -======= - Annotation Date :: 12/21/2022, 19:53:31 ->>>>>>> 195c8410c (change option for plot):tools/bakta/test-data/TEST_1/TEST_1.gbff - 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 -// diff -r 44fb905481f0 -r f77ebe2e4df0 test-data/tmp/TEST_1.gff3 --- a/test-data/tmp/TEST_1.gff3 Thu Jan 12 11:25:17 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,36 +0,0 @@ -##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 diff -r 44fb905481f0 -r f77ebe2e4df0 test-data/tmp/TEST_1.hypotheticals.faa --- a/test-data/tmp/TEST_1.hypotheticals.faa Thu Jan 12 11:25:17 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ ->IHHALP_00005 hypothetical protein -MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD ->IHHALP_00010 hypothetical protein -MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI diff -r 44fb905481f0 -r f77ebe2e4df0 test-data/tmp/TEST_1.hypotheticals.tsv --- a/test-data/tmp/TEST_1.hypotheticals.tsv Thu Jan 12 11:25:17 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -#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 diff -r 44fb905481f0 -r f77ebe2e4df0 test-data/tmp/TEST_1.json --- a/test-data/tmp/TEST_1.json Thu Jan 12 11:25:17 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,105 +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": 0.6203007518796992 - }, - "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": { -<<<<<<< HEAD:tools/bakta/test-data/tmp/TEST_1.json -<<<<<<< HEAD:tools/bakta/test-data/TEST_1/TEST_1.json - "start": "2022-12-19 10:20:24", - "end": "2022-12-19 10:20:25" -======= -<<<<<<< HEAD:tools/bakta/test-data/TEST_4/TEST_4.json - "start": "2022-09-16 07:32:48", - "end": "2022-09-16 07:32:50" -======= - "start": "2022-12-21 14:34:38", - "end": "2022-12-21 14:34:39" ->>>>>>> f1bb03fb2 (update bakta for plot output and to reduce number of output files):tools/bakta/test-data/tmp/TEST_1.json ->>>>>>> 17d4de2b8 (update bakta for plot output and to reduce number of output files):tools/bakta/test-data/tmp/TEST_1.json -======= - "start": "2022-12-21 19:53:30", - "end": "2022-12-21 19:53:31" ->>>>>>> 195c8410c (change option for plot):tools/bakta/test-data/TEST_1/TEST_1.json - }, - "version": { - "bakta": "1.6.1", - "db": "4.0" - } -} \ No newline at end of file diff -r 44fb905481f0 -r f77ebe2e4df0 test-data/tmp/TEST_1.log --- a/test-data/tmp/TEST_1.log Thu Jan 12 11:25:17 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,119 +0,0 @@ -14:34:38.821 - INFO - UTILS - version=1.6.1 -14:34:38.821 - INFO - UTILS - developer: Oliver Schwengers, github.com/oschwengers -14:34:38.821 - INFO - UTILS - command: /home/pierre/miniconda3/envs/__bakta@1.6.1/bin/bakta --threads 6 --db ./database_path --min-contig-length 1 --prefix TEST_1 --translation-table 11 --gram ? ../NC_002127.1.fna -14:34:38.821 - INFO - UTILS - local time: 2022-12-21 14:34:38 -14:34:38.822 - INFO - UTILS - machine: type=x86_64, cores=8 -14:34:38.822 - INFO - UTILS - system: type=Linux, release=5.15.0-56-generic -14:34:38.822 - INFO - UTILS - python: version=3.10.8, implementation=CPython -14:34:38.822 - INFO - CONFIG - threads=6 -14:34:38.822 - INFO - CONFIG - verbose=False -14:34:38.822 - INFO - CONFIG - debug=False -14:34:38.822 - INFO - CONFIG - database: type=parameter, path=/home/pierre/tools-iuc/tools/bakta/test-data/tmp/database_path -14:34:38.823 - INFO - CONFIG - tmp-path=/tmp/tmpxm45i679 -14:34:38.823 - INFO - CONFIG - genome-path=/home/pierre/tools-iuc/tools/bakta/test-data/NC_002127.1.fna -14:34:38.823 - INFO - CONFIG - min_contig_length=1 -14:34:38.823 - INFO - CONFIG - prefix=TEST_1 -14:34:38.823 - INFO - CONFIG - output-path=/home/pierre/tools-iuc/tools/bakta/test-data/tmp -14:34:38.823 - INFO - CONFIG - genus=None -14:34:38.823 - INFO - CONFIG - species=None -14:34:38.823 - INFO - CONFIG - strain=None -14:34:38.823 - INFO - CONFIG - plasmid=None -14:34:38.823 - INFO - CONFIG - complete=False -14:34:38.823 - INFO - CONFIG - prodigal_tf=None -14:34:38.823 - INFO - CONFIG - translation_table=11 -14:34:38.823 - INFO - CONFIG - gram=? -14:34:38.823 - INFO - CONFIG - compliant=False -14:34:38.823 - INFO - CONFIG - locus=None -14:34:38.823 - INFO - CONFIG - locus-tag=None -14:34:38.823 - INFO - CONFIG - keep_contig_headers=False -14:34:38.823 - INFO - CONFIG - replicon-table=None -14:34:38.823 - INFO - CONFIG - skip-tRNA=False -14:34:38.823 - INFO - CONFIG - skip-tmRNA=False -14:34:38.823 - INFO - CONFIG - skip-rRNA=False -14:34:38.823 - INFO - CONFIG - skip-ncRNA=False -14:34:38.823 - INFO - CONFIG - skip-ncRNA-region=False -14:34:38.823 - INFO - CONFIG - skip-CRISPR=False -14:34:38.823 - INFO - CONFIG - skip-CDS=False -14:34:38.823 - INFO - CONFIG - skip-pseudo=False -14:34:38.823 - INFO - CONFIG - skip-sORF=False -14:34:38.823 - INFO - CONFIG - skip-gap=False -14:34:38.823 - INFO - CONFIG - skip-ori=False -14:34:38.823 - INFO - CONFIG - skip-plot=False -14:34:38.823 - INFO - DB - detected: major=4, minor=0, date=2022-08-25 -14:34:38.883 - INFO - UTILS - dependency: tool=tRNAscan-SE, version=v2.0.11 -14:34:38.884 - INFO - UTILS - dependency: tool=aragorn, version=v1.2.41 -14:34:38.887 - INFO - UTILS - dependency: tool=cmscan, version=v1.1.4 -14:34:38.888 - INFO - UTILS - dependency: tool=pilercr, version=v1.6.0 -14:34:38.889 - INFO - UTILS - dependency: tool=amrfinder, version=v3.11.2 -14:34:38.914 - INFO - UTILS - dependency: tool=hmmsearch, version=v3.3.2 -14:34:38.919 - INFO - UTILS - dependency: tool=diamond, version=v2.0.15 -14:34:38.955 - INFO - UTILS - dependency: tool=blastn, version=v2.13.0 -14:34:39.223 - INFO - UTILS - dependency: tool=circos, version=v1.6.1 -14:34:39.227 - INFO - FASTA - imported: id=NC_002127.1, length=1330, description=Escherichia coli O157:H7 str. Sakai plasmid pOSAK1, complete sequence, genomic=True, dna=True -14:34:39.227 - INFO - MAIN - imported sequences=1 -14:34:39.227 - INFO - UTILS - qc: revised sequence: id=contig_1, orig-id=NC_002127.1, type=plasmid, complete=True, topology=circular, name=unnamed1, description='[completeness=complete] [topology=circular] [gcode=11]', orig-description='Escherichia coli O157:H7 str. Sakai plasmid pOSAK1, complete sequence' -14:34:39.227 - INFO - FASTA - write genome sequences: path=/tmp/tmpxm45i679/contigs.fna, description=False, wrap=False -14:34:39.338 - INFO - T_RNA - predicted=0 -14:34:39.340 - INFO - TM_RNA - predicted=0 -14:34:39.346 - INFO - R_RNA - predicted=0 -14:34:39.352 - INFO - NC_RNA - predicted=0 -14:34:39.357 - INFO - NC_RNA_REGION - predicted=0 -14:34:39.359 - INFO - CRISPR - predicted=0 -14:34:39.359 - INFO - CDS - skip creation of prodigal training info object: meta=True, closed=False -14:34:39.379 - INFO - CDS - contig=contig_1, start=1, stop=141, strand=-, frame=2, truncated=3-prime, start-type=ATG, RBS-motif=AGGA/GGAG/GAGG -14:34:39.380 - INFO - CDS - contig=contig_1, start=413, stop=736, strand=+, frame=2, truncated=no, start-type=ATG, RBS-motif=GGAG/GAGG -14:34:39.380 - INFO - CDS - contig=contig_1, start=971, stop=1330, strand=-, frame=1, truncated=5-prime, start-type=Edge, RBS-motif=None -14:34:39.380 - INFO - CDS - edge CDS: contig=contig_1, start=971, stop=141, strand=-, frame=1, start-type=ATG, RBS-motif=AGGA/GGAG/GAGG, aa-hexdigest=1e7027cbe48346e06a83e802a9385584, aa=[MNKQQQTALN..SFALKKGIPI] -14:34:39.380 - INFO - CDS - contig=contig_1, start=413, stop=736, strand=+, nt=[ATGACAAAAC..GGCAGATTAG] -14:34:39.380 - INFO - CDS - contig=contig_1, start=971, stop=141, strand=-, nt=[ATGAACAAGC..TCCAATATAA] -14:34:39.384 - INFO - CDS - predicted=2 -14:34:39.384 - INFO - ORF - write internal aa seqs: # seqs=2, path=/tmp/tmpxm45i679/cds.spurious.faa -14:34:39.391 - INFO - ORF - discarded=0 -14:34:39.392 - INFO - UPS - looked-up=0 -14:34:39.392 - INFO - IPS - looked-up=0 -14:34:39.392 - INFO - ORF - write internal aa seqs: # seqs=2, path=/tmp/tmpxm45i679/cds.psc.faa -14:34:39.466 - INFO - PSC - found: PSC=0, PSCC=0 -14:34:39.467 - INFO - PSC - looked-up=0 -14:34:39.467 - INFO - PSCC - looked-up=0 -14:34:39.467 - INFO - ORF - write internal aa seqs: # seqs=2, path=/tmp/tmpxm45i679/cds.expert.faa -14:34:39.548 - INFO - EXPERT-AMRFINDER - found=0 -14:34:39.624 - INFO - EXPERT_AA_SEQ - found=0 -14:34:39.624 - INFO - ORF - write internal aa seqs: # seqs=1, path=/tmp/tmpxm45i679/cds.pseudo.candidates.faa -14:34:39.697 - INFO - CDS - found: pseudogene-candidates=0 -14:34:39.698 - INFO - PSC - looked-up=0 -14:34:39.698 - INFO - PSCC - looked-up=0 -14:34:39.698 - INFO - ORF - write internal aa seqs: # seqs=2, path=/tmp/tmpxm45i679/hypotheticals.faa -14:34:39.704 - INFO - CDS - predicted-pfams=0, CDS-w/-pfams=0 -14:34:39.706 - INFO - S_ORF - predicted=22 -14:34:39.706 - INFO - S_ORF - sORF filter: # valid=20, # discarded=2 -14:34:39.706 - INFO - ORF - write internal aa seqs: # seqs=20, path=/tmp/tmpxm45i679/sorf.spurious.faa -14:34:39.712 - INFO - ORF - discarded=0 -14:34:39.716 - INFO - UPS - looked-up=0 -14:34:39.716 - INFO - IPS - looked-up=0 -14:34:39.716 - INFO - ORF - write internal aa seqs: # seqs=20, path=/tmp/tmpxm45i679/sorf.faa -14:34:39.795 - INFO - S_ORF - found=0 -14:34:39.796 - INFO - PSC - looked-up=0 -14:34:39.833 - INFO - ORI - predicted=0 -14:34:39.871 - INFO - ORI - predicted=0 -14:34:39.872 - INFO - UTILS - generated sequence tag prefix: prefix=IHHALPPJCH, length=10, MD5=211A5993C1DD2EA7E96312462C14806B -14:34:39.872 - INFO - MAIN - selected features=2 -14:34:39.872 - INFO - UTILS - generated sequence tag prefix: prefix=IHHALP, length=6, MD5=211A5993C1DD2EA7E96312462C14806B -14:34:39.872 - INFO - MAIN - locus tag prefix=IHHALP -14:34:39.872 - INFO - UTILS - genome-size=1330 -14:34:39.872 - INFO - UTILS - GC=0.452 -14:34:39.872 - INFO - UTILS - N=0.000 -14:34:39.872 - INFO - UTILS - N50=1330 -14:34:39.872 - INFO - UTILS - coding-ratio=0.620 -14:34:39.872 - INFO - TSV - write tsv: path=/home/pierre/tools-iuc/tools/bakta/test-data/tmp/TEST_1.tsv -14:34:39.872 - INFO - GFF - write GFF3: path=/home/pierre/tools-iuc/tools/bakta/test-data/tmp/TEST_1.gff3 -14:34:39.873 - INFO - INSDC - write GenBank: path=/home/pierre/tools-iuc/tools/bakta/test-data/tmp/TEST_1.gbff -14:34:39.873 - INFO - INSDC - write EMBL: path=/home/pierre/tools-iuc/tools/bakta/test-data/tmp/TEST_1.embl -14:34:39.874 - INFO - FASTA - write genome sequences: path=/home/pierre/tools-iuc/tools/bakta/test-data/tmp/TEST_1.fna, description=True, wrap=True -14:34:39.874 - INFO - FASTA - write feature nucleotide sequences: path=/home/pierre/tools-iuc/tools/bakta/test-data/tmp/TEST_1.ffn -14:34:39.874 - INFO - FASTA - write translated CDS/sORF: path=/home/pierre/tools-iuc/tools/bakta/test-data/tmp/TEST_1.faa -14:34:39.874 - INFO - PLOT - split edge feature: contig=contig_1, start=971, stop=141, strand=-, edge=True -14:34:39.878 - INFO - PLOT - write circular genome plot: file-name=TEST_1, output-dir=/home/pierre/tools-iuc/tools/bakta/test-data/tmp -14:34:41.980 - INFO - TSV - write hypothetical tsv: path=/home/pierre/tools-iuc/tools/bakta/test-data/tmp/TEST_1.hypotheticals.tsv -14:34:41.980 - INFO - FASTA - write translated CDS/sORF: path=/home/pierre/tools-iuc/tools/bakta/test-data/tmp/TEST_1.hypotheticals.faa -14:34:41.981 - INFO - JSON - write JSON: path=/home/pierre/tools-iuc/tools/bakta/test-data/tmp/TEST_1.json -14:34:41.982 - INFO - MAIN - removed tmp dir: /tmp/tmpxm45i679 diff -r 44fb905481f0 -r f77ebe2e4df0 test-data/tmp/TEST_1.png Binary file test-data/tmp/TEST_1.png has changed diff -r 44fb905481f0 -r f77ebe2e4df0 test-data/tmp/TEST_1.svg --- a/test-data/tmp/TEST_1.svg Thu Jan 12 11:25:17 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2408 +0,0 @@ - - - - - - - - - -0 bp - - - - - - - - - - -25 bp - - - - - - - - - - -50 bp - - - - - - - - - - -75 bp - - - - - - - - - - -100 bp - - - - - - - - - - -125 bp - - - - - - - - - - -150 bp - - - - - - - - - - -175 bp - - - - - - - - - - -200 bp - - - - - - - - - - -225 bp - - - - - - - - - - -250 bp - - - - - - - - - - -275 bp - - - - - - - - - - -300 bp - - - - - - - - - - -325 bp - - - - - - - - - - -350 bp - - - - - - - - - - -375 bp - - - - - 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+0000 @@ -1,5 +0,0 @@ -#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 diff -r 44fb905481f0 -r f77ebe2e4df0 test-data/tmp/TEST_1.txt --- a/test-data/tmp/TEST_1.txt Thu Jan 12 11:25:17 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -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: v1.6.1 -Database: v4.0 -DOI: 10.1099/mgen.0.000685 -URL: github.com/oschwengers/bakta diff -r 44fb905481f0 -r f77ebe2e4df0 test-data/tmp/database_path/antifam.h3f Binary file test-data/tmp/database_path/antifam.h3f has changed diff -r 44fb905481f0 -r f77ebe2e4df0 test-data/tmp/database_path/antifam.h3i Binary file test-data/tmp/database_path/antifam.h3i has changed diff -r 44fb905481f0 -r f77ebe2e4df0 test-data/tmp/database_path/antifam.h3m Binary file test-data/tmp/database_path/antifam.h3m has changed diff -r 44fb905481f0 -r f77ebe2e4df0 test-data/tmp/database_path/antifam.h3p Binary file test-data/tmp/database_path/antifam.h3p has changed diff -r 44fb905481f0 -r f77ebe2e4df0 test-data/tmp/database_path/bakta.db Binary file test-data/tmp/database_path/bakta.db has changed diff -r 44fb905481f0 -r f77ebe2e4df0 test-data/tmp/database_path/expert-protein-sequences.dmnd Binary file test-data/tmp/database_path/expert-protein-sequences.dmnd has changed diff -r 44fb905481f0 -r f77ebe2e4df0 test-data/tmp/database_path/ncRNA-genes.i1f Binary file test-data/tmp/database_path/ncRNA-genes.i1f has changed diff -r 44fb905481f0 -r f77ebe2e4df0 test-data/tmp/database_path/ncRNA-genes.i1i Binary file test-data/tmp/database_path/ncRNA-genes.i1i has changed diff -r 44fb905481f0 -r f77ebe2e4df0 test-data/tmp/database_path/ncRNA-genes.i1m Binary file test-data/tmp/database_path/ncRNA-genes.i1m has changed diff -r 44fb905481f0 -r f77ebe2e4df0 test-data/tmp/database_path/ncRNA-genes.i1p Binary file test-data/tmp/database_path/ncRNA-genes.i1p has changed diff -r 44fb905481f0 -r f77ebe2e4df0 test-data/tmp/database_path/ncRNA-regions.i1f Binary file test-data/tmp/database_path/ncRNA-regions.i1f has changed diff -r 44fb905481f0 -r f77ebe2e4df0 test-data/tmp/database_path/ncRNA-regions.i1i Binary file test-data/tmp/database_path/ncRNA-regions.i1i has changed diff -r 44fb905481f0 -r f77ebe2e4df0 test-data/tmp/database_path/ncRNA-regions.i1m Binary file test-data/tmp/database_path/ncRNA-regions.i1m has changed diff -r 44fb905481f0 -r f77ebe2e4df0 test-data/tmp/database_path/ncRNA-regions.i1p Binary file test-data/tmp/database_path/ncRNA-regions.i1p has changed diff -r 44fb905481f0 -r f77ebe2e4df0 test-data/tmp/database_path/oric.fna --- a/test-data/tmp/database_path/oric.fna Thu Jan 12 11:25:17 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ ->ORI10010001 -TATTCTTCTATAACATTGTCAAGAATGATAGTTAAAATTCTCGAAATTGGGATATTAACTGCTTTGGAGTAATTTCTAACTTTTTGTCATACTCTTTGACTTGTATAGAAGTGTACACCTGTATCTAGTTTTTCTTGGCGTTCAACAGGAACTATTCCTGGTATTTTTGTTTTAGGTTGGGGAGGAATAGGCTGTGGTTGTGTGAATTGTTGTTGAAAATTTTGATTTTTTTGCTGTAAGAAACCATTATTATGATATTGAAAATTTTGTTCCTCTTGAAAATATCTCTCTTTTTTTGGTTTTCCAGAAAAATTTGATGAAAAAGATTTTTCTTCATTTCAATTTTCAAGATTATTTTCATTTTGTTGATTTATTTGCTCAGGCTGTTGAAATGAATTATTTTTTGATCAAAAAGATTTTGGAAAGGTTTTTTCAAAAGCAGATAAAGGTCCAAAATCAAATGAAGATGAATCTTTGTCAAAAGATGTTTCTTCTCTTTTTGACAAATTTTGTTTTTGATTAAACTTATTTTTATTTTGGGGTGTTACTTTTTCTTTTATGGAAAACAAATCTTCTTCTAAAAGACTTTGTTCTGGGTCATCATCTTGTGCTAAATCAAAGAAAAAACGTTTCTTTTTGTTA ->ORI10010003 -GGCGTAGACACTGAATTCGATGGGGATAAGTGGTGGATAAAAGAATATAAATTAGTCATTACACTTTACTCACGAATATCCCCCTTTTTTTAGAGAAAAAATATACTTTCTTCACAAGCTTGTGTGCGGTTTTTGTTTGGTAATTCTCGAGACATAAGCACTTATCCAGATATTCACAGTTACTATTATGTGATACGACTACATTCTTTATACTTATAAGATTAATAAGGAGGAAACTAACT diff -r 44fb905481f0 -r f77ebe2e4df0 test-data/tmp/database_path/orit.fna --- a/test-data/tmp/database_path/orit.fna Thu Jan 12 11:25:17 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ ->CP019995|MOBP -GTAGAATCGTTTAGTATGAGAATAGAAAACCAACGGTTTTCATGAACTTACTAAACGATTCTAC ->CP012386|MOBP -AGAACAATCAACAACTAATTAGGCAAATTAAGGGGTGCTAAACAACTGCTAGTAGGTGCTAGAGATGTGCTATAAAGGGTGCTAGTTTGGTGCTAGTTACTGCTAAATACGTGCTAGTTTAGGTGCTAGAAACGTGCTATATGGTGCTAAAAAGGTGCTAGTTTGCATGAAGTTACCTGCTAGCCAAGTGCTAGTGGCGTTCGTTTTTGGGTCCCACGGGAAAGCCTTGCACTGCAAGGCGGGTCAGCTTGTCTGACCCCCATTTCCCCTTATGCTCTTCCGAAACACAAAGCGCAATTAAGCGAATACTAGAGAATAAATA diff -r 44fb905481f0 -r f77ebe2e4df0 test-data/tmp/database_path/pfam.h3f Binary file test-data/tmp/database_path/pfam.h3f has changed diff -r 44fb905481f0 -r f77ebe2e4df0 test-data/tmp/database_path/pfam.h3i Binary file test-data/tmp/database_path/pfam.h3i has changed diff -r 44fb905481f0 -r f77ebe2e4df0 test-data/tmp/database_path/pfam.h3m Binary file test-data/tmp/database_path/pfam.h3m has changed diff -r 44fb905481f0 -r f77ebe2e4df0 test-data/tmp/database_path/pfam.h3p Binary file test-data/tmp/database_path/pfam.h3p has changed diff -r 44fb905481f0 -r f77ebe2e4df0 test-data/tmp/database_path/psc.dmnd Binary file test-data/tmp/database_path/psc.dmnd has changed diff -r 44fb905481f0 -r f77ebe2e4df0 test-data/tmp/database_path/rRNA.i1f Binary file test-data/tmp/database_path/rRNA.i1f has changed diff -r 44fb905481f0 -r f77ebe2e4df0 test-data/tmp/database_path/rRNA.i1i Binary file test-data/tmp/database_path/rRNA.i1i has changed diff -r 44fb905481f0 -r f77ebe2e4df0 test-data/tmp/database_path/rRNA.i1m Binary file test-data/tmp/database_path/rRNA.i1m has changed diff -r 44fb905481f0 -r f77ebe2e4df0 test-data/tmp/database_path/rRNA.i1p Binary file test-data/tmp/database_path/rRNA.i1p has changed diff -r 44fb905481f0 -r f77ebe2e4df0 test-data/tmp/database_path/rfam-go.tsv --- a/test-data/tmp/database_path/rfam-go.tsv Thu Jan 12 11:25:17 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -Rfam:RF00001 GO:0003735 diff -r 44fb905481f0 -r f77ebe2e4df0 test-data/tmp/database_path/sorf.dmnd Binary file test-data/tmp/database_path/sorf.dmnd has changed diff -r 44fb905481f0 -r f77ebe2e4df0 test-data/tmp/database_path/version.json --- a/test-data/tmp/database_path/version.json Thu Jan 12 11:25:17 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,53 +0,0 @@ -{ - "date": "2022-08-25", - "major": 4, - "minor": 0, - "dependencies": [ - { - "name": "AMRFinderPlus", - "release": "2020-09-22.2" - }, - { - "name": "COG", - "release": "2014" - }, - { - "name": "DoriC", - "release": "10" - }, - { - "name": "ISFinder", - "release": "2019-09-25" - }, - { - "name": "Mob-suite", - "release": "2.0" - }, - { - "name": "Pfam", - "release": "33.1" - }, - { - "name": "RefSeq", - "release": "r202" - }, - { - "name": "Rfam", - "release": "14.2" - }, - { - "name": "UniProtKB/Swiss-Prot", - "release": "2020_04" - } - ], - "experts": [ - { - "name": "AMRFinderPlus", - "release": "3.10.1" - }, - { - "name": "NCBI BlastRules", - "release": "4.0" - } - ] -}