| Previous changeset 6:92eee5f31117 (2024-02-11) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2 |
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modified:
bakta.xml macro.xml test-data/bakta_database.loc tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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added:
test-data/V5.1_light_2024-01-19/antifam.h3f test-data/V5.1_light_2024-01-19/antifam.h3i test-data/V5.1_light_2024-01-19/antifam.h3m test-data/V5.1_light_2024-01-19/antifam.h3p test-data/V5.1_light_2024-01-19/bakta.db test-data/V5.1_light_2024-01-19/expert-protein-sequences.dmnd test-data/V5.1_light_2024-01-19/ncRNA-genes.i1f test-data/V5.1_light_2024-01-19/ncRNA-genes.i1i test-data/V5.1_light_2024-01-19/ncRNA-genes.i1m test-data/V5.1_light_2024-01-19/ncRNA-genes.i1p test-data/V5.1_light_2024-01-19/ncRNA-regions.i1f test-data/V5.1_light_2024-01-19/ncRNA-regions.i1i test-data/V5.1_light_2024-01-19/ncRNA-regions.i1m test-data/V5.1_light_2024-01-19/ncRNA-regions.i1p test-data/V5.1_light_2024-01-19/oric.fna test-data/V5.1_light_2024-01-19/orit.fna test-data/V5.1_light_2024-01-19/pfam.h3f test-data/V5.1_light_2024-01-19/pfam.h3i test-data/V5.1_light_2024-01-19/pfam.h3m test-data/V5.1_light_2024-01-19/pfam.h3p test-data/V5.1_light_2024-01-19/psc.dmnd test-data/V5.1_light_2024-01-19/pscc.dmnd test-data/V5.1_light_2024-01-19/rRNA.i1f test-data/V5.1_light_2024-01-19/rRNA.i1i test-data/V5.1_light_2024-01-19/rRNA.i1m test-data/V5.1_light_2024-01-19/rRNA.i1p test-data/V5.1_light_2024-01-19/rfam-go.tsv test-data/V5.1_light_2024-01-19/sorf.dmnd test-data/V5.1_light_2024-01-19/version.json test-data/amrfinderplus-db/AMR.LIB test-data/amrfinderplus-db/AMR.LIB.h3f test-data/amrfinderplus-db/AMR.LIB.h3i test-data/amrfinderplus-db/AMR.LIB.h3m test-data/amrfinderplus-db/AMR.LIB.h3p test-data/amrfinderplus-db/AMRProt test-data/amrfinderplus-db/AMRProt-mutation.tab test-data/amrfinderplus-db/AMRProt-suppress test-data/amrfinderplus-db/AMRProt-susceptible.tab test-data/amrfinderplus-db/AMRProt.pdb test-data/amrfinderplus-db/AMRProt.phr test-data/amrfinderplus-db/AMRProt.pin test-data/amrfinderplus-db/AMRProt.pjs test-data/amrfinderplus-db/AMRProt.psq test-data/amrfinderplus-db/AMRProt.ptf test-data/amrfinderplus-db/AMRProt.pto test-data/amrfinderplus-db/AMR_CDS test-data/amrfinderplus-db/AMR_CDS.ndb test-data/amrfinderplus-db/AMR_CDS.nhr test-data/amrfinderplus-db/AMR_CDS.nin test-data/amrfinderplus-db/AMR_CDS.njs test-data/amrfinderplus-db/AMR_CDS.not test-data/amrfinderplus-db/AMR_CDS.nsq test-data/amrfinderplus-db/AMR_CDS.ntf test-data/amrfinderplus-db/AMR_CDS.nto test-data/amrfinderplus-db/AMR_DNA-Escherichia test-data/amrfinderplus-db/AMR_DNA-Escherichia.ndb test-data/amrfinderplus-db/AMR_DNA-Escherichia.nhr test-data/amrfinderplus-db/AMR_DNA-Escherichia.nin test-data/amrfinderplus-db/AMR_DNA-Escherichia.njs test-data/amrfinderplus-db/AMR_DNA-Escherichia.not test-data/amrfinderplus-db/AMR_DNA-Escherichia.nsq test-data/amrfinderplus-db/AMR_DNA-Escherichia.ntf test-data/amrfinderplus-db/AMR_DNA-Escherichia.nto test-data/amrfinderplus-db/AMR_DNA-Escherichia.tab test-data/amrfinderplus-db/ReferenceGeneCatalog.txt test-data/amrfinderplus-db/ReferenceGeneHierarchy.txt test-data/amrfinderplus-db/amr_targets.fa test-data/amrfinderplus-db/bla.tsv test-data/amrfinderplus-db/changelog.txt test-data/amrfinderplus-db/changes.txt test-data/amrfinderplus-db/database_format_version.txt test-data/amrfinderplus-db/fam.tab test-data/amrfinderplus-db/mcr.tsv test-data/amrfinderplus-db/qnr.tsv test-data/amrfinderplus-db/taxgroup.tab test-data/amrfinderplus-db/version.txt test-data/amrfinderplus_versioned_database.loc tool-data/amrfinderplus_versioned_database.loc.sample |
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removed:
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.tsv test-data/TEST_1/TEST_1.txt test-data/TEST_1/TEST_1_plot.svg test-data/TEST_2/TEST_2.ffn test-data/TEST_2/TEST_2.gff3 test-data/TEST_2/TEST_2.tsv test-data/TEST_2/TEST_2_plot.svg test-data/TEST_3/TEST_3.ffn test-data/TEST_3/TEST_3.gff3 test-data/TEST_3/TEST_3.tsv test-data/TEST_4/TEST_4.ffn test-data/TEST_4/TEST_4.gff3 test-data/TEST_4/TEST_4.tsv test-data/TEST_4/TEST_4_plot.svg test-data/TEST_5/TEST_5.txt test-data/TEST_6/TEST_6.embl test-data/TEST_6/TEST_6.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.tsv test-data/TEST_6/TEST_6.txt test-data/TEST_6/TEST_6_plot.svg test-data/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3f test-data/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3i test-data/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3m test-data/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3p test-data/amrfinderplus-db/2021-09-30.1/AMRProt-mutation.tab test-data/amrfinderplus-db/2021-09-30.1/AMRProt-suppress test-data/amrfinderplus-db/2021-09-30.1/AMRProt-susceptible.tab test-data/amrfinderplus-db/2021-09-30.1/AMRProt.pdb test-data/amrfinderplus-db/2021-09-30.1/AMRProt.phr test-data/amrfinderplus-db/2021-09-30.1/AMRProt.pin test-data/amrfinderplus-db/2021-09-30.1/AMRProt.psq test-data/amrfinderplus-db/2021-09-30.1/AMRProt.ptf test-data/amrfinderplus-db/2021-09-30.1/AMRProt.pto test-data/amrfinderplus-db/2021-09-30.1/AMR_CDS.ndb test-data/amrfinderplus-db/2021-09-30.1/AMR_CDS.nhr test-data/amrfinderplus-db/2021-09-30.1/AMR_CDS.nin test-data/amrfinderplus-db/2021-09-30.1/AMR_CDS.not test-data/amrfinderplus-db/2021-09-30.1/AMR_CDS.nsq test-data/amrfinderplus-db/2021-09-30.1/AMR_CDS.ntf test-data/amrfinderplus-db/2021-09-30.1/AMR_CDS.nto test-data/amrfinderplus-db/2021-09-30.1/database_format_version.txt test-data/amrfinderplus-db/2021-09-30.1/fam.tab test-data/amrfinderplus-db/2021-09-30.1/taxgroup.tab test-data/amrfinderplus-db/2021-09-30.1/version.txt test-data/amrfinderplus_database.loc tool-data/amrfinderplus_database.loc.sample |
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| diff -r 92eee5f31117 -r ba6990f72184 bakta.xml --- a/bakta.xml Sun Feb 11 00:56:12 2024 +0000 +++ b/bakta.xml Wed Jun 05 14:22:02 2024 +0000 |
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| b'@@ -1,111 +1,109 @@\n <tool id="bakta" name="Bakta" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n <description>\n- Genome annotation via alignment-free sequence identification\n+ Rapid and standardized annotation of bacterial genomes, MAGs and plasmids\n </description>\n <macros>\n <import>macro.xml</import>\n </macros>\n- <expand macro=\'edam\'/>\n- <expand macro=\'xrefs\'/>\n+ <expand macro="xrefs"/>\n <expand macro="requirements"/>\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 --verbose\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 \n- #*======================================\n- CPU option\n- ======================================*#\n- --threads \\${GALAXY_SLOTS:-1}\n- #*======================================\n- Bakta database\n- ======================================*#\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- --min-contig-length 200\n- #else\n- --min-contig-length 1\n- #end if\n- --prefix bakta_output\n- #*======================================\n- Organism options\n- genus/species/strain/plasmid\n- ======================================*#\n- #if $organism.genus\n- --genus \'$organism.genus\'\n- #end if\n- #if $organism.species\n- --species \'$organism.species\'\n- #end if\n- #if $organism.strain\n- --strain \'$organism.strain\'\n- #end if\n- #if $organism.plasmid\n- --plasmid \'$organism.plasmid\'\n- #end if\n- #*======================================\n- Annotation options\n- gram type, prodigal/protein file\n- ======================================*#\n- $annotation.complete\n- #if $annotation.prodigal\n- --prodigal-tf \'$annotation.prodigal\'\n- #end if\n- #if $annotation.translation_table\n- --translation-table \'$annotation.translation_table\'\n- #end if\n- --gram \'?\'\n- $annotation.keep_contig_headers\n- #if $annotation.replicons\n- --replicons \'$annotation.replicons\'\n- #end if\n- $annotation.compliant\n- #if $annotation.proteins\n- --proteins \'$annotation.proteins\'\n- #end if\n- #if $annotation.regions\n- --regions \'$annotation.regions\'\n- #end if\n- #*======================================\n- Workflow OPTIONS\n- skip some step of the bakta analysis\n- ======================================*#\n+bakta \n+ --verbose\n+#*======================================\n+ CPU option\n+======================================*#\n+ --threads \\${GALAXY_SLOTS:-1}\n+#*======================================\n+ Bakta database\n+======================================*#\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+ --min-contig-length 200\n+#else\n+ --min-contig-length 1\n+#end if\n+ --prefix bakta_output\n+#*======================================\n+ Organism options\n+ genus/species/strain/plasmid\n+======================================*#\n'..b'fy informations about analysed fasta as text input for:\n+- genus\n+- species\n+- strain\n+- plasmid\n \n- **Annotation options**\n- 1. You can specify if all sequences (chromosome or plasmids) are complete or not\n- 2. You can add your own prodigal training file for CDS prediction\xc5\x93\n- 3. The translation table could be modified, default is the 11th for bacteria\n- 4. You can specify if bacteria is gram -/+ or unknonw (default value is unknow)\n- 5. You can keep the name of contig present in the input file\n- 6. You can specify your own replicon table as a TSV/CSV file\n- 7. The compliance option is for ready to submit annotation file to Public database\n- as ENA, Genbank EMBL\n- 8. You can specify a protein sequence file for annotation in GenBank or fasta formats\n- Using the Fasta format, each reference sequence can be provided in a short or long format:\n+**Annotation options**\n+1. You can specify if all sequences (chromosome or plasmids) are complete or not\n+2. You can add your own prodigal training file for CDS prediction\xc5\x93\n+3. The translation table could be modified, default is the 11th for bacteria\n+4. You can specify if bacteria is gram -/+ or unknonw (default value is unknow)\n+5. You can keep the name of contig present in the input file\n+6. You can specify your own replicon table as a TSV/CSV file\n+7. The compliance option is for ready to submit annotation file to Public database\n+as ENA, Genbank EMBL\n+8. You can specify a protein sequence file for annotation in GenBank or fasta formats\n+Using the Fasta format, each reference sequence can be provided in a short or long format:\n \n- # short:\n- >id gene~~~product~~~dbxrefs\n- MAQ...\n+# short:\n+>id gene~~~product~~~dbxrefs\n+MAQ...\n \n- # long:\n- >id min_identity~~~min_query_cov~~~min_subject_cov~~~gene~~~product~~~dbxrefs\n- MAQ...\n+# long:\n+>id min_identity~~~min_query_cov~~~min_subject_cov~~~gene~~~product~~~dbxrefs\n+MAQ...\n \n- **Skip steps**\n- Some steps could be skiped:\n- - skip-trna Skip tRNA detection & annotation\n- - skip-tmrna Skip tmRNA detection & annotation\n- - skip-rrna Skip rRNA detection & annotation\n- - skip-ncrna Skip ncRNA detection & annotation\n- - skip-ncrna-region Skip ncRNA region detection & annotation\n- - skip-crispr Skip CRISPR array detection & annotation\n- - skip-cds Skip CDS detection & annotation\n- - skip-pseudo Skip pseudogene detection & annotation\n- - skip-sorf Skip sORF detection & annotation\n- - skip-gap Skip gap detection & annotation\n- - skip-ori Skip oriC/oriT detection & annotation\n+**Skip steps**\n+Some steps could be skiped:\n+- skip-trna Skip tRNA detection & annotation\n+- skip-tmrna Skip tmRNA detection & annotation\n+- skip-rrna Skip rRNA detection & annotation\n+- skip-ncrna Skip ncRNA detection & annotation\n+- skip-ncrna-region Skip ncRNA region detection & annotation\n+- skip-crispr Skip CRISPR array detection & annotation\n+- skip-cds Skip CDS detection & annotation\n+- skip-pseudo Skip pseudogene detection & annotation\n+- skip-sorf Skip sORF detection & annotation\n+- skip-gap Skip gap detection & annotation\n+- skip-ori Skip oriC/oriT detection & annotation\n \n- **Output options**\n- Bakta produce numbers of output files, you can select what type of file you want:\n- - Summary of the annotation\n- - Annotated files\n- - Sequence files for nucleotide and/or amino acid\n+**Output options**\n+Bakta produce numbers of output files, you can select what type of file you want:\n+- Summary of the annotation\n+- Annotated files\n+- Sequence files for nucleotide and/or amino acid\n ]]></help>\n <expand macro="citations"/>\n </tool>\n' |
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| diff -r 92eee5f31117 -r ba6990f72184 macro.xml --- a/macro.xml Sun Feb 11 00:56:12 2024 +0000 +++ b/macro.xml Wed Jun 05 14:22:02 2024 +0000 |
| [ |
| @@ -1,20 +1,15 @@ <macros> - <token name="@TOOL_VERSION@">1.9.2</token> + <token name="@TOOL_VERSION@">1.9.3</token> <token name="@COMPATIBLE_BAKTA_VERSION@">1.7</token> <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">21.05</token> <xml name="version_command"> <version_command><![CDATA[bakta --version]]></version_command> </xml> - <xml name="edam"> - <edam_topics> - <edam_topic>topic_3174</edam_topic> - </edam_topics> - </xml> <xml name="xrefs"> <xrefs> - <xref type='bio.tools'>Bakta</xref> + <xref type="bio.tools">bakta</xref> </xrefs> </xml> <xml name="requirements"> @@ -27,7 +22,6 @@ <citation type="doi">10.1099/mgen.0.000685</citation> </citations> </xml> - <xml name="assert_content_test"> <assert_contents> <has_text text="Options and arguments"/> |
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| diff -r 92eee5f31117 -r ba6990f72184 test-data/TEST_1/TEST_1.embl --- a/test-data/TEST_1/TEST_1.embl Sun Feb 11 00:56:12 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,85 +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: v1.9.2 -CC Database: v5.0, full -CC DOI: 10.1099/mgen.0.000685 -CC URL: github.com/oschwengers/bakta -CC -CC ##Genome Annotation Summary:## -CC Annotation Date :: 02/11/2024, 00:24:56 -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 -// |
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| diff -r 92eee5f31117 -r ba6990f72184 test-data/TEST_1/TEST_1.faa --- a/test-data/TEST_1/TEST_1.faa Sun Feb 11 00:56:12 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,4 +0,0 @@ ->IHHALP_00005 hypothetical protein -MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD ->IHHALP_00010 hypothetical protein -MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI |
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| diff -r 92eee5f31117 -r ba6990f72184 test-data/TEST_1/TEST_1.ffn --- a/test-data/TEST_1/TEST_1.ffn Sun Feb 11 00:56:12 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,4 +0,0 @@ ->IHHALP_00005 hypothetical protein -ATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAG ->IHHALP_00010 hypothetical protein -ATGAACAAGCAGCAGCAAACTGCACTCAACATGGCGGGATTCATAAAAAGCCAGAGCCTGACGCTGCTCGAAAAACTGGACGCACTCGATGCTGACGAGCAGGCCACCATGTGTGAGAAGCTGCACGAACTCGCAGAAGAACAAATAGAAGCAATAAAAAATAAAGATAAAACTTTATTTATTGTCTATGCTACTGATATTTATAGCCCGAGCGAATTTTTCTCAAAAATCGAATCCGACTTGAAGAAAAAGAAAAGCAAGGGTGATGTTTTTTTTGATTTAATAATTCCTAACGGTGGAAAAAAAGATCGTTACGTCTATACGTCATTTAATGGCGAGAAGTTTTCAAGTTACACATTAAACAAAGTTACGAAAACTGATGAATATAATGATTTATCTGAGCTCTCGGCTTCGTTCTTTAAAAAAAACTTTGATAAGATCAACGTAAACCTTCTATCCAAAGCCACATCATTTGCTTTGAAAAAAGGCATTCCAATATAA |
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| diff -r 92eee5f31117 -r ba6990f72184 test-data/TEST_1/TEST_1.fna --- a/test-data/TEST_1/TEST_1.fna Sun Feb 11 00:56:12 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,24 +0,0 @@ ->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 92eee5f31117 -r ba6990f72184 test-data/TEST_1/TEST_1.gbff --- a/test-data/TEST_1/TEST_1.gbff Sun Feb 11 00:56:12 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,81 +0,0 @@ -LOCUS contig_1 1330 bp DNA circular BCT 11-FEB-2024 -DEFINITION plasmid unnamed1, complete sequence. -ACCESSION contig_1 -VERSION contig_1 -KEYWORDS . -SOURCE None - ORGANISM . - . -COMMENT Annotated with Bakta - Software: v1.9.2 - Database: v5.0, full - DOI: 10.1099/mgen.0.000685 - URL: github.com/oschwengers/bakta - - ##Genome Annotation Summary:## - Annotation Date :: 02/11/2024, 00:24:56 - 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 92eee5f31117 -r ba6990f72184 test-data/TEST_1/TEST_1.gff3 --- a/test-data/TEST_1/TEST_1.gff3 Sun Feb 11 00:56:12 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -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: v1.9.2 -# 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 92eee5f31117 -r ba6990f72184 test-data/TEST_1/TEST_1.hypotheticals.faa --- a/test-data/TEST_1/TEST_1.hypotheticals.faa Sun Feb 11 00:56:12 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ ->IHHALP_00005 hypothetical protein -MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD ->IHHALP_00010 hypothetical protein -MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/TEST_1/TEST_1.hypotheticals.tsv --- a/test-data/TEST_1/TEST_1.hypotheticals.tsv Sun Feb 11 00:56:12 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,5 +0,0 @@ -#Annotated with Bakta v1.9.2, https://github.com/oschwengers/bakta -#Database v5.0, https://doi.org/10.5281/zenodo.4247252 -#Sequence Id Start Stop Strand Locus Tag Mol Weight [kDa] Iso El. Point Pfam hits Dbxrefs -contig_1 413 736 + IHHALP_00005 12.1 10.4 -contig_1 971 141 - IHHALP_00010 18.9 7.7 |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/TEST_1/TEST_1.json --- a/test-data/TEST_1/TEST_1.json Sun Feb 11 00:56:12 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,95 +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": "+", - "frame": 2, - "gene": null, - "product": "hypothetical protein", - "db_xrefs": [], - "nt": "ATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAG", - "aa": "MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD", - "aa_hexdigest": "d9bdebc84195542e775c3d22458b507e", - "start_type": "ATG", - "rbs_motif": "GGAG/GAGG", - "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": "-", - "frame": 1, - "gene": null, - "product": "hypothetical protein", - "db_xrefs": [], - "nt": "ATGAACAAGCAGCAGCAAACTGCACTCAACATGGCGGGATTCATAAAAAGCCAGAGCCTGACGCTGCTCGAAAAACTGGACGCACTCGATGCTGACGAGCAGGCCACCATGTGTGAGAAGCTGCACGAACTCGCAGAAGAACAAATAGAAGCAATAAAAAATAAAGATAAAACTTTATTTATTGTCTATGCTACTGATATTTATAGCCCGAGCGAATTTTTCTCAAAAATCGAATCCGACTTGAAGAAAAAGAAAAGCAAGGGTGATGTTTTTTTTGATTTAATAATTCCTAACGGTGGAAAAAAAGATCGTTACGTCTATACGTCATTTAATGGCGAGAAGTTTTCAAGTTACACATTAAACAAAGTTACGAAAACTGATGAATATAATGATTTATCTGAGCTCTCGGCTTCGTTCTTTAAAAAAAACTTTGATAAGATCAACGTAAACCTTCTATCCAAAGCCACATCATTTGCTTTGAAAAAAGGCATTCCAATATAA", - "aa": "MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI", - "aa_hexdigest": "1e7027cbe48346e06a83e802a9385584", - "start_type": "ATG", - "rbs_motif": "AGGA/GGAG/GAGG", - "edge": true, - "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": "2024-02-11 00:24:53", - "end": "2024-02-11 00:25:06" - }, - "version": { - "bakta": "1.9.2", - "db": { - "version": "5.0", - "type": "full" - } - } -} \ No newline at end of file |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/TEST_1/TEST_1.tsv --- a/test-data/TEST_1/TEST_1.tsv Sun Feb 11 00:56:12 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,8 +0,0 @@ -# Annotated with Bakta -# Software: v1.9.2 -# 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 92eee5f31117 -r ba6990f72184 test-data/TEST_1/TEST_1.txt --- a/test-data/TEST_1/TEST_1.txt Sun Feb 11 00:56:12 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -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: v1.9.2 -Database: v5.0, full -DOI: 10.1099/mgen.0.000685 -URL: github.com/oschwengers/bakta |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/TEST_1/TEST_1_plot.svg --- a/test-data/TEST_1/TEST_1_plot.svg Sun Feb 11 00:56:12 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,2400 +0,0 @@\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 92eee5f31117 -r ba6990f72184 test-data/TEST_2/TEST_2.ffn --- a/test-data/TEST_2/TEST_2.ffn Sun Feb 11 00:56:12 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,4 +0,0 @@ ->IHHALP_00005 hypothetical protein -ATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAG ->IHHALP_00010 hypothetical protein -ATGAACAAGCAGCAGCAAACTGCACTCAACATGGCGGGATTCATAAAAAGCCAGAGCCTGACGCTGCTCGAAAAACTGGACGCACTCGATGCTGACGAGCAGGCCACCATGTGTGAGAAGCTGCACGAACTCGCAGAAGAACAAATAGAAGCAATAAAAAATAAAGATAAAACTTTATTTATTGTCTATGCTACTGATATTTATAGCCCGAGCGAATTTTTCTCAAAAATCGAATCCGACTTGAAGAAAAAGAAAAGCAAGGGTGATGTTTTTTTTGATTTAATAATTCCTAACGGTGGAAAAAAAGATCGTTACGTCTATACGTCATTTAATGGCGAGAAGTTTTCAAGTTACACATTAAACAAAGTTACGAAAACTGATGAATATAATGATTTATCTGAGCTCTCGGCTTCGTTCTTTAAAAAAAACTTTGATAAGATCAACGTAAACCTTCTATCCAAAGCCACATCATTTGCTTTGAAAAAAGGCATTCCAATATAA |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/TEST_2/TEST_2.gff3 --- a/test-data/TEST_2/TEST_2.gff3 Sun Feb 11 00:56:12 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,37 +0,0 @@ -##gff-version 3 -##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: v1.9.2 -# Database: v5.0, full -# DOI: 10.1099/mgen.0.000685 -# URL: github.com/oschwengers/bakta -##sequence-region NC_002127.1 1 1330 -NC_002127.1 Bakta region 1 1330 . + . ID=NC_002127.1;Name=NC_002127.1;Is_circular=true -NC_002127.1 Prodigal CDS 413 736 . + 0 ID=IHHALP_00005;Name=hypothetical protein;locus_tag=IHHALP_00005;product=hypothetical protein -NC_002127.1 Prodigal CDS 971 1471 . - 0 ID=IHHALP_00010;Name=hypothetical protein;locus_tag=IHHALP_00010;product=hypothetical protein -##FASTA ->NC_002127.1 -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 92eee5f31117 -r ba6990f72184 test-data/TEST_2/TEST_2.tsv --- a/test-data/TEST_2/TEST_2.tsv Sun Feb 11 00:56:12 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,8 +0,0 @@ -# Annotated with Bakta -# Software: v1.9.2 -# 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 |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/TEST_2/TEST_2_plot.svg --- a/test-data/TEST_2/TEST_2_plot.svg Sun Feb 11 00:56:12 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
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| diff -r 92eee5f31117 -r ba6990f72184 test-data/TEST_3/TEST_3.gff3 --- a/test-data/TEST_3/TEST_3.gff3 Sun Feb 11 00:56:12 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,34 +0,0 @@ -##gff-version 3 -##feature-ontology https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/v3.1/so.obo -# Annotated with Bakta -# Software: v1.9.2 -# 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 -##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 |
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| diff -r 92eee5f31117 -r ba6990f72184 test-data/TEST_3/TEST_3.tsv --- a/test-data/TEST_3/TEST_3.tsv Sun Feb 11 00:56:12 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,6 +0,0 @@ -# Annotated with Bakta -# Software: v1.9.2 -# 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 92eee5f31117 -r ba6990f72184 test-data/TEST_4/TEST_4.ffn --- a/test-data/TEST_4/TEST_4.ffn Sun Feb 11 00:56:12 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ ->IHHALP_00005 hypothetical protein -ATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAG ->IHHALP_00010 hypothetical protein -ATGAACAAGCAGCAGCAAACTGCACTCAACATGGCGGGATTCATAAAAAGCCAGAGCCTGACGCTGCTCGAAAAACTGGACGCACTCGATGCTGACGAGCAGGCCACCATGTGTGAGAAGCTGCACGAACTCGCAGAAGAACAAATAGAAGCAATAAAAAATAAAGATAAAACTTTATTTATTGTCTATGCTACTGATATTTATAGCCCGAGCGAATTTTTCTCAAAAATCGAATCCGACTTGAAGAAAAAGAAAAGCAAGGGTGATGTTTTTTTTGATTTAATAATTCCTAACGGTGGAAAAAAAGATCGTTACGTCTATACGTCATTTAATGGCGAGAAGTTTTCAAGTTACACATTAAACAAAGTTACGAAAACTGATGAATATAATGATTTATCTGAGCTCTCGGCTTCGTTCTTTAAAAAAAACTTTGATAAGATCAACGTAAACCTTCTATCCAAAGCCACATCATTTGCTTTGAAAAAAGGCATTCCAATATAA |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/TEST_4/TEST_4.gff3 --- a/test-data/TEST_4/TEST_4.gff3 Sun Feb 11 00:56:12 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,13 +0,0 @@ -##gff-version 3 -##feature-ontology https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/v3.1/so.obo -# Annotated with Bakta -# Software: v1.9.2 -# Database: v5.0, full -# DOI: 10.1099/mgen.0.000685 -# URL: github.com/oschwengers/bakta -##sequence-region p2 1 1330 -p2 Bakta region 1 1330 . + . ID=p2;Name=p2;Is_circular=true -p2 Prodigal gene 413 736 . + . ID=IHHALP_00005_gene;locus_tag=IHHALP_00005 -p2 Prodigal CDS 413 736 . + 0 ID=IHHALP_00005;Name=hypothetical protein;locus_tag=IHHALP_00005;product=hypothetical protein;Parent=IHHALP_00005_gene;inference=ab initio prediction:Prodigal:2.6 -p2 Prodigal gene 971 1471 . - . ID=IHHALP_00010_gene;locus_tag=IHHALP_00010 -p2 Prodigal CDS 971 1471 . - 0 ID=IHHALP_00010;Name=hypothetical protein;locus_tag=IHHALP_00010;product=hypothetical protein;Parent=IHHALP_00010_gene;inference=ab initio prediction:Prodigal:2.6 |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/TEST_4/TEST_4.tsv --- a/test-data/TEST_4/TEST_4.tsv Sun Feb 11 00:56:12 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,8 +0,0 @@ -# Annotated with Bakta -# Software: v1.9.2 -# 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 |
| b |
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| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/TEST_5/TEST_5.txt --- a/test-data/TEST_5/TEST_5.txt Sun Feb 11 00:56:12 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,30 +0,0 @@ -Sequence(s): -Length: 1330 -Count: 1 -GC: 45.2 -N50: 1330 -N ratio: 0.0 -coding density: 0.0 - -Annotation: -tRNAs: 0 -tmRNAs: 0 -rRNAs: 0 -ncRNAs: 0 -ncRNA regions: 0 -CRISPR arrays: 0 -CDSs: 0 -pseudogenes: 0 -hypotheticals: 0 -signal peptides: 0 -sORFs: 0 -gaps: 0 -oriCs: 0 -oriVs: 0 -oriTs: 0 - -Bakta: -Software: v1.9.2 -Database: v5.0, full -DOI: 10.1099/mgen.0.000685 -URL: github.com/oschwengers/bakta |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/TEST_6/TEST_6.embl --- a/test-data/TEST_6/TEST_6.embl Sun Feb 11 00:56:12 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,85 +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: v1.9.2 -CC Database: v5.0, full -CC DOI: 10.1099/mgen.0.000685 -CC URL: github.com/oschwengers/bakta -CC -CC ##Genome Annotation Summary:## -CC Annotation Date :: 02/11/2024, 00:27:34 -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 92eee5f31117 -r ba6990f72184 test-data/TEST_6/TEST_6.faa --- a/test-data/TEST_6/TEST_6.faa Sun Feb 11 00:56:12 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ ->IHHALP_00005 hypothetical protein -MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD ->IHHALP_00010 hypothetical protein -MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/TEST_6/TEST_6.ffn --- a/test-data/TEST_6/TEST_6.ffn Sun Feb 11 00:56:12 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ ->IHHALP_00005 hypothetical protein -ATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAG ->IHHALP_00010 hypothetical protein -ATGAACAAGCAGCAGCAAACTGCACTCAACATGGCGGGATTCATAAAAAGCCAGAGCCTGACGCTGCTCGAAAAACTGGACGCACTCGATGCTGACGAGCAGGCCACCATGTGTGAGAAGCTGCACGAACTCGCAGAAGAACAAATAGAAGCAATAAAAAATAAAGATAAAACTTTATTTATTGTCTATGCTACTGATATTTATAGCCCGAGCGAATTTTTCTCAAAAATCGAATCCGACTTGAAGAAAAAGAAAAGCAAGGGTGATGTTTTTTTTGATTTAATAATTCCTAACGGTGGAAAAAAAGATCGTTACGTCTATACGTCATTTAATGGCGAGAAGTTTTCAAGTTACACATTAAACAAAGTTACGAAAACTGATGAATATAATGATTTATCTGAGCTCTCGGCTTCGTTCTTTAAAAAAAACTTTGATAAGATCAACGTAAACCTTCTATCCAAAGCCACATCATTTGCTTTGAAAAAAGGCATTCCAATATAA |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/TEST_6/TEST_6.fna --- a/test-data/TEST_6/TEST_6.fna Sun Feb 11 00:56:12 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,24 +0,0 @@ ->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 92eee5f31117 -r ba6990f72184 test-data/TEST_6/TEST_6.gbff --- a/test-data/TEST_6/TEST_6.gbff Sun Feb 11 00:56:12 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,81 +0,0 @@ -LOCUS contig_1 1330 bp DNA circular BCT 11-FEB-2024 -DEFINITION plasmid unnamed1, complete sequence. -ACCESSION contig_1 -VERSION contig_1 -KEYWORDS . -SOURCE None - ORGANISM . - . -COMMENT Annotated with Bakta - Software: v1.9.2 - Database: v5.0, full - DOI: 10.1099/mgen.0.000685 - URL: github.com/oschwengers/bakta - - ##Genome Annotation Summary:## - Annotation Date :: 02/11/2024, 00:27:34 - 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 92eee5f31117 -r ba6990f72184 test-data/TEST_6/TEST_6.gff3 --- a/test-data/TEST_6/TEST_6.gff3 Sun Feb 11 00:56:12 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -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: v1.9.2 -# 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 92eee5f31117 -r ba6990f72184 test-data/TEST_6/TEST_6.hypotheticals.faa --- a/test-data/TEST_6/TEST_6.hypotheticals.faa Sun Feb 11 00:56:12 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ ->IHHALP_00005 hypothetical protein -MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD ->IHHALP_00010 hypothetical protein -MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/TEST_6/TEST_6.hypotheticals.tsv --- a/test-data/TEST_6/TEST_6.hypotheticals.tsv Sun Feb 11 00:56:12 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,5 +0,0 @@ -#Annotated with Bakta v1.9.2, https://github.com/oschwengers/bakta -#Database v5.0, https://doi.org/10.5281/zenodo.4247252 -#Sequence Id Start Stop Strand Locus Tag Mol Weight [kDa] Iso El. Point Pfam hits Dbxrefs -contig_1 413 736 + IHHALP_00005 12.1 10.4 -contig_1 971 141 - IHHALP_00010 18.9 7.7 |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/TEST_6/TEST_6.json --- a/test-data/TEST_6/TEST_6.json Sun Feb 11 00:56:12 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,95 +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": "+", - "frame": 2, - "gene": null, - "product": "hypothetical protein", - "db_xrefs": [], - "nt": "ATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAG", - "aa": "MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD", - "aa_hexdigest": "d9bdebc84195542e775c3d22458b507e", - "start_type": "ATG", - "rbs_motif": "GGAG/GAGG", - "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": "-", - "frame": 1, - "gene": null, - "product": "hypothetical protein", - "db_xrefs": [], - "nt": "ATGAACAAGCAGCAGCAAACTGCACTCAACATGGCGGGATTCATAAAAAGCCAGAGCCTGACGCTGCTCGAAAAACTGGACGCACTCGATGCTGACGAGCAGGCCACCATGTGTGAGAAGCTGCACGAACTCGCAGAAGAACAAATAGAAGCAATAAAAAATAAAGATAAAACTTTATTTATTGTCTATGCTACTGATATTTATAGCCCGAGCGAATTTTTCTCAAAAATCGAATCCGACTTGAAGAAAAAGAAAAGCAAGGGTGATGTTTTTTTTGATTTAATAATTCCTAACGGTGGAAAAAAAGATCGTTACGTCTATACGTCATTTAATGGCGAGAAGTTTTCAAGTTACACATTAAACAAAGTTACGAAAACTGATGAATATAATGATTTATCTGAGCTCTCGGCTTCGTTCTTTAAAAAAAACTTTGATAAGATCAACGTAAACCTTCTATCCAAAGCCACATCATTTGCTTTGAAAAAAGGCATTCCAATATAA", - "aa": "MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI", - "aa_hexdigest": "1e7027cbe48346e06a83e802a9385584", - "start_type": "ATG", - "rbs_motif": "AGGA/GGAG/GAGG", - "edge": true, - "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": "2024-02-11 00:27:31", - "end": "2024-02-11 00:27:43" - }, - "version": { - "bakta": "1.9.2", - "db": { - "version": "5.0", - "type": "full" - } - } -} \ No newline at end of file |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/TEST_6/TEST_6.tsv --- a/test-data/TEST_6/TEST_6.tsv Sun Feb 11 00:56:12 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,8 +0,0 @@ -# Annotated with Bakta -# Software: v1.9.2 -# 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 92eee5f31117 -r ba6990f72184 test-data/TEST_6/TEST_6.txt --- a/test-data/TEST_6/TEST_6.txt Sun Feb 11 00:56:12 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -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: v1.9.2 -Database: v5.0, full -DOI: 10.1099/mgen.0.000685 -URL: github.com/oschwengers/bakta |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/TEST_6/TEST_6_plot.svg --- a/test-data/TEST_6/TEST_6_plot.svg Sun Feb 11 00:56:12 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -0,0 +1,4 @@ +>ORI10010001 +TATTCTTCTATAACATTGTCAAGAATGATAGTTAAAATTCTCGAAATTGGGATATTAACTGCTTTGGAGTAATTTCTAACTTTTTGTCATACTCTTTGACTTGTATAGAAGTGTACACCTGTATCTAGTTTTTCTTGGCGTTCAACAGGAACTATTCCTGGTATTTTTGTTTTAGGTTGGGGAGGAATAGGCTGTGGTTGTGTGAATTGTTGTTGAAAATTTTGATTTTTTTGCTGTAAGAAACCATTATTATGATATTGAAAATTTTGTTCCTCTTGAAAATATCTCTCTTTTTTTGGTTTTCCAGAAAAATTTGATGAAAAAGATTTTTCTTCATTTCAATTTTCAAGATTATTTTCATTTTGTTGATTTATTTGCTCAGGCTGTTGAAATGAATTATTTTTTGATCAAAAAGATTTTGGAAAGGTTTTTTCAAAAGCAGATAAAGGTCCAAAATCAAATGAAGATGAATCTTTGTCAAAAGATGTTTCTTCTCTTTTTGACAAATTTTGTTTTTGATTAAACTTATTTTTATTTTGGGGTGTTACTTTTTCTTTTATGGAAAACAAATCTTCTTCTAAAAGACTTTGTTCTGGGTCATCATCTTGTGCTAAATCAAAGAAAAAACGTTTCTTTTTGTTA +>ORI10010003 +GGCGTAGACACTGAATTCGATGGGGATAAGTGGTGGATAAAAGAATATAAATTAGTCATTACACTTTACTCACGAATATCCCCCTTTTTTTAGAGAAAAAATATACTTTCTTCACAAGCTTGTGTGCGGTTTTTGTTTGGTAATTCTCGAGACATAAGCACTTATCCAGATATTCACAGTTACTATTATGTGATACGACTACATTCTTTATACTTATAAGATTAATAAGGAGGAAACTAACT |
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| @@ -0,0 +1,4 @@ +>CP019995|MOBP +GTAGAATCGTTTAGTATGAGAATAGAAAACCAACGGTTTTCATGAACTTACTAAACGATTCTAC +>CP012386|MOBP +AGAACAATCAACAACTAATTAGGCAAATTAAGGGGTGCTAAACAACTGCTAGTAGGTGCTAGAGATGTGCTATAAAGGGTGCTAGTTTGGTGCTAGTTACTGCTAAATACGTGCTAGTTTAGGTGCTAGAAACGTGCTATATGGTGCTAAAAAGGTGCTAGTTTGCATGAAGTTACCTGCTAGCCAAGTGCTAGTGGCGTTCGTTTTTGGGTCCCACGGGAAAGCCTTGCACTGCAAGGCGGGTCAGCTTGTCTGACCCCCATTTCCCCTTATGCTCTTCCGAAACACAAAGCGCAATTAAGCGAATACTAGAGAATAAATA |
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| [ |
| @@ -0,0 +1,54 @@ +{ + "date": "2023-02-20", + "major": 5, + "minor": 0, + "type": "light", + "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" + } + ] +} |
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| @@ -1,2 +0,0 @@ -#taxgroup accession_version mutation_position mutation_symbol class subclass mutated_protein_name -Escherichia WP_000019358.1 12 soxS_A12S MULTIDRUG AMPICILLIN/CHLORAMPHENICOL/QUINOLONE/RIFAMPIN/TETRACYCLINE Escherichia_ampicillin/chloramphenicol/quinolone/rifampin/tetracycline_resistant_SoxS |
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| diff -r 92eee5f31117 -r ba6990f72184 test-data/amrfinderplus-db/2021-09-30.1/AMRProt-suppress --- a/test-data/amrfinderplus-db/2021-09-30.1/AMRProt-suppress Sun Feb 11 00:56:12 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,2 +0,0 @@ -#taxgroup protein_accession protein_gi -Escherichia AAA21095.1 151858 |
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| @@ -1,2 +0,0 @@ -#taxgroup gene_symbol accession_version resistance_cutoff class subclass resistance_protein_name -Streptococcus_pneumoniae pbp1a WP_001040013.1 99.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP1A |
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| @@ -1,1 +0,0 @@ -3.10.16 |
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| b'@@ -1,1744 +0,0 @@\n-#node_id\tparent_node_id\tgene_symbol\thmm_id\thmm_tc1\thmm_tc2\tblastrule_complete_ident\tblastrule_complete_wp_coverage\tblastrule_complete_br_coverage\tblastrule_partial_ident\tblastrule_partial_wp_coverage\tblastrule_partial_br_coverage\treportable\ttype\tsubtype\tclass\tsubclass\tfamily_name\n-ACID\tSTRESS\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tACID\t\t\t\n-ALL\t\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\t\t\t\t\t\n-AME\tAMR\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\taminoglycoside modifying enzymes\n-AMR\tALL\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\t\n-BIOCIDE\tSTRESS\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tBIOCIDE\t\t\t\n-BcII\tbla-B1\tbla2\tNF033095.1\t500.00\t500.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tBETA-LACTAM\tCARBAPENEM\tBcII family subclass B1 metallo-beta-lactamase\n-CDF_efflux\tMETAL\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tMETAL\t\t\tCDF family cation efflux transporter\n-CMY2-MIR-ACT-EC\tbla-C\tampC\tNF012173.1\t680.00\t680.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tBETA-LACTAM\tBETA-LACTAM\tCMY2/MIR/ACT/EC family class C beta-lactamase\n-EFFLUX\tAMR\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\tefflux\n-HARLDQ_not_B3\tbla-B3\t-\tNF000405.1\t350.00\t350.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\tHARLDQ motif MBL-fold protein\n-HEAT\tSTRESS\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tHEAT\t\t\t\n-HTH_5\tMETAL\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tMETAL\t\t\tArsR/SmtB family metalloregulatory transcriptional repressor\n-LHR_hdeD\tHEAT\thdeD-GI\t-\t0.00\t0.00\t90.00\t90.00\t90.00\t93.00\t90.00\t25.00\t1\tSTRESS\tHEAT\t\t\theat resistance membrane protein HdeD-GI\n-LHR_hsp20A\tHEAT\thsp20\t-\t0.00\t0.00\t94.00\t90.00\t90.00\t96.00\t90.00\t25.00\t1\tSTRESS\tHEAT\t\t\tsmall heat shock protein sHSP20\n-LHR_hsp20B\tHEAT\tshsP\t-\t0.00\t0.00\t93.00\t90.00\t90.00\t94.00\t90.00\t25.00\t1\tSTRESS\tHEAT\t\t\tsmall heat shock protein sHSP20-GI\n-LHR_kefB\tHEAT\tkefB-GI\t-\t0.00\t0.00\t86.00\t90.00\t90.00\t90.00\t90.00\t25.00\t1\tSTRESS\tHEAT\t\t\theat resistance system K+/H+ antiporter KefB-GI\n-LHR_psiE\tHEAT\tpsi-GI\t-\t0.00\t0.00\t88.00\t90.00\t90.00\t90.00\t90.00\t25.00\t1\tSTRESS\tHEAT\t\t\theat resistance protein PsiE-GI\n-LHR_trx\tHEAT\ttrxLHR\t-\t0.00\t0.00\t85.00\t90.00\t90.00\t90.00\t90.00\t25.00\t1\tSTRESS\tHEAT\t\t\theat resistance system thioredoxin Trx-GI\n-LHR_yfdX1\tHEAT\tyfdX1\t-\t0.00\t0.00\t88.00\t90.00\t90.00\t90.00\t90.00\t25.00\t1\tSTRESS\tHEAT\t\t\theat resistance protein YfdX1\n-LHR_yfdX2\tHEAT\tyfdX2\t-\t0.00\t0.00\t90.00\t90.00\t90.00\t90.00\t90.00\t25.00\t1\tSTRESS\tHEAT\t\t\theat resistance protein YfdX2\n-MATE_efflux\tEFFLUX\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\tmultidrug efflux MATE transporter\n-METAL-RND-IM\tMETAL\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tMETAL\t\t\tcation efflux RND transporter permease subunit\n-METAL\tSTRESS\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tMETAL\t\t\tMetal Resistance\n-MFS_efflux_CHL\tMFS_efflux\tcml\t-\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tPHENICOL\tCHLORAMPHENICOL\tchloramphenicol efflux MFS transporter\n-MFS_efflux_qac\tBIOCIDE\tqac\tNF000089.1\t900.00\t900.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tSTRESS\tBIOCIDE\tQUATERNARY AMMONIUM\tQUATERNARY AMMONIUM\tQacA/B family quaternary ammonium compound efflux MFS transporter\n-MFS_efflux\tEFFLUX\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\tmultidrug efflux MFS transporter\n-MerP_Gneg\tmerP\tmerP\tTIGR02052.1\t92.55\t92.55\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t1\tSTRESS\tMETAL\tMERCURY\tMERCURY\tmercury resistance system periplasmic binding protein MerP\n-OM_sidero\tVIRULENCE_Ecoli\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tVIRULENCE\tVIRULENCE\t\t\tTonB-dependent siderophore receptor\n-P-type_ATPase\tMETAL\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tMETAL\t\t\tmetal-translocating P-type ATPase\n-PERI-SENSOR\tMETAL\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tMETAL\t\t\tperiplasmic heavy metal sensor\n-RESPONSE_REG\tAMR\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\tDNA-binding response regulator\n-RND-IM\tEFFLUX\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\tmultidrug efflux RND transporter permease subunit\n-RND-OM\tEFFLUX\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\tmultidrug'..b'ferase Vat(A)\n-vat(B)\tvat\tvat(B)\t-\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin A O-acetyltransferase Vat(B)\n-vat(C)\tvat\tvat(C)\tNF000097.1\t425.00\t425.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin A O-acetyltransferase Vat(C)\n-vat(D)\tvat\tvat(D)\tNF000111.1\t400.00\t400.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin A O-acetyltransferase Vat(D)\n-vat(E)\tvat\tvat(E)\tNF000020.1\t450.00\t450.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin A O-acetyltransferase Vat(E)\n-vat(F)\tvat\tvat(F)\tNF000147.1\t400.00\t400.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin A O-acetyltransferase Vat(F)\n-vat(H)\tvat\tvat(H)\tNF000504.1\t475.00\t425.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin A O-acetyltransferase Vat(H)\n-vat(I)\tvat\tvatI\tNF033468.1\t415.00\t415.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin A O-acetyltransferase Vat(I)\n-vat\tAMR\tvat\tNF000311.1\t300.00\t300.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tVat family streptogramin A O-acetyltransferase\n-vga(A)\tvga\tvga(A)\t-\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tLINCOSAMIDE\tLINCOSAMIDE\tABC-F type ribosomal protection protein Vga(A)\n-vga(B)\tvga\tvga(B)\t-\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tLINCOSAMIDE\tLINCOSAMIDE\tABC-F type ribosomal protection protein Vga(B)\n-vga(C)\tvga\tvga(C)\t-\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tLINCOSAMIDE\tLINCOSAMIDE\tABC-F type ribosomal protection protein Vga(C)\n-vga(D)\tvga\tvga(D)\t-\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tLINCOSAMIDE\tLINCOSAMIDE\tABC-F type ribosomal protection protein Vga(D)\n-vga(E)\tvga\tvga(E)\t-\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tLINCOSAMIDE\tLINCOSAMIDE\tABC-F type ribosomal protection protein Vga(E)\n-vga\tabc-f\tvga\tNF000170.1\t800.00\t800.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tLINCOSAMIDE\tLINCOSAMIDE\tVga family ABC-F type ribosomal protection protein\n-vgb(A)\tvgb\tvgb(A)\tNF000022.1\t600.00\t600.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin B lyase Vgb(A)\n-vgb(B)\tvgb\tvgb(B)\tNF000096.1\t600.00\t600.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin B lyase Vgb(B)\n-vgb(C)\tvgb\tvgbC\t-\t0.00\t0.00\t84.00\t90.00\t90.00\t88.00\t90.00\t25.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin B lyase Vgb(C)\n-vgb\tAMR\tvgb\t-\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin B lyase\n-virF\tVIRULENCE_Ecoli\tvirF\t-\t0.00\t0.00\t94.00\t90.00\t90.00\t96.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\tAraC family invasion system transcriptional regulator VirF\n-vmlR\tabc-f\tvmlR\t-\t0.00\t0.00\t90.00\t90.00\t90.00\t96.00\t90.00\t25.00\t2\tAMR\tAMR\tMACROLIDE/PLEUROMUTILIN\tLINCOSAMIDE/STREPTOGRAMIN/TIAMULIN\tABC-F type ribosomal protection protein VmlR\n-vph\tAMR\tvph\tNF000088.1\t400.00\t400.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tTUBERACTINOMYCIN\tVIOMYCIN\tviomycin phosphotransferase\n-ybtP\tVIRULENCE\tybtP\t-\t0.00\t0.00\t85.00\t90.00\t90.00\t96.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\tyersiniabactin ABC transporter ATP-binding/permease protein YbtP\n-ybtQ\tVIRULENCE\tybtQ\t-\t0.00\t0.00\t85.00\t90.00\t90.00\t96.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\tyersiniabactin ABC transporter ATP-binding/permease protein YbtQ\n-yfeA\tVIRULENCE\tyfeA\t-\t0.00\t0.00\t83.00\t90.00\t90.00\t88.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\tiron/manganese ABC transporter substrate-binding protein YfeA\n-yfeB\tVIRULENCE\tyfeB\t-\t0.00\t0.00\t86.00\t90.00\t90.00\t96.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\tiron/manganese ABC transporter ATP-binding protein YfeB\n-yfeD\tVIRULENCE\tyfeD\t-\t0.00\t0.00\t88.00\t90.00\t90.00\t92.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\tiron/manganese ABC transporter permease subunit YfeD\n-zbmA\tble\tzbmA\tNF000479.1\t280.00\t280.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tBLEOMYCIN\tZORBAMYCIN\tzorbamycin binding protein ZbmA\n' |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/amrfinderplus-db/2021-09-30.1/taxgroup.tab --- a/test-data/amrfinderplus-db/2021-09-30.1/taxgroup.tab Sun Feb 11 00:56:12 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -#taxgroup gpipe_taxgroup number_of_nucl_ref_genes -Acinetobacter_baumannii Acinetobacter 0 |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/amrfinderplus-db/2021-09-30.1/version.txt --- a/test-data/amrfinderplus-db/2021-09-30.1/version.txt Sun Feb 11 00:56:12 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -2021-09-30.1 |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/amrfinderplus-db/AMR.LIB --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amrfinderplus-db/AMR.LIB Wed Jun 05 14:22:02 2024 +0000 |
| [ |
| b'@@ -0,0 +1,6500 @@\n+HMMER3/f [3.1b2 | February 2015]\n+NAME tet_ABC_46_A-NCBIFAM\n+ACC NF000474.1\n+DESC NCBIFAM: tetracycline efflux ABC transporter Tet(46) subunit A\n+LENG 574\n+ALPH amino\n+RF no\n+MM no\n+CONS yes\n+CS no\n+MAP yes\n+DATE Tue Aug 27 12:39:42 2019\n+NSEQ 5\n+EFFN 0.405273\n+CKSUM 3622448626\n+GA 1250 1250\n+TC 1250 1250\n+NC 1250 1250\n+STATS LOCAL MSV -11.9374 0.69736\n+STATS LOCAL VITERBI -12.7561 0.69736\n+STATS LOCAL FORWARD -6.3343 0.69736\n+HMM A C D E F G H I K L M N P Q R S T V W Y\n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 2.55881 4.49993 2.93380 2.79370 3.15097 2.79672 3.88777 2.66977 2.78373 2.28694 3.58134 3.28220 3.63499 3.01909 2.94342 2.68638 2.91336 2.54646 4.47664 3.36127\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.03386 3.79821 4.52056 0.61958 0.77255 0.00000 *\n+ 1 2.91318 4.47450 3.97049 3.55992 3.17917 3.77862 4.31234 2.34751 3.33143 1.78660 1.52825 3.84610 4.24023 3.71911 3.54516 3.25380 3.21778 2.34458 5.00913 3.76340 1 m - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.03386 3.79821 4.52056 0.61958 0.77255 0.48576 0.95510\n+ 2 2.97337 4.41526 4.22623 3.84078 3.32614 3.98301 4.58395 1.17512 3.66729 1.92971 3.27541 4.09660 4.42309 4.02442 3.87247 3.47271 3.27462 1.84971 5.20019 3.93072 2 i - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.03386 3.79821 4.52056 0.61958 0.77255 0.48576 0.95510\n+ 3 2.92484 4.76558 3.40824 2.93741 4.10136 3.42467 3.77613 3.63946 2.21581 3.16909 4.17302 3.30193 3.93250 3.00174 1.09842 3.01366 3.19695 3.36708 5.21564 4.04667 3 r - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.03386 3.79821 4.52056 0.61958 0.77255 0.48576 0.95510\n+ 4 1.12649 4.15831 3.38969 3.17968 3.98066 2.98437 4.21016 3.09535 3.19405 2.98009 4.02182 3.34729 3.71677 3.54255 3.44855 2.51011 2.78241 2.76278 5.41537 4.20774 4 a - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.03386 3.79821 4.52056 0.61958 0.77255 0.48576 0.95510\n+ 5 2.97337 4.41526 4.22623 3.84078 3.32614 3.98301 4.58395 1.17512 3.66729 1.92971 3.27541 4.09660 4.42309 4.02442 3.87247 3.47271 3.27462 1.84971 5.20019 3.93072 5 i - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.03386 3.79821 4.52056 0.61958 0.77255 0.48576 0.95510\n+ 6 2.99964 4.50080 4.00607 3.53243 2.44313 3.84920 3.70593 2.75832 3.23546 1.92151 3.40968 3.71304 4.23894 3.59102 3.42742 3.24662 3.24963 2.68949 1.89475 2.50247 6 w - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.03386 3.79821 4.52056 0.61958 0.77255 0.4857'..b' 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.03150 3.86924 4.59158 0.61958 0.77255 0.48576 0.95510\n+ 69 3.00176 4.84118 3.49207 3.00377 4.19494 3.49042 3.82184 3.73640 2.23595 3.25291 4.25315 3.36377 3.99313 3.04230 0.98334 3.08607 3.26792 3.46048 5.27927 4.12297 69 r - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.03150 3.86924 4.59158 0.61958 0.77255 0.48576 0.95510\n+ 70 3.06303 4.43114 4.56086 4.00550 2.29264 4.26987 4.49404 1.76885 3.89021 1.37484 2.93679 4.24143 4.52117 4.04233 4.04916 3.59690 3.29171 2.02951 4.90105 3.65166 70 l - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.03150 3.86924 4.59158 0.61958 0.77255 0.48576 0.95510\n+ 71 2.65042 4.97394 2.37397 2.19864 4.29764 3.25354 3.52746 3.75233 2.48616 3.31296 4.12641 2.21008 2.87483 2.78288 2.97899 2.40564 2.91436 3.37837 5.51475 4.12630 71 e - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.03150 3.86924 4.59158 0.61958 0.77255 0.48576 0.95510\n+ 72 2.82684 4.88742 2.87978 2.57959 4.09001 3.37774 3.71718 3.66771 2.31091 3.17751 4.14238 3.04321 3.89612 1.44141 2.52973 2.86017 3.09908 3.37580 5.32568 4.00751 72 q - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.03150 3.86924 4.59158 0.61958 0.77255 0.48576 0.95510\n+ 73 2.92668 4.90873 3.33473 2.80010 4.09553 3.52772 3.41052 3.72365 2.03412 3.22001 4.14409 3.19096 3.96785 2.83868 1.26161 2.97224 3.14928 3.42956 5.22372 3.95221 73 r - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.03150 3.86924 4.59158 0.61958 0.77255 0.48576 0.95510\n+ 74 1.76274 4.21184 3.24777 2.84993 4.03533 2.69407 3.93978 3.42446 2.85365 3.10422 3.94125 3.14352 3.67086 3.18028 3.07071 2.06815 2.26336 2.99396 5.37683 4.13523 74 a - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.03150 3.86924 4.59158 0.61958 0.77255 0.48576 0.95510\n+ 75 3.02858 4.44817 4.33114 3.94679 3.37197 4.06309 4.67549 1.08191 3.77487 1.95864 3.30780 4.19259 4.49458 4.12347 3.97181 3.55805 3.32779 1.84575 5.26216 4.00020 75 i - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.03150 3.86924 4.59158 0.61958 0.77255 0.48576 0.95510\n+ 76 3.04189 4.44450 4.41667 3.97756 3.31747 4.17934 4.68449 1.15539 3.78471 1.83984 3.23210 4.23183 4.55416 4.12248 3.98786 3.60498 3.32259 1.79603 5.24865 3.97929 76 i - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.03150 3.86924 4.59158 0.61958 0.77255 0.48576 0.95510\n' |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/amrfinderplus-db/AMR.LIB.h3f |
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| Binary file test-data/amrfinderplus-db/AMR.LIB.h3f has changed |
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| diff -r 92eee5f31117 -r ba6990f72184 test-data/amrfinderplus-db/AMR.LIB.h3i |
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| Binary file test-data/amrfinderplus-db/AMR.LIB.h3i has changed |
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| diff -r 92eee5f31117 -r ba6990f72184 test-data/amrfinderplus-db/AMR.LIB.h3m |
| b |
| Binary file test-data/amrfinderplus-db/AMR.LIB.h3m has changed |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/amrfinderplus-db/AMR.LIB.h3p |
| b |
| Binary file test-data/amrfinderplus-db/AMR.LIB.h3p has changed |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/amrfinderplus-db/AMRProt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amrfinderplus-db/AMRProt Wed Jun 05 14:22:02 2024 +0000 |
| b |
| @@ -0,0 +1,79 @@ +>1028082228|WP_063841495.1|1|1|aph(3')-IIIa|aph(3')-IIIa|phosphotransferase|2|AMIKACIN/KANAMYCIN|AMINOGLYCOSIDE|aminoglycoside_O-phosphotransferase_APH(3')-IIIa +MAKMRISPELKKLIEKYRCVKDTEGMSPAKVYKLVGENENLYLKMTDSRYKGTTYDVEREKDMMLWLEGKLPVPKVLHFE +RHDGWSNLLMSEADGVLCSEEYEDEQSPEKIIELYAECIRLFHSIDISDCPYTNSLDSRLAELDYLLNNDLADVDCENWE +EDTPFKDPRELYDFLKTEKPEEELVFSHGDLGDSNIFVKDGKVSGFIDLGRSGRADKWYDIAFCIRSIREDIGEEQYVEL +FFDLLGIKPDWEKIKYYILLDELF* +>1028082240|WP_063841507.1|1|1|aph(3')-IIIa|aph(3')-IIIa|phosphotransferase|2|AMIKACIN/KANAMYCIN|AMINOGLYCOSIDE|aminoglycoside_O-phosphotransferase_APH(3')-IIIa +MAKMRISPELKKLIEKYRCVKDTEGMSPAKVYKLVGENENLYLKMTDSRYKGTTYDVEREKDMMLWLEGKLPVPKVLHFE +RHDGWSNLLMSEADGVLCSEEYEDEQSPEKIIELYAECIRLFHSIDISDCPYTNSLNSRLAELDYLLNNDLADVDCENWE +EDTPFKDPRELYDFLKTEKPEEELVFSHGDLGDSNIFVKDGKVSGFIDLGRSGRADKWYDIAFCVRSIREDIGEEQYVEL +FFDLLGIKPDWEKIKYYILLDELF* +>1028084243|WP_063843211.1|1|1|catA7|catA7|acetyltransferase|2|CHLORAMPHENICOL|PHENICOL|type_A-7_chloramphenicol_O-acetyltransferase +MTFNIIKLENWDRKEYFEHYFNQQTTYSITKEIDITLFKDMIKKKGYEIYPSLIYAIMEVVNKNKVFRTGINSENKLGYW +DKLNPLYTVFNKQTEKFTNIWTESDNNFTSFYNNYKNDLFEYKDKEEMFPKKPIPENTIPISMIPWIDFSSFNLNIGNNS +SFLLPIITIGKFYSENNKIYIPVALQLHHAVCDGYHASLFINEFQDIIKKVDDWI* +>1028086162|WP_063844601.1|1|1|erm(B)|erm(B)|target_modification|2|CLINDAMYCIN/ERYTHROMYCIN/STREPTOGRAMIN_B|LINCOSAMIDE/MACROLIDE/STREPTOGRAMIN|23S_rRNA_(adenine(2058)-N(6))-methyltransferase_Erm(B) +MNKNIKYSQNFLTNEKVLNQIIKQLNLKETDTVYEIGTGKGHLTTKLAKISKQVTSIELDSHLFNLSSEKLKLNTRVTLI +HQDILQFQFPNKQRYKIVGSIPYHLSTQIIKKVVFESHASDIYLIVEEGFYKRTLDIHRTLGLLLHTQVSIQQLLKLPAE +CFHPKPKVNSVLIKLTRHTTDVPDKYWKLYTYFVSKWVNREYRQLFTKNQFHQAMKHAKVNNLSTVTYEQVLSIFNSYLL +FNGRK* +>1028097810|WP_063854488.1|1|1|mupB|mupB|insensitivity|2|MUPIROCIN|MUPIROCIN|mupirocin-resistant_isoleucine--tRNA_ligase_MupB +MENENIIEEQKILNFWKEENIFKKSIDNRKNDNPFVFYDGPPTANGLPHTGHVLGRVIKDLFARYKTMQGFYVERKAGWD +THGLPVELGVEKKLGIKDKNEIEKYGIEKFINECKNSVFMYEKQWREFSELIGYWVDMEKPYKTMDNTYIESIWYILSDF +HKKGLLYKGHKVTPYCPSCETSLSSHEVAQGYKEVKDISVILKFPILDSDENFLVWTTTPWSLPGNIALAINAEEIYVKV +NYDNEIFIIMESLLQSVFKDEDNIDIVSKHKGKEFVGKEYLAPFPNKSLMNNENSYKVLPADFVTNKDGTGIVHIAPAYG +EDDYKLVQENNIPFINVIDSRGKYNQDSPIFKGELAKESDINIIKELTHLNLLFKKEKYEHSYPFCWRCDNPLIYYAMEG +WFIKTTAYKNEIKENNQKIEWYPDHIKNGRFGNFLDNMIDWNIGRKRYWGTPLNIWKCSTCSHEFSPKSINDLIQHSIED +IPSDIELHRPYIDNVKCKCQNCGGDMCREEEVIDVWFDSGSMPFAQNHYPFSGPIQNSYPADFIAEGVDQTRGWFYSLLV +ISTIFKGEAPYKNALSLGHILDSNGQKMSKSKGNVIDPISMIKTYGADSLRWTLVSDSVPWTNKRFSENMVAQSKSRVID +TLKNIFNFYNMYQKIDNYDYTRDTPKQLNLLDNWAISRMNSVIKEVELHLEKYNPTNASRAIGEFINEISNWYIRRSRSR +FWSSEMNEDKKSAYFTLRLILINTCKIIAPFTPFTSEEIHLNLTKKSVHLEDFPQAKEEYINLKLEEDMNKVLDIVEKSR +SIRNNINIKTKQPLSNMYIYDNNNLDNEFLRKYKDIIKDEINVKKINIVSDLDNFLEYDVKPNFSTLGPKLGKDMKQFQI +LFKNIKKEEMNKLINDFDKLQKVFDSLGVTIEEKDFIISKIPKKGFSLSSNDSDRLIILDTNLTQELIREGFVRELIRVI +QQLRKQQNFNIEERINVVIDIDSDGLLSIKNNINILKENVLINNLKFEKRETMKYFKINQKEIGIQLMSSFTN* +>1028097848|WP_063854496.1|1|1|optrA|optrA|target_protection|2|FLORFENICOL/OXAZOLIDINONE|PHENICOL/OXAZOLIDINONE|ABC-F_type_ribosomal_protection_protein_OptrA +MSKATFAIASTNAKEDMKMQYKIINGAVYYDGNMVLENIGIEINDNEKIAIVGRNGCGKTTLLKAIIGEIELEEGTGESE +FQVIKTGNPYISYLRQMPFEDESISMVDEVRTVFKTLIDMENKMKQLIDKMENQYDDKIINEYSDISERYMALGGLTYQK +EYETMIRSMGFTEADYKKPISEFSGGQRTKIAFIKILLTKPDILLLDEPTNHLDIETIQWLESYLRSYKSTLVIISHDRM +FLNRIVDKVYEIEWGETKCYKGNYSAFEEQKRENHIKQQKDYDLQQIEIERITRLIERFRYKPTKAKMVQSKIKLLQRMQ +ILNAPDQYDTKTYMSKFQPRISSSRQVLSASELVIGYDTPLAKVNFNLERGQKLGIVGSNGIGKSTLLKTLMGGVAALSG +DFKFGYNVEISYFDQQLAQISGDDTLFEIFQSEYPELNDTEVRTALGSFQFSGDDVFRPVSSLSGGEKVRLTLCKLLYKR +TNVLILDEPTNHMDIIGKENLENILCSYQGTIIFVSHDRYFTNKIADRLLVFDKDGVEFVQSTYGEYEKKRMNSEKPFNN +IKVEQKVEKNNTVKGDRNSIEKEKVKKEKRIEKLEVLINQYDEELERLNKIISEPNNSSDYIVLTEIQKSIDDVKRCQGN +YFNEWEQLMRELEVM* +>1028098403|WP_063854934.1|1|1|sat4|sat4|acetyltransferase|2|STREPTOTHRICIN|STREPTOTHRICIN|streptothricin_N-acetyltransferase_Sat4 +MITEMKAEHLKDIDKPSEPFEVIGKIIPRYENENWTFTELLYEAPYLKSYQDEEDEEDEEADCLEYIDNTDKIIYLYYQD +DKCVGKVKLRKNWNRYAYIEDIAVCKDFRGQGIGSALINISIEWAKHKNLHGLMLETQDNNLIACKFYHNCGFKIGSVDT +MLYANFENNFEKAVFWYLRF* +>1028099083|WP_063855540.1|1|1|sul2|sul2|insensitivity|2|SULFONAMIDE|SULFONAMIDE|sulfonamide-resistant_dihydropteroate_synthase_Sul2 +MNKSLIIFGIVNITSDSFSDGGRYLAPDAAIAQARKLMAEGADVIDLGPASSNPDAAPVSSDTEIARIAPVLDALKADGI +PVSLDSYQPATQAYALSRGVAYLNDIRGFPDAAFYPQLAKSSAKLVVMHSVQDGQADRREAPAGDIMDHIAAFFDARIAA +LTGAGIKRNRLVLDPGMGFFLGAAPETSLSVLARFDELRVRFDLPVLLSVSRKSFLRALTGRGPGDVGAATLAAELAAAA +GGADFIRTHEPRPLRDGLAVLAALKETARIR* +>1028099808|WP_063856080.1|1|1|tet(L)|tet(L)|efflux|2|TETRACYCLINE|TETRACYCLINE|tetracycline_efflux_MFS_transporter_Tet(L) +MNTSYSQSNLRHNQILIWLCILSFFSVLNEMVLNVSLPDIANDFNKPPASTNWVNTAFMLTFSIGTAVYGKLSDQLGIKR +LLLFGIIINCFGSVIGFVGHSFFSLLIMARFIQGAGAAAFPALVMVVVARYIPKENRGKAFGLIGSIVAMGEGVGPAIGG +MIAHYIHWSYLLLIPMITIITVPFLMKLLKKEVRIKGHFDIKGIILMSVGIVFFMLFTTSYSISFLIVSVLSFLIFVKHI +RKVTDPFVDPGLGKNIPFMIGVLCGGIIFGTVAGFVSMVPYMMKDVHQLSTAEIGSVIIFPGTMSVIIFGYIGGILVDRR +GPLYVLNIGVTFLSVSFLTASFLLETTSWFMTIIIVFVLGGLLFTKTVISTIVSSSLKQQEAGAGMSLLNFTSFLSEGTG +IAIVGGLLSIPLLDQRLLPMEVDQSTYLYSNLLLLFSGIIVISWLVTLNVYKHSQRDF* +>1028100174|WP_063856395.1|1|1|tet(M)|tet(M)|target_protection|2|TETRACYCLINE|TETRACYCLINE|tetracycline_resistance_ribosomal_protection_protein_Tet(M) +MKIINIGVLAHVDAGKTTLTESLLYNSGAITELGSVDKGTTRTDNTLLERQRGITIQTGITSFQWENTKVNIIDTPGHMD +FLAEVYRSLSVLDGAILLISAKDGVQAQTRILFHALRKMGIPTIFFINKIDQNGIDLSTVYQDIKEKLSAEIVIKQKVEL +YPNMCVTNFTESEQWDTVIEGNDDLLEKYMSGKSLEALELEQEESIRFQNCSLFPVYHGSAKNNIGIDNLIEVITNKFYS +STHRGQSELCGNVFKIEYTKKRQRLAYIRLYSGVLHLRDSVRISEKEKIKITEMYTSINGELCKIDKAYSGEIVILQNEF +LKLNSVLGDTKLLPQRERIENPLPLLQTTVEPSKPQQREMLLDALLEISDSDPLLRYYVDSTTHEIILSFLGKVQMEVIS +ALLQEKYHVEIELKEPTVIYMERPLKNAEYTIHIEVPPNPFWASIGLSVSPLPLGSGVQYESSVSLGYLNQSFQNAVMEG +IRYGCEQGLYGWNVTDCKICFKYGLYYSPVSTPADFRMLAPIVLEQVLKKAGTELLEPYLSFKIYAPQEYLSRAYNDAPK +YCANIVDTQFKNNEVILSGEIPARCIQEYRSDLTFFTNGRSVCLTELKGYHVTTGEPVCQPRRPNSRIDKVRYMFNKIT* +>1028100560|WP_063856695.1|1|1|vanG|vanG|re-structuring_of_the_cell_wall|2|VANCOMYCIN|GLYCOPEPTIDE|D-alanine--D-serine_ligase_VanG +MQNKKIAVIFGGNSTEYEVSLQSASAVFENINTNKFDIIPIGITRSGEWYHYTGEKEKILNNTWFEDSKNLCPVVVSQNR +SVKGFLEIASDKYRIIKVDLVFPVLHGKNGENGTLQGIFELAGIPVVGCDTLSSALCMDKDRAHKLVSLAGISVPKSVTF +KRFNEEAAMKEIEANLTYPLFIKPVRAGSSFGITKVIEKQELDAAIELAFEHDTEVIVEETINGFEVGCAVLGIDELIVG +RVDEIELSSGFFDYTEKYTLKSSKIYMPARIDAEAEKRIQEAAVTIYKALGCSGFSRVDMFYTPSGEIVFNEVNTIPGFT +SHSRYPNMMKGIGLSFSQMLDKLIGLYVE* +>1028109707|WP_063864110.1|1|1|blaOXA-484|blaOXA-48_fam|hydrolase|2|CARBAPENEM|BETA-LACTAM|OXA-48_family_carbapenem-hydrolyzing_class_D_beta-lactamase_OXA-484 +MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIA +LDLGVVKDEHQVFKWDGQTRDIAAWNRDHDLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDG +GIRISATQQIAFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTGIEPKIGWWVGWVELDDNVWFFAMNMD +MPTSDGLGLRQAITKEVLKQEKIIP* |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/amrfinderplus-db/AMRProt-mutation.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amrfinderplus-db/AMRProt-mutation.tab Wed Jun 05 14:22:02 2024 +0000 |
| b |
| b'@@ -0,0 +1,1208 @@\n+#taxgroup\taccession_version\tmutation_position\tmutation_symbol\tclass\tsubclass\tmutated_protein_name\n+Escherichia\tWP_000019358.1\t12\tsoxS_A12S\tMULTIDRUG\tAMPICILLIN/CHLORAMPHENICOL/QUINOLONE/RIFAMPIN/TETRACYCLINE\tEscherichia_ampicillin/chloramphenicol/quinolone/rifampin/tetracycline_resistant_SoxS\n+Salmonella\tWP_000019483.1\t52\tsoxS_E52K\tMULTIDRUG\tAMPICILLIN/CHLORAMPHENICOL/QUINOLONE/RIFAMPIN/TETRACYCLINE\tSalmonella_ampicillin/chloramphenicol/quinolone/rifampin/tetracycline_resistant_SoxS\n+Streptococcus_pneumoniae\tWP_000024543.1\t65\trplD_WR65del\tMACROLIDE/OXAZOLIDINONE/PHENICOL\tAZITHROMYCIN/CHLORAMPHENICOL/CLARITHROMYCIN/ERYTHROMYCIN/LINEZOLID\tStreptococcus_pneumoniae_azithromycin/chloramphenicol/clarithromycin/erythromycin/linezolid_resistant_RplD\n+Streptococcus_pneumoniae\tWP_000024543.1\t68\trplD_KG68del\tMACROLIDE/OXAZOLIDINONE/PHENICOL\tAZITHROMYCIN/CHLORAMPHENICOL/CLARITHROMYCIN/ERYTHROMYCIN/LINEZOLID\tStreptococcus_pneumoniae_azithromycin/chloramphenicol/clarithromycin/erythromycin/linezolid_resistant_RplD\n+Escherichia\tWP_000031783.1\t121\ttufA_L121Q\tPOLYKETIDE\tKIRROMYCIN\tEscherichia_kirromycin_resistant_TufA\n+Escherichia\tWP_000031783.1\t125\ttufA_Q125E\tPOLYKETIDE\tKIRROMYCIN\tEscherichia_kirromycin_resistant_TufA\n+Escherichia\tWP_000031783.1\t125\ttufA_Q125K\tPOLYKETIDE\tKIRROMYCIN\tEscherichia_kirromycin_resistant_TufA\n+Escherichia\tWP_000031783.1\t125\ttufA_Q125R\tPOLYKETIDE\tKIRROMYCIN\tEscherichia_kirromycin_resistant_TufA\n+Escherichia\tWP_000031783.1\t161\ttufA_Y161C\tPOLYKETIDE\tKIRROMYCIN\tEscherichia_kirromycin_resistant_TufA\n+Escherichia\tWP_000031783.1\t161\ttufA_Y161D\tPOLYKETIDE\tKIRROMYCIN\tEscherichia_kirromycin_resistant_TufA\n+Escherichia\tWP_000031783.1\t161\ttufA_Y161N\tPOLYKETIDE\tKIRROMYCIN\tEscherichia_kirromycin_resistant_TufA\n+Escherichia\tWP_000031783.1\t231\ttufA_R231C\tPOLYKETIDE\tPULVOMYCIN\tEscherichia_pulvomycin_resistant_TufA\n+Escherichia\tWP_000031783.1\t231\ttufA_R231V\tPOLYKETIDE\tPULVOMYCIN\tEscherichia_pulvomycin_resistant_TufA\n+Escherichia\tWP_000031783.1\t234\ttufA_R234F\tPOLYKETIDE\tPULVOMYCIN\tEscherichia_pulvomycin_resistant_TufA\n+Escherichia\tWP_000031783.1\t234\ttufA_R234S\tPOLYKETIDE\tPULVOMYCIN\tEscherichia_pulvomycin_resistant_TufA\n+Escherichia\tWP_000031783.1\t317\ttufA_G317D\tPOLYKETIDE\tKIRROMYCIN\tEscherichia_kirromycin_resistant_TufA\n+Escherichia\tWP_000031783.1\t330\ttufA_Q330H\tPOLYKETIDE\tKIRROMYCIN\tEscherichia_kirromycin_resistant_TufA\n+Escherichia\tWP_000031783.1\t334\ttufA_R334C\tPOLYKETIDE\tPULVOMYCIN\tEscherichia_pulvomycin_resistant_TufA\n+Escherichia\tWP_000031783.1\t335\ttufA_T335A\tPOLYKETIDE\tPULVOMYCIN\tEscherichia_pulvomycin_resistant_TufA\n+Escherichia\tWP_000031783.1\t376\ttufA_A376S\tPOLYKETIDE\tKIRROMYCIN\tEscherichia_kirromycin_resistant_TufA\n+Escherichia\tWP_000031783.1\t376\ttufA_A376T\tPOLYKETIDE\tKIRROMYCIN\tEscherichia_kirromycin_resistant_TufA\n+Escherichia\tWP_000031783.1\t376\ttufA_A376V\tPOLYKETIDE\tKIRROMYCIN\tEscherichia_kirromycin_resistant_TufA\n+Escherichia\tWP_000031783.1\t379\ttufA_E379K\tPOLYKETIDE\tKIRROMYCIN\tEscherichia_kirromycin_resistant_TufA\n+Acinetobacter_baumannii\tWP_000064875.1\t68\tlpxA_G68D\tCOLISTIN\tCOLISTIN\tAcinetobacter_baumannii_colistin_resistant_LpxA\n+Acinetobacter_baumannii\tWP_000064875.1\t72\tlpxA_Q72K\tCOLISTIN\tCOLISTIN\tAcinetobacter_baumannii_colistin_resistant_LpxA\n+Acinetobacter_baumannii\tWP_000064875.1\t159\tlpxA_H159D\tCOLISTIN\tCOLISTIN\tAcinetobacter_baumannii_colistin_resistant_LpxA\n+Acinetobacter_baumannii\tWP_000064875.1\t233\tlpxA_D233STOP\tCOLISTIN\tCOLISTIN\tAcinetobacter_baumannii_colistin_resistant_LpxA\n+Salmonella\tWP_000072047.1\t421\tgyrB_Y421C\tQUINOLONE\tQUINOLONE\tSalmonella_quinolone_resistant_GyrB\n+Salmonella\tWP_000072047.1\t438\tgyrB_R438L\tQUINOLONE\tQUINOLONE\tSalmonella_quinolone_resistant_GyrB\n+Salmonella\tWP_000072047.1\t464\tgyrB_S464F\tQUINOLONE\tQUINOLONE\tSalmonella_quinolone_resistant_GyrB\n+Salmonella\tWP_000072047.1\t464\tgyrB_S464T\tQUINOLONE\tQUINOLONE\tSalmonella_quinolone_resistant_GyrB\n+Salmonella\tWP_000072047.1\t464\tgyrB_S464Y\tQUINOLONE\tQUINOLONE\tSalmonella_quinolone_resistant_GyrB\n+Salmonella\tWP_000072047.1\t466\tgy'..b'OMYCIN\tStaphylococcus_aureus_daptomycin_resistant_MprF\n+Staphylococcus_aureus\tWP_111724484.1\t347\tmprF_M347R\tLIPOPEPTIDE\tDAPTOMYCIN\tStaphylococcus_aureus_daptomycin_resistant_MprF\n+Staphylococcus_aureus\tWP_111724484.1\t351\tmprF_V351E\tLIPOPEPTIDE\tDAPTOMYCIN\tStaphylococcus_aureus_daptomycin_resistant_MprF\n+Staphylococcus_aureus\tWP_111724484.1\t420\tmprF_I420N\tLIPOPEPTIDE\tDAPTOMYCIN\tStaphylococcus_aureus_daptomycin_resistant_MprF\n+Staphylococcus_aureus\tWP_111724484.1\t472\tmprF_T472K\tLIPOPEPTIDE\tDAPTOMYCIN\tStaphylococcus_aureus_daptomycin_resistant_MprF\n+Staphylococcus_aureus\tWP_111724484.1\t826\tmprF_L826F\tLIPOPEPTIDE\tDAPTOMYCIN\tStaphylococcus_aureus_daptomycin_resistant_MprF\n+Enterococcus_faecium\tWP_115256011.1\t82\tparC_S80I\tQUINOLONE\tQUINOLONE\tEnterococcus_faecium_quinolone_resistant_ParC\n+Enterococcus_faecium\tWP_115256011.1\t82\tparC_S80R\tQUINOLONE\tQUINOLONE\tEnterococcus_faecium_quinolone_resistant_ParC\n+Enterococcus_faecium\tWP_115256011.1\t86\tparC_E84A\tQUINOLONE\tQUINOLONE\tEnterococcus_faecium_quinolone_resistant_ParC\n+Enterococcus_faecium\tWP_115256011.1\t86\tparC_E84K\tQUINOLONE\tQUINOLONE\tEnterococcus_faecium_quinolone_resistant_ParC\n+Enterococcus_faecium\tWP_115256011.1\t86\tparC_E84T\tQUINOLONE\tQUINOLONE\tEnterococcus_faecium_quinolone_resistant_ParC\n+Klebsiella_pneumoniae\tWP_117036963.1\t83\tgyrA_S83F\tQUINOLONE\tQUINOLONE\tKlebsiella_pneumoniae_quinolone_resistant_GyrA\n+Klebsiella_pneumoniae\tWP_117036963.1\t83\tgyrA_S83I\tQUINOLONE\tQUINOLONE\tKlebsiella_pneumoniae_quinolone_resistant_GyrA\n+Klebsiella_pneumoniae\tWP_117036963.1\t83\tgyrA_S83L\tQUINOLONE\tQUINOLONE\tKlebsiella_pneumoniae_quinolone_resistant_GyrA\n+Klebsiella_pneumoniae\tWP_117036963.1\t83\tgyrA_S83T\tQUINOLONE\tQUINOLONE\tKlebsiella_pneumoniae_quinolone_resistant_GyrA\n+Klebsiella_pneumoniae\tWP_117036963.1\t83\tgyrA_S83Y\tQUINOLONE\tQUINOLONE\tKlebsiella_pneumoniae_quinolone_resistant_GyrA\n+Klebsiella_pneumoniae\tWP_117036963.1\t87\tgyrA_D87A\tQUINOLONE\tQUINOLONE\tKlebsiella_pneumoniae_quinolone_resistant_GyrA\n+Klebsiella_pneumoniae\tWP_117036963.1\t87\tgyrA_D87G\tQUINOLONE\tQUINOLONE\tKlebsiella_pneumoniae_quinolone_resistant_GyrA\n+Klebsiella_pneumoniae\tWP_117036963.1\t87\tgyrA_D87H\tQUINOLONE\tQUINOLONE\tKlebsiella_pneumoniae_quinolone_resistant_GyrA\n+Klebsiella_pneumoniae\tWP_117036963.1\t87\tgyrA_D87N\tQUINOLONE\tQUINOLONE\tKlebsiella_pneumoniae_quinolone_resistant_GyrA\n+Klebsiella_pneumoniae\tWP_117036963.1\t87\tgyrA_D87Y\tQUINOLONE\tQUINOLONE\tKlebsiella_pneumoniae_quinolone_resistant_GyrA\n+Staphylococcus_aureus\tWP_123090655.1\t183\tpbp4_E183A\tBETA-LACTAM\tCEPHALOSPORIN\tStaphylococcus_aureus_cephalosporin_resistant_Pbp4\n+Staphylococcus_aureus\tWP_123090655.1\t200\tpbp4_R200L\tBETA-LACTAM\tCEPHALOSPORIN\tStaphylococcus_aureus_cephalosporin_resistant_Pbp4\n+Staphylococcus_aureus\tWP_123090655.1\t218\tpbp4_E218K\tBETA-LACTAM\tCEPHALOSPORIN\tStaphylococcus_aureus_cephalosporin_resistant_Pbp4\n+Staphylococcus_aureus\tWP_123090655.1\t241\tpbp4_F241R\tBETA-LACTAM\tCEPHALOSPORIN\tStaphylococcus_aureus_cephalosporin_resistant_Pbp4\n+Enterococcus_faecium\tWP_137277832.1\t84\tgyrA_S83I\tQUINOLONE\tQUINOLONE\tEnterococcus_faecium_quinolone_resistant_GyrA\n+Enterococcus_faecium\tWP_137277832.1\t84\tgyrA_S83L\tQUINOLONE\tQUINOLONE\tEnterococcus_faecium_quinolone_resistant_GyrA\n+Enterococcus_faecium\tWP_137277832.1\t84\tgyrA_S83N\tQUINOLONE\tQUINOLONE\tEnterococcus_faecium_quinolone_resistant_GyrA\n+Enterococcus_faecium\tWP_137277832.1\t84\tgyrA_S83R\tQUINOLONE\tQUINOLONE\tEnterococcus_faecium_quinolone_resistant_GyrA\n+Enterococcus_faecium\tWP_137277832.1\t84\tgyrA_S83Y\tQUINOLONE\tQUINOLONE\tEnterococcus_faecium_quinolone_resistant_GyrA\n+Enterococcus_faecium\tWP_137277832.1\t88\tgyrA_E87G\tQUINOLONE\tQUINOLONE\tEnterococcus_faecium_quinolone_resistant_GyrA\n+Enterococcus_faecium\tWP_137277832.1\t88\tgyrA_E87K\tQUINOLONE\tQUINOLONE\tEnterococcus_faecium_quinolone_resistant_GyrA\n+Enterococcus_faecium\tWP_137277832.1\t88\tgyrA_E87L\tQUINOLONE\tQUINOLONE\tEnterococcus_faecium_quinolone_resistant_GyrA\n+Enterococcus_faecium\tWP_137277832.1\t98\tgyrA_S97N\tQUINOLONE\tQUINOLONE\tEnterococcus_faecium_quinolone_resistant_GyrA\n' |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/amrfinderplus-db/AMRProt-suppress --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amrfinderplus-db/AMRProt-suppress Wed Jun 05 14:22:02 2024 +0000 |
| b |
| @@ -0,0 +1,17 @@ +#taxgroup protein_accession protein_gi +Escherichia AAA21095.1 151858 +Escherichia AAA21096.1 151859 +Escherichia AAB09628.1 1061418 +Escherichia BAA24823.1 2879920 +Escherichia BAA24824.1 2879921 +Escherichia BAA15331.2 85675040 +Escherichia BAE77395.1 85676145 +Escherichia BAE77620.1 85676370 +Escherichia BAE77793.1 85676543 +Klebsiella_oxytoca BAA24824.1 2879921 +Klebsiella_oxytoca BAB89353.1 20152201 +Klebsiella_pneumoniae ABR76310.1 150954280 +Salmonella BAE77395.1 85676145 +Staphylococcus_pseudintermedius AAA25637.1 150728 +Staphylococcus_pseudintermedius AAA27588.1 155345 +Vibrio_cholerae ABQ18953.1 146314413 |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/amrfinderplus-db/AMRProt-susceptible.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amrfinderplus-db/AMRProt-susceptible.tab Wed Jun 05 14:22:02 2024 +0000 |
| b |
| @@ -0,0 +1,27 @@ +#taxgroup gene_symbol accession_version resistance_cutoff class subclass resistance_protein_name +Neisseria_gonorrhoeae pbp2 WP_003703066.1 94.000000 BETA-LACTAM BETA-LACTAM Neisseria_gonorrhoeae_beta-lactam_resistant_PBP2 +Streptococcus_pneumoniae pbp1a WP_001039998.1 99.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP1A +Streptococcus_pneumoniae pbp1a WP_001040004.1 99.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP1A +Streptococcus_pneumoniae pbp1a WP_001040010.1 99.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP1A +Streptococcus_pneumoniae pbp1a WP_001040013.1 99.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP1A +Streptococcus_pneumoniae pbp1a WP_050078510.1 99.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP1A +Streptococcus_pneumoniae pbp1a WP_050208712.1 99.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP1A +Streptococcus_pneumoniae pbp1a WP_054370471.1 99.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP1A +Streptococcus_pneumoniae pbp2b WP_001224867.1 99.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP2B +Streptococcus_pneumoniae pbp2b WP_001224871.1 99.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP2B +Streptococcus_pneumoniae pbp2b WP_001224884.1 99.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP2B +Streptococcus_pneumoniae pbp2b WP_001224885.1 99.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP2B +Streptococcus_pneumoniae pbp2b WP_001224886.1 99.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP2B +Streptococcus_pneumoniae pbp2b WP_061634854.1 99.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP2B +Streptococcus_pneumoniae pbp2x WP_000872264.1 98.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP2X +Streptococcus_pneumoniae pbp2x WP_000872267.1 98.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP2X +Streptococcus_pneumoniae pbp2x WP_000872270.1 98.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP2X +Streptococcus_pneumoniae pbp2x WP_000872271.1 98.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP2X +Streptococcus_pneumoniae pbp2x WP_000872273.1 98.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP2X +Streptococcus_pneumoniae pbp2x WP_000872275.1 98.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP2X +Streptococcus_pneumoniae pbp2x WP_000872277.1 98.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP2X +Streptococcus_pneumoniae pbp2x WP_000872282.1 98.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP2X +Streptococcus_pneumoniae pbp2x WP_033707918.1 98.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP2X +Streptococcus_pneumoniae pbp2x WP_050293540.1 98.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP2X +Streptococcus_pneumoniae pbp2x WP_054364452.1 98.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP2X +Streptococcus_pneumoniae pbp2x WP_061745305.1 98.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP2X |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/amrfinderplus-db/AMRProt.pdb |
| b |
| Binary file test-data/amrfinderplus-db/AMRProt.pdb has changed |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/amrfinderplus-db/AMRProt.phr |
| b |
| Binary file test-data/amrfinderplus-db/AMRProt.phr has changed |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/amrfinderplus-db/AMRProt.pin |
| b |
| Binary file test-data/amrfinderplus-db/AMRProt.pin has changed |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/amrfinderplus-db/AMRProt.pjs --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amrfinderplus-db/AMRProt.pjs Wed Jun 05 14:22:02 2024 +0000 |
| [ |
| @@ -0,0 +1,22 @@ +{ + "version": "1.2", + "dbname": "AMRProt", + "dbtype": "Protein", + "db-version": 5, + "description": "/Users/bebatut/Documents/projects/galaxyproject/tools-iuc/data_managers/data_manager_build_amrfinderplus/amrfinderplus-db/AMRProt", + "number-of-letters": 4850, + "number-of-sequences": 12, + "last-updated": "2024-05-28T13:31:00", + "number-of-volumes": 1, + "bytes-total": 44751, + "bytes-to-cache": 5175, + "files": [ + "AMRProt.pdb", + "AMRProt.phr", + "AMRProt.pin", + "AMRProt.pot", + "AMRProt.psq", + "AMRProt.ptf", + "AMRProt.pto" + ] +} |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/amrfinderplus-db/AMRProt.psq |
| b |
| Binary file test-data/amrfinderplus-db/AMRProt.psq has changed |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/amrfinderplus-db/AMRProt.ptf |
| b |
| Binary file test-data/amrfinderplus-db/AMRProt.ptf has changed |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/amrfinderplus-db/AMRProt.pto |
| b |
| Binary file test-data/amrfinderplus-db/AMRProt.pto has changed |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/amrfinderplus-db/AMR_CDS --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amrfinderplus-db/AMR_CDS Wed Jun 05 14:22:02 2024 +0000 |
| b |
| b"@@ -0,0 +1,199 @@\n+>1028082228|WP_063841495.1|NG_047419.1|1|1|aph(3')-IIIa|aph(3')-IIIa|aminoglycoside_O-phosphotransferase_APH(3')-IIIa NG_047419.1:101-895\n+atggctaaaatgagaatatcaccggaattgaaaaaactgatcgaaaaataccgctgcgtaaaagatacggaaggaatgtc\n+tcctgctaaggtatataagctggtgggagaaaatgaaaacctatatttaaaaatgacggacagccggtataaagggacca\n+cctatgatgtggaacgggaaaaggacatgatgctatggctggaaggaaagctgcctgttccaaaggtcctgcactttgaa\n+cggcatgatggctggagcaatctgctcatgagtgaggccgatggcgtcctttgctcggaagagtatgaagatgaacaaag\n+ccctgaaaagattatcgagctgtatgcggagtgcatcaggctctttcactccatcgacatatcggattgtccctatacga\n+atagcttagacagccgcttagccgaattggattacttactgaataacgatctggccgatgtggattgcgaaaactgggaa\n+gaagacactccatttaaagatccgcgcgagctgtatgattttttaaagacggaaaagcccgaagaggaacttgtcttttc\n+ccacggcgacctgggagacagcaacatctttgtgaaagatggcaaagtaagtggctttattgatcttgggagaagcggca\n+gggcggacaagtggtatgacattgccttctgcatccggtcgatcagggaggatatcggggaagaacagtatgtcgagcta\n+ttttttgacttactggggatcaagcctgattgggagaaaataaaatattatattttactggatgaattgttttag\n+>1028082240|WP_063841507.1|NG_047420.1|1|1|aph(3')-IIIa|aph(3')-IIIa|aminoglycoside_O-phosphotransferase_APH(3')-IIIa NG_047420.1:101-895\n+atggctaaaatgagaatatcaccggaattgaaaaaactgatcgaaaaataccgctgcgtaaaagatacggaaggaatgtc\n+tcctgctaaggtatataagctggtgggagaaaatgaaaacctatatttaaaaatgacggacagccggtataaagggacca\n+cctatgatgtggaacgggaaaaggacatgatgctatggctggaaggaaagctgcctgttccaaaggtcctgcactttgaa\n+cggcatgatggctggagcaatctgctcatgagtgaggccgatggcgtcctttgctcggaagagtatgaagatgaacaaag\n+ccctgaaaagattatcgagctgtatgcggagtgcatcaggctctttcactccatcgacatatcggattgtccctatacga\n+atagcttaaacagccgcttagccgaattggattacttactgaataacgatctggccgatgtggattgcgaaaactgggaa\n+gaagacactccatttaaagatccgcgcgagctgtatgattttttaaagacggaaaagcccgaagaggaacttgtcttttc\n+ccacggcgacctgggagacagcaacatctttgtgaaagatggcaaagtaagtggctttattgatcttgggagaagcggca\n+gggcggacaagtggtatgacattgccttctgcgtccggtcgatcagggaggatatcggggaagaacagtatgtcgagcta\n+ttttttgacttactggggatcaagcctgattgggagaaaataaaatattatattttactggatgaattgttttag\n+>1028084243|WP_063843211.1|NG_047572.1|1|1|catA7|catA7|type_A-7_chloramphenicol_O-acetyltransferase NG_047572.1:101-748\n+atgacttttaatattatcaaattagaaaattgggatagaaaagaatattttgaacactattttaaccagcaaactacgta\n+tagcattactaaagaaattgatattactttgtttaaagatatgataaaaaagaaaggatatgaaatttatccttctttga\n+tttatgcaattatggaagttgtaaataaaaataaagtgtttagaacaggaattaatagtgagaataaattaggctattgg\n+gataagttaaatcctttgtatacagtttttaataagcaaactgaaaaatttactaacatttggactgaatctgataacaa\n+cttcacttctttttataataattataaaaatgacttgtttgaatataaagataaagaagaaatgtttcctaaaaaaccga\n+tacctgaaaacaccataccgatttcaatgattccttggattgattttagttcatttaatttaaacattggtaacaatagc\n+agctttttattgcctattattacgataggtaaattttatagtgagaataataaaatttatataccagttgccttacagct\n+tcatcatgctgtatgtgatggttaccatgcttcattatttataaatgaatttcaagatataattaagaaggtagatgatt\n+ggatttag\n+>1028086162|WP_063844601.1|NG_047793.1|1|1|erm(B)|erm(B)|23S_rRNA_(adenine(2058)-N(6))-methyltransferase_Erm(B) NG_047793.1:101-838\n+atgaacaaaaatataaaatattctcaaaactttttaacgaatgaaaaagtactcaaccaaataataaaacaattgaattt\n+aaaagaaaccgataccgtttacgaaattggaacaggtaaagggcatttaacgacgaaactggctaaaataagtaaacagg\n+taacgtctattgaattagacagtcatctattcaacttatcgtcagaaaaattaaaactgaatactcgtgtcactttaatt\n+caccaagatattctacagtttcaattccctaacaaacagaggtataaaattgttgggagtattccttaccatttaagcac\n+acaaattattaaaaaagtggtttttgaaagccatgcgtctgacatctatctgattgttgaagaaggattctacaagcgta\n+ccttggatattcaccgaacactagggttgctcttgcacactcaagtctcgattcagcaattgcttaagctgccagcggaa\n+tgctttcatcctaaaccaaaagtaaacagtgtcttaataaaacttacccgccataccacagatgttccagataaatattg\n+gaagctatatacgtactttgtttcaaaatgggtcaatcgagaatatcgtcaactgtttactaaaaatcagtttcatcaag\n+caatgaaacacgccaaagtaaacaatttaagtaccgttacttatgagcaagtattgtctatttttaatagttatctatta\n+tttaacgggaggaaataa\n+>1028097810|WP_063854488.1|NG_048009.1|1|1|mupB|mupB|mupirocin-resistant_isoleucine--tRNA_ligase_MupB NG_048009.1:91-3192\n+ttggaaaacgagaatataatagaagaacaaaaaatcttaaatttttggaaagaagaaaacattttcaaaaagagtattga\n+taatagaaaaaatgataatccatttgttttttacgatggtcctccaactgccaatggcttaccacatacaggtcacgtgt\n+taggaagagtaataaaagatttatttgctcgatataagacaatgcaaggattttatgttgaaagaaaagctgggtgggat\n+acccatggactacctgtagaacttg"..b'ggacggataatacgcttttagaacgtcagagaggaa\n+ttacaattcagacaggaataacctcttttcagtgggaaaatacgaaggtgaacatcatagacacgccaggacatatggat\n+ttcttagcagaagtatatcgttcattatcagttttagatggggcaattctactgatttctgcaaaagatggcgtacaagc\n+acaaactcgtatattatttcatgcacttaggaaaatggggattcccacaatcttttttatcaataagattgaccaaaatg\n+gaattgatttatcaacggtttatcaggatattaaagagaaactttctgccgaaattgtaatcaaacagaaggtagaactg\n+tatcctaatatgtgtgtgacgaactttaccgaatctgaacaatgggatacggtaatagagggaaacgatgaccttttaga\n+gaaatatatgtccggtaaatcattagaagcattggaactcgaacaagaggaaagcataagatttcagaattgttccctgt\n+tccctgtttatcacggaagtgcaaaaaacaatatagggattgataaccttatagaagtgattacgaataaattttattca\n+tcaacacatcgaggtcagtctgaactttgcggaaatgttttcaaaattgaatatacaaaaaaaagacaacgtcttgcata\n+tatacgtctttatagtggcgtactgcatttgcgagattcggttagaatatcggaaaaggaaaaaataaaaattacagaaa\n+tgtatacttcaataaatggtgaattatgtaaaatcgataaggcttattccggggaaattgttattttgcagaatgagttt\n+ttgaagttaaatagtgttcttggagatacaaagctattgccacagagagagagaattgaaaatcccctccctctgctgca\n+aacgactgttgaaccgagcaaacctcaacaaagggaaatgttgcttgatgcccttttggaaatctcagatagtgatccgc\n+ttctacgatattacgtggattctacgacacatgaaattatactttctttcttagggaaagtacaaatggaagtgattagt\n+gcactgttgcaagaaaagtatcatgtggagatagaactaaaagagcctacagtcatttatatggagagaccgttaaaaaa\n+tgcagaatataccattcacatcgaagtgccgccaaatcctttctgggcttccattggtttatctgtatcaccgcttccat\n+tagggagcggagtgcagtatgagagctcggtttctcttggatacttaaatcaatcgtttcaaaatgcagttatggagggg\n+atacgctatggctgtgaacaaggattgtatggttggaatgtgacggactgtaaaatctgttttaagtatggcttatacta\n+tagccctgttagtaccccagcagattttcggatgcttgctcctattgtattggaacaagtcttaaaaaaagctggaacag\n+aattgttagagccatatcttagttttaaaatttatgcgccacaggaatatctttcacgagcatacaacgatgctcctaaa\n+tattgtgcgaacatcgtagacactcaattcaaaaataatgaggtcattcttagtggagaaatccctgctcggtgtattca\n+agaatatcgtagtgatttaactttctttacaaatggacgtagtgtttgtttaacagagttaaaagggtaccatgttacta\n+ccggtgaacctgtttgccagccccgtcgtccaaatagtcggatagataaagtacgatatatgttcaataaaataacttag\n+>1028100560|WP_063856695.1|NG_048368.1|1|1|vanG|vanG|D-alanine--D-serine_ligase_VanG NG_048368.1:101-1150\n+atgcaaaataaaaaaatagcagttatttttggaggcaattcaacagagtacgaggtgtcattgcaatcggcatccgctgt\n+ttttgaaaatatcaataccaataaatttgacataattccaataggaattacaagaagtggtgaatggtatcactatacgg\n+gagaaaaggagaaaatcctaaacaatacttggtttgaagatagcaaaaatctatgccctgttgtcgtttcccaaaatcgt\n+tccgttaaaggctttttagaaattgcttcagacaaataccgtattataaaagttgatttggtattccccgtattgcatgg\n+caaaaacggcgaaaatgggactttgcagggcatatttgaattggcaggaatacctgttgttggctgcgatacactctcat\n+cagctctttgtatggataaggacagggcacataaactcgttagccttgcgggtatatctgttcctaaatcggtaacattc\n+aaacgctttaacgaagaagcagcgatgaaagagattgaagcgaatttaacttatccgctgtttattaaacctgttcgtgc\n+aggctcttcctttggaataacaaaagtaattgaaaagcaagagcttgatgctgccatagagttggcatttgaacacgata\n+cagaagtcatcgttgaagaaacaataaacggctttgaagtcggttgtgccgtacttggcatagatgagctcattgttggc\n+agagttgatgaaatcgaactgtcaagcggcttttttgattatacagagaaatatacgcttaaatcttcaaagatatatat\n+gcctgcaaggattgatgccgaagcagaaaaacggatacaagaagcggctgtaaccatatataaagctctgggctgttcgg\n+gtttttccagagtggatatgttttatacaccgtctggcgaaattgtatttaatgaggtaaacacaataccaggctttacc\n+tcgcacagtcgctatccaaatatgatgaaaggcattggtctatcgttctcccaaatgttggataagctgataggtctgta\n+tgtggaatga\n+>1028109707|WP_063864110.1|NG_049766.1|1|1|blaOXA-484|blaOXA-48_fam|OXA-48_family_carbapenem-hydrolyzing_class_D_beta-lactamase_OXA-484 NG_049766.1:1-798\n+atgcgtgtattagccttatcggctgtgtttttggtggcatcgattatcggaatgccagcggtagcaaaggaatggcaaga\n+aaacaaaagttggaatgctcactttactgaacataaatcacagggcgtagttgtgctctggaatgagaataagcagcaag\n+gatttaccaataatcttaaacgggcgaaccaagcatttttacccgcatctacctttaaaattcccaatagcttgatcgcc\n+ctcgatttgggcgtggttaaggatgaacaccaagtctttaagtgggatggacagacgcgtgatatcgccgcttggaatcg\n+tgaccatgacttaattaccgcgatgaagtactcagttgtgcctgtttatcaagaatttgcccgccaaattggtgaggcac\n+gtatgagtaaaatgctgcacgccttcgattatggcaatgaggatatctcgggcaatgtagacagtttttggctcgatggt\n+ggtattcgcatttcggctacccagcaaatcgcttttttacgcaagctgtatcacaacaagctgcacgtttctgagcgtag\n+tcagcgcatcgtgaaacaagccatgctgaccgaagccaatggcgactatattattcgggctaaaacgggatactcgactg\n+gaatcgaacctaagattggctggtgggttggttgggttgaacttgatgataatgtgtggttttttgcgatgaatatggat\n+atgcccacatcggatggtttagggctgcgccaagccatcacaaaagaagtgctcaaacaggagaaaattattccctag\n' |
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| diff -r 92eee5f31117 -r ba6990f72184 test-data/amrfinderplus-db/AMR_CDS.ndb |
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| Binary file test-data/amrfinderplus-db/AMR_CDS.ndb has changed |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/amrfinderplus-db/AMR_CDS.nhr |
| b |
| Binary file test-data/amrfinderplus-db/AMR_CDS.nhr has changed |
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| diff -r 92eee5f31117 -r ba6990f72184 test-data/amrfinderplus-db/AMR_CDS.nin |
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| Binary file test-data/amrfinderplus-db/AMR_CDS.nin has changed |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/amrfinderplus-db/AMR_CDS.njs --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amrfinderplus-db/AMR_CDS.njs Wed Jun 05 14:22:02 2024 +0000 |
| [ |
| @@ -0,0 +1,22 @@ +{ + "version": "1.2", + "dbname": "AMR_CDS", + "dbtype": "Nucleotide", + "db-version": 5, + "description": "/Users/bebatut/Documents/projects/galaxyproject/tools-iuc/data_managers/data_manager_build_amrfinderplus/amrfinderplus-db/AMR_CDS", + "number-of-letters": 14550, + "number-of-sequences": 12, + "last-updated": "2024-05-28T13:31:00", + "number-of-volumes": 1, + "bytes-total": 43342, + "bytes-to-cache": 4010, + "files": [ + "AMR_CDS.ndb", + "AMR_CDS.nhr", + "AMR_CDS.nin", + "AMR_CDS.not", + "AMR_CDS.nsq", + "AMR_CDS.ntf", + "AMR_CDS.nto" + ] +} |
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| diff -r 92eee5f31117 -r ba6990f72184 test-data/amrfinderplus-db/AMR_CDS.not |
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| Binary file test-data/amrfinderplus-db/AMR_CDS.not has changed |
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| diff -r 92eee5f31117 -r ba6990f72184 test-data/amrfinderplus-db/AMR_CDS.nsq |
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| Binary file test-data/amrfinderplus-db/AMR_CDS.nsq has changed |
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| Binary file test-data/amrfinderplus-db/AMR_CDS.ntf has changed |
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| diff -r 92eee5f31117 -r ba6990f72184 test-data/amrfinderplus-db/AMR_CDS.nto |
| b |
| Binary file test-data/amrfinderplus-db/AMR_CDS.nto has changed |
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| diff -r 92eee5f31117 -r ba6990f72184 test-data/amrfinderplus-db/AMR_DNA-Escherichia --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amrfinderplus-db/AMR_DNA-Escherichia Wed Jun 05 14:22:02 2024 +0000 |
| b |
| @@ -0,0 +1,101 @@ +>NC_000913.3@16S_ribosomal_RNA@16S_rrsB:4166659-4168201 +aaattgaagagtttgatcatggctcagattgaacgctggcggcaggcctaacacatgcaagtcgaacggtaacaggaaga +agcttgcttctttgctgacgagtggcggacgggtgagtaatgtctgggaaactgcctgatggagggggataactactgga +aacggtagctaataccgcataacgtcgcaagaccaaagagggggaccttcgggcctcttgccatcggatgtgcccagatg +ggattagctagtaggtggggtaacggctcacctaggcgacgatccctagctggtctgagaggatgaccagccacactgga +actgagacacggtccagactcctacgggaggcagcagtggggaatattgcacaatgggcgcaagcctgatgcagccatgc +cgcgtgtatgaagaaggccttcgggttgtaaagtactttcagcggggaggaagggagtaaagttaatacctttgctcatt +gacgttacccgcagaagaagcaccggctaactccgtgccagcagccgcggtaatacggagggtgcaagcgttaatcggaa +ttactgggcgtaaagcgcacgcaggcggtttgttaagtcagatgtgaaatccccgggctcaacctgggaactgcatctga +tactggcaagcttgagtctcgtagaggggggtagaattccaggtgtagcggtgaaatgcgtagagatctggaggaatacc +ggtggcgaaggcggccccctggacgaagactgacgctcaggtgcgaaagcgtggggagcaaacaggattagataccctgg +tagtccacgccgtaaacgatgtcgacttggaggttgtgcccttgaggcgtggcttccggagctaacgcgttaagtcgacc +gcctggggagtacggccgcaaggttaaaactcaaatgaattgacgggggcccgcacaagcggtggagcatgtggtttaat +tcgatgcaacgcgaagaaccttacctggtcttgacatccacggaagttttcagagatgagaatgtgccttcgggaaccgt +gagacaggtgctgcatggctgtcgtcagctcgtgttgtgaaatgttgggttaagtcccgcaacgagcgcaacccttatcc +tttgttgccagcggtccggccgggaactcaaaggagactgccagtgataaactggaggaaggtggggatgacgtcaagtc +atcatggcccttacgaccagggctacacacgtgctacaatggcgcatacaaagagaagcgacctcgcgagagcaagcgga +cctcataaagtgcgtcgtagtccggattggagtctgcaactcgactccatgaagtcggaatcgctagtaatcgtggatca +gaatgccacggtgaatacgttcccgggccttgtacacaccgcccgtcacaccatgggagtgggttgcaaaagaagtaggt +agcttaaccttcgggagggcgcttaccactttgtgattcatgactggggtgaagtcgtaacaaggtaaccgtaggggaac +ctgcggttggatcacctccttac +>NC_000913.3@16S_ribosomal_RNA@16S_rrsC:3941808-3943350 +aaattgaagagtttgatcatggctcagattgaacgctggcggcaggcctaacacatgcaagtcgaacggtaacaggaaac +agcttgctgtttcgctgacgagtggcggacgggtgagtaatgtctgggaaactgcctgatggagggggataactactgga +aacggtagctaataccgcataacgtcgcaagaccaaagagggggaccttcgggcctcttgccatcagatgtgcccagatg +ggattagctagtaggtggggtaacggctcacctaggcgacgatccctagctggtctgagaggatgaccagccacactgga +actgagacacggtccagactcctacgggaggcagcagtggggaatattgcacaatgggcgcaagcctgatgcagccatgc +cgcgtgtatgaagaaggccttcgggttgtaaagtactttcagcggggaggaagggagtaaagttaatacctttgctcatt +gacgttacccgcagaagaagcaccggctaactccgtgccagcagccgcggtaatacggagggtgcaagcgttaatcggaa +ttactgggcgtaaagcgcacgcaggcggtttgttaagtcagatgtgaaatccccgggctcaacctgggaactgcatctga +tactggcaagcttgagtctcgtagaggggggtagaattccaggtgtagcggtgaaatgcgtagagatctggaggaatacc +ggtggcgaaggcggccccctggacgaagactgacgctcaggtgcgaaagcgtggggagcaaacaggattagataccctgg +tagtccacgccgtaaacgatgtcgacttggaggttgtgcccttgaggcgtggcttccggagctaacgcgttaagtcgacc +gcctggggagtacggccgcaaggttaaaactcaaatgaattgacgggggcccgcacaagcggtggagcatgtggtttaat +tcgatgcaacgcgaagaaccttacctggtcttgacatccacggaagttttcagagatgagaatgtgccttcgggaaccgt +gagacaggtgctgcatggctgtcgtcagctcgtgttgtgaaatgttgggttaagtcccgcaacgagcgcaacccttatcc +tttgttgccagcggtccggccgggaactcaaaggagactgccagtgataaactggaggaaggtggggatgacgtcaagtc +atcatggcccttacgaccagggctacacacgtgctacaatggcgcatacaaagagaagcgacctcgcgagagcaagcgga +cctcataaagtgcgtcgtagtccggattggagtctgcaactcgactccatgaagtcggaatcgctagtaatcgtggatca +gaatgccacggtgaatacgttcccgggccttgtacacaccgcccgtcacaccatgggagtgggttgcaaaagaagtaggt +agcttaaccttcgggagggcgcttaccactttgtgattcatgactggggtgaagtcgtaacaaggtaaccgtaggggaac +ctgcggttggatcacctccttac +>NC_004431.1@23S_ribosomal_RNA@23S:237160-240064 +ggttaagcgactaagcgtacacggtggatgccctggcagtcagaggcgatgaaggacgtgctaatctgcgataagcgtcg +gtaaggtgatatgaaccgttataaccggcgatttccgaatggggaaacccagtgtgtttcgacacactatcattaactga +atccataggttaatgaggcgaaccgggggaactgaaacatctaagtaccccgaggaaaagaaatcaaccgagattccccc +agtagcggcgagcgaacggggaggagcccagagcctgaatcagtgtgtgtgttagtggaagcgtctggaaaggcgcgcga +tacagggtgacagccccgtacacaaaaatgcacatgctgtgagctcgatgagtagggcgggacacgtggtatcctgtctg +aatatggggggaccatcctccaaggctaaatactcctgactgaccgatagtgaaccagtaccgtgagggaaaggcgaaaa +gaaccccggcgaggggagtgaaaaagaacctgaaaccgtgtacgtacaagcagtgggagcatgcttaggcgtgtgactgc +gtaccttttgtataatgggtcagcgacttatattctgtagcaaggttaaccgaataggggagccgaagggaaaccgagtc +ttaactgggcgttaagttgcagggtatagacccgaaacccggtgatctagccatgggcaggttgaaggttgggtaacact +aactggaggaccgaaccgactaatgttgaaaaattagcggatgacttgtggctgggggtgaaaggccaatcaaaccggga +gatagctggttctccccgaaagctatttaggtagcgcctcgtgaactcatctccgggggtagagcactgtttcggcaagg +gggtcatcccgacttaccaacccgatgcaaactgcgaataccggagaatgttatcacgggagacacacggcgggtgctaa +cgtccgtcgngaagagggaaacaacccagaccgccagctaaggtcccaaagtcatggttaagtgggaaacgatgtgggaa +ggcccagacagccaggatgttggcttagaagcagccatcatttaaagaaagcgtaatagctcactggtcgagtcggcctg +cgcggaagatgtaacggggctaaaccatgcaccgaagctgcggcagcgacgcttatgcgttgttgggtaggggagcgttc +tgtaagcctgtgaaggtgtactgtgaggtatgctggaggtatcagaagtgcgaatgctgacataagtaacgataaagcgg +gtgaaaagcccgctcgccggaagaccaagggttcctgtccaacgttaatcggggcagggtgagtcgacccctaaggcgag +gccgaaaggcgtagtcgatgggaaacaggttaatattcctgtacttggtgttactgcgaaggggggacggagaaggctat +gttggccgggcgacggttgtcccggtttaagcgtgtaggctggttttccaggcaaatccggaaaatcaaggctgaggcgt +gatgacgaggcactacggtgctgaagcaacaaatgccctgcttccaggaaaagcctctaagcatcaggtaacatcaaatc +gtaccccaaaccgacacaggtggtcaggtagagaataccaaggcgcttgagagaactcgggtgaaggaactaggcaaaat +ggtgccgtaacttcgggagaaggcacgctgatatgtaggtgaagcgacttgctcgtggagctgaaatcagtcgaagatac +cagctggctgcaactgtttattaaaaacacagcactgtgcaaacacgaaagtggacgtatacggtgtgacgcctgcccgg +tgccggaaggttaattgatggggttagcgcaagcgaagctcttgatcgaagccccggtaaacggcggccgtaactataac +ggtcctaaggtagcgaaattccttgtcgggtaagttccgacctgcacgaatggcgtaatgatggccaggctgtctccacc +cgagactcagtgaaattgaactcgctgtgaagatgcagtgtacccgcggcaagacggaaagaccccgtgaacctttacta +tagcttgacactgaacattgagccttgatgtgtaggataggtgggaggctttgaagtgtggacgccagtctgcatggagc +cgaccttgaaataccaccctttaatgtttgatgttctaacgttgacccgtaatccgggttgcggacagtgtctggtgggt +agtttgactggggcggtctcctcctaaagagtaacggaggagcacgaaggttggctaatcctggtcggacatcaggaggt +tagtgcaatggcataagccagcttgactgcgagcgtgacggcgcgagcaggtgcgaaagcaggtcatagtgatccggtgg +ttctgaatggaagggccatcgctcaacggataaaaggtactccggggataacaggctgataccgcccaagagttcatatc +gacggcggtgtttggcacctcgatgtcggctcatcacatcctggggctgaagtaggtcccaagggtatggctgttcgcca +tttaaagtggtacgcgagctgggtttagaacgtcgtgagacagttcggtccctatctgccgtgggcgctggagaactgag +gggggctgctcctagtacgagaggaccggagtggacgcatcactggtgttcgggttgtcatgccaatggcactgcccggt +agctaaatgcggaagagataagtgctgaaagcatctaagcacgaaacttgccccgagatgagttctccctgactccttga +gggtcctgaaggaacgttgaagacgacgacgttgataggccgggtgtgtaagcgcagcgatgcgttgagctaaccggtac +taatgaaccgtgaggcttaacctta +>NZ_CP041538.1@ampC/blaEC_promoter_region@ampC:1149245-1149489 +tggctgctatcctgacagttgtcacgctgattggtgtcgttacaatctaacgcatcgccaatgtaaatccggcccgccta +tggcgggccgttttgtatggaaaccagaccctatgttcaaaacgacgctctgcaccttattaattaccgcctcttgctcc +acatttgccgcccctcaacaaatcaacgatattgtgcatcgcacaattaccccgcttatagagcaacaaaagatccccgg +tatgg +>NZ_CP095603.1@blaTEM_promoter_region@blaTEM:148777-149952 +ttcttgaagacgaaagggcctcgtgatacgcctatttttataggttaatgtcatgataataatggtttcttagacgtcag +gtggcacttttcggggaaatgtgcgcggaacccctatttgtttatttttctaaatacattcaaatatgtatccgctcatg +agacaataaccctgataaatgcttcaataatattgaaaaaggaagagtatgagtattcaacatttccgtgtcgcccttat +tcccttttttgcggcattttgccttcctgtttttgctcacccagaaacgctggtgaaagtaaaagatgctgaagatcagt +tgggtgcacgagtgggttacatcgaactggatctcaacagcggtaagatccttgagagttttcgccccgaagaacgtttt +ccaatgatgagcacttttaaagttctgctatgtggcgcggtattatcccgtgttgacgccgggcaagagcaactcggtcg +ccgcatacactattctcagaatgacttggttgagtactcaccagtcacagaaaagcatcttacggatggcatgacagtaa +gagaattatgcagtgctgccataaccatgagtgataacactgcggccaacttacttctgacaacgatcggaggaccgaag +gagctaaccgcttttttgcacaacatgggggatcatgtaactcgccttgatcgttgggaaccggagctgaatgaagccat +accaaacgacgagcgtgacaccacgatgcctgcagcaatggcaacaacgttgcgcaaactattaactggcgaactactta +ctctagcttcccggcaacaattaatagactggatggaggcggataaagttgcaggaccacttctgcgctcggcccttccg +gctggctggtttattgctgataaatctggagccggtgagcgtgggtctcgcggtatcattgcagcactggggccagatgg +taagccctcccgtatcgtagttatctacacgacggggagtcaggcaactatggatgaacgaaatagacagatcgctgaga +taggtgcctcactgattaagcattggtaactgtcagaccaagtttactcatatatactttagattgatttaaaacttcat +ttttaatttaaaaggatctaggtgaagatcctttttgataatctcatgaccaaaat |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/amrfinderplus-db/AMR_DNA-Escherichia.ndb |
| b |
| Binary file test-data/amrfinderplus-db/AMR_DNA-Escherichia.ndb has changed |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/amrfinderplus-db/AMR_DNA-Escherichia.nhr |
| b |
| Binary file test-data/amrfinderplus-db/AMR_DNA-Escherichia.nhr has changed |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/amrfinderplus-db/AMR_DNA-Escherichia.nin |
| b |
| Binary file test-data/amrfinderplus-db/AMR_DNA-Escherichia.nin has changed |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/amrfinderplus-db/AMR_DNA-Escherichia.njs --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amrfinderplus-db/AMR_DNA-Escherichia.njs Wed Jun 05 14:22:02 2024 +0000 |
| [ |
| @@ -0,0 +1,22 @@ +{ + "version": "1.2", + "dbname": "AMR_DNA-Escherichia", + "dbtype": "Nucleotide", + "db-version": 5, + "description": "/Users/bebatut/Documents/projects/galaxyproject/tools-iuc/data_managers/data_manager_build_amrfinderplus/amrfinderplus-db/AMR_DNA-Escherichia", + "number-of-letters": 7412, + "number-of-sequences": 5, + "last-updated": "2024-05-28T13:31:00", + "number-of-volumes": 1, + "bytes-total": 39713, + "bytes-to-cache": 2169, + "files": [ + "AMR_DNA-Escherichia.ndb", + "AMR_DNA-Escherichia.nhr", + "AMR_DNA-Escherichia.nin", + "AMR_DNA-Escherichia.not", + "AMR_DNA-Escherichia.nsq", + "AMR_DNA-Escherichia.ntf", + "AMR_DNA-Escherichia.nto" + ] +} |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/amrfinderplus-db/AMR_DNA-Escherichia.not |
| b |
| Binary file test-data/amrfinderplus-db/AMR_DNA-Escherichia.not has changed |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/amrfinderplus-db/AMR_DNA-Escherichia.nsq |
| b |
| Binary file test-data/amrfinderplus-db/AMR_DNA-Escherichia.nsq has changed |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/amrfinderplus-db/AMR_DNA-Escherichia.ntf |
| b |
| Binary file test-data/amrfinderplus-db/AMR_DNA-Escherichia.ntf has changed |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/amrfinderplus-db/AMR_DNA-Escherichia.nto |
| b |
| Binary file test-data/amrfinderplus-db/AMR_DNA-Escherichia.nto has changed |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/amrfinderplus-db/AMR_DNA-Escherichia.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amrfinderplus-db/AMR_DNA-Escherichia.tab Wed Jun 05 14:22:02 2024 +0000 |
| b |
| @@ -0,0 +1,50 @@ +#accesion_version@gene_name@gene_symbol:start-stop mutation_position mutation_symbol class subclass mutated_gene_name +NC_000913.3@16S_ribosomal_RNA@16S_rrsB:4166659-4168201 523 16S_A523C AMINOGLYCOSIDE STREPTOMYCIN Escherichia_streptomycin_resistant_16S_rrsB +NC_000913.3@16S_ribosomal_RNA@16S_rrsB:4166659-4168201 527 16S_G527T AMINOGLYCOSIDE STREPTOMYCIN Escherichia_streptomycin_resistant_16S_rrsB +NC_000913.3@16S_ribosomal_RNA@16S_rrsB:4166659-4168201 528 16S_C528T AMINOGLYCOSIDE STREPTOMYCIN Escherichia_streptomycin_resistant_16S_rrsB +NC_000913.3@16S_ribosomal_RNA@16S_rrsB:4166659-4168201 964 16S_A964G TETRACYCLINE TETRACYCLINE Escherichia_tetracycline_resistant_16S_rrsB +NC_000913.3@16S_ribosomal_RNA@16S_rrsB:4166659-4168201 1053 16S_G1053A TETRACYCLINE TETRACYCLINE Escherichia_tetracycline_resistant_16S_rrsB +NC_000913.3@16S_ribosomal_RNA@16S_rrsB:4166659-4168201 1054 16S_C1054T TETRACYCLINE TETRACYCLINE Escherichia_tetracycline_resistant_16S_rrsB +NC_000913.3@16S_ribosomal_RNA@16S_rrsB:4166659-4168201 1055 16S_A1055G TETRACYCLINE TETRACYCLINE Escherichia_tetracycline_resistant_16S_rrsB +NC_000913.3@16S_ribosomal_RNA@16S_rrsB:4166659-4168201 1058 16S_G1058C TETRACYCLINE TETRACYCLINE Escherichia_tetracycline_resistant_16S_rrsB +NC_000913.3@16S_ribosomal_RNA@16S_rrsB:4166659-4168201 1064 16S_G1064A AMINOGLYCOSIDE SPECTINOMYCIN Escherichia_spectinomycin_resistant_16S_rrsB +NC_000913.3@16S_ribosomal_RNA@16S_rrsB:4166659-4168201 1064 16S_G1064C AMINOGLYCOSIDE SPECTINOMYCIN Escherichia_spectinomycin_resistant_16S_rrsB +NC_000913.3@16S_ribosomal_RNA@16S_rrsB:4166659-4168201 1064 16S_G1064T AMINOGLYCOSIDE SPECTINOMYCIN Escherichia_spectinomycin_resistant_16S_rrsB +NC_000913.3@16S_ribosomal_RNA@16S_rrsB:4166659-4168201 1066 16S_C1066T AMINOGLYCOSIDE SPECTINOMYCIN Escherichia_spectinomycin_resistant_16S_rrsB +NC_000913.3@16S_ribosomal_RNA@16S_rrsB:4166659-4168201 1068 16S_G1068A AMINOGLYCOSIDE SPECTINOMYCIN Escherichia_spectinomycin_resistant_16S_rrsB +NC_000913.3@16S_ribosomal_RNA@16S_rrsB:4166659-4168201 1192 16S_C1192A AMINOGLYCOSIDE SPECTINOMYCIN Escherichia_spectinomycin_resistant_16S_rrsB +NC_000913.3@16S_ribosomal_RNA@16S_rrsB:4166659-4168201 1192 16S_C1192G AMINOGLYCOSIDE SPECTINOMYCIN Escherichia_spectinomycin_resistant_16S_rrsB +NC_000913.3@16S_ribosomal_RNA@16S_rrsB:4166659-4168201 1192 16S_C1192T AMINOGLYCOSIDE SPECTINOMYCIN Escherichia_spectinomycin_resistant_16S_rrsB +NC_000913.3@16S_ribosomal_RNA@16S_rrsB:4166659-4168201 1406 16S_T1406A AMINOGLYCOSIDE G418/TOBRAMYCIN Escherichia_g418/tobramycin_resistant_16S_rrsB +NC_000913.3@16S_ribosomal_RNA@16S_rrsB:4166659-4168201 1408 16S_A1408G AMINOGLYCOSIDE GENTAMICIN_C/NEOMYCIN/PAROMOMYCIN Escherichia_gentamicin_c/neomycin/paromomycin_resistant_16S_rrsB +NC_000913.3@16S_ribosomal_RNA@16S_rrsB:4166659-4168201 1499 16S_A1499G EDEINE EDEINE Escherichia_edeine_resistant_16S_rrsB +NC_000913.3@16S_ribosomal_RNA@16S_rrsC:3941808-3943350 794 16S_A794G AMINOGLYCOSIDE KASUGAMYCIN Escherichia_kasugamycin_resistant_16S_rrsC +NC_000913.3@16S_ribosomal_RNA@16S_rrsC:3941808-3943350 794 16S_A794T AMINOGLYCOSIDE KASUGAMYCIN Escherichia_kasugamycin_resistant_16S_rrsC +NC_000913.3@16S_ribosomal_RNA@16S_rrsC:3941808-3943350 926 16S_G926A AMINOGLYCOSIDE KASUGAMYCIN Escherichia_kasugamycin_resistant_16S_rrsC +NC_000913.3@16S_ribosomal_RNA@16S_rrsC:3941808-3943350 926 16S_G926C AMINOGLYCOSIDE KASUGAMYCIN Escherichia_kasugamycin_resistant_16S_rrsC +NC_000913.3@16S_ribosomal_RNA@16S_rrsC:3941808-3943350 926 16S_G926T AMINOGLYCOSIDE KASUGAMYCIN Escherichia_kasugamycin_resistant_16S_rrsC +NC_000913.3@16S_ribosomal_RNA@16S_rrsC:3941808-3943350 1519 16S_A1519C AMINOGLYCOSIDE KASUGAMYCIN Escherichia_kasugamycin_resistant_16S_rrsC +NC_000913.3@16S_ribosomal_RNA@16S_rrsC:3941808-3943350 1519 16S_A1519G AMINOGLYCOSIDE KASUGAMYCIN Escherichia_kasugamycin_resistant_16S_rrsC +NC_000913.3@16S_ribosomal_RNA@16S_rrsC:3941808-3943350 1519 16S_A1519T AMINOGLYCOSIDE KASUGAMYCIN Escherichia_kasugamycin_resistant_16S_rrsC +NC_004431.1@23S_ribosomal_RNA@23S:237160-240064 754 23S_T754A MACROLIDE ERYTHROMYCIN/TELITHROMYCIN Escherichia_erythromycin/telithromycin_resistant_23S +NC_004431.1@23S_ribosomal_RNA@23S:237160-240064 2032 23S_G2032A LINCOSAMIDE/OXAZOLIDINONE CLINDAMYCIN/LINEZOLID Escherichia_clindamycin/linezolid_resistant_23S +NC_004431.1@23S_ribosomal_RNA@23S:237160-240064 2032 23S_G2032C OXAZOLIDINONE LINEZOLID Escherichia_linezolid_resistant_23S +NC_004431.1@23S_ribosomal_RNA@23S:237160-240064 2032 23S_G2032T MACROLIDE/OXAZOLIDINONE CLARITHROMYCIN/LINEZOLID Escherichia_clarithromycin/linezolid_resistant_23S +NC_004431.1@23S_ribosomal_RNA@23S:237160-240064 2057 23S_G2057A MULTIDRUG CHLORAMPHENICOL/ERYTHROMYCIN/TELITHROMYCIN Escherichia_chloramphenicol/erythromycin/telithromycin_resistant_23S +NC_004431.1@23S_ribosomal_RNA@23S:237160-240064 2058 23S_A2058G MACROLIDE AZITHROMYCIN/ERYTHROMYCIN/TELITHROMYCIN Escherichia_azithromycin/erythromycin/telithromycin_resistant_23S +NC_004431.1@23S_ribosomal_RNA@23S:237160-240064 2058 23S_A2058T MACROLIDE AZITHROMYCIN/ERYTHROMYCIN/TELITHROMYCIN Escherichia_azithromycin/erythromycin/telithromycin_resistant_23S +NC_004431.1@23S_ribosomal_RNA@23S:237160-240064 2447 23S_G2447T OXAZOLIDINONE LINEZOLID Escherichia_linezolid_resistant_23S +NC_004431.1@23S_ribosomal_RNA@23S:237160-240064 2609 23S_T2609C MACROLIDE TELITHROMYCIN Escherichia_telithromycin_resistant_23S +NC_004431.1@23S_ribosomal_RNA@23S:237160-240064 2611 23S_C2611T MACROLIDE ERYTHROMYCIN/TELITHROMYCIN Escherichia_erythromycin/telithromycin_resistant_23S +NZ_CP041538.1@ampC/blaEC_promoter_region@ampC:1149245-1149489 12 ampC_C-42A BETA-LACTAM CEPHALOSPORIN Escherichia_cephalosporin_resistant_ampC +NZ_CP041538.1@ampC/blaEC_promoter_region@ampC:1149245-1149489 12 ampC_C-42G BETA-LACTAM CEPHALOSPORIN Escherichia_cephalosporin_resistant_ampC +NZ_CP041538.1@ampC/blaEC_promoter_region@ampC:1149245-1149489 12 ampC_C-42T BETA-LACTAM CEPHALOSPORIN Escherichia_cephalosporin_resistant_ampC +NZ_CP041538.1@ampC/blaEC_promoter_region@ampC:1149245-1149489 22 ampC_T-32A BETA-LACTAM CEPHALOSPORIN Escherichia_cephalosporin_resistant_ampC +NZ_CP041538.1@ampC/blaEC_promoter_region@ampC:1149245-1149489 22 ampC_T-32C BETA-LACTAM CEPHALOSPORIN Escherichia_cephalosporin_resistant_ampC +NZ_CP041538.1@ampC/blaEC_promoter_region@ampC:1149245-1149489 22 ampC_T-32G BETA-LACTAM CEPHALOSPORIN Escherichia_cephalosporin_resistant_ampC +NZ_CP041538.1@ampC/blaEC_promoter_region@ampC:1149245-1149489 39 ampC_G-15GG BETA-LACTAM CEPHALOSPORIN Escherichia_cephalosporin_resistant_ampC +NZ_CP041538.1@ampC/blaEC_promoter_region@ampC:1149245-1149489 40 ampC_T-14TGT BETA-LACTAM CEPHALOSPORIN Escherichia_cephalosporin_resistant_ampC +NZ_CP041538.1@ampC/blaEC_promoter_region@ampC:1149245-1149489 43 ampC_C-11T BETA-LACTAM CEPHALOSPORIN Escherichia_cephalosporin_resistant_ampC +NZ_CP095603.1@blaTEM_promoter_region@blaTEM:148777-149952 32 blaTEMp_C32T BETA-LACTAM AMOXICILLIN-CLAVULANIC_ACID/PIPERACILLIN-TAZOBACTAM/TICARCILLIN-CLAVULANIC_ACID Escherichia_amoxicillin-clavulanic_acid/piperacillin-tazobactam/ticarcillin-clavulanic_acid_resistant_blaTEM +NZ_CP095603.1@blaTEM_promoter_region@blaTEM:148777-149952 141 blaTEMp_C141G BETA-LACTAM AMOXICILLIN-CLAVULANIC_ACID/PIPERACILLIN-TAZOBACTAM/TICARCILLIN-CLAVULANIC_ACID Escherichia_amoxicillin-clavulanic_acid/piperacillin-tazobactam/ticarcillin-clavulanic_acid_resistant_blaTEM +NZ_CP095603.1@blaTEM_promoter_region@blaTEM:148777-149952 162 blaTEMp_G162T BETA-LACTAM AMOXICILLIN-CLAVULANIC_ACID/PIPERACILLIN-TAZOBACTAM/TICARCILLIN-CLAVULANIC_ACID Escherichia_amoxicillin-clavulanic_acid/piperacillin-tazobactam/ticarcillin-clavulanic_acid_resistant_blaTEM |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/amrfinderplus-db/ReferenceGeneCatalog.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amrfinderplus-db/ReferenceGeneCatalog.txt Wed Jun 05 14:22:02 2024 +0000 |
| b |
| @@ -0,0 +1,14 @@ +allele gene_family whitelisted_taxa product_name scope type subtype class subclass refseq_protein_accession refseq_nucleotide_accession curated_refseq_start genbank_protein_accession genbank_nucleotide_accession genbank_strand genbank_start genbank_stop refseq_strand refseq_start refseq_stop pubmed_reference blacklisted_taxa synonyms hierarchy_node db_version + aph(3')-IIIa aminoglycoside O-phosphotransferase APH(3')-IIIa core AMR AMR AMINOGLYCOSIDE AMIKACIN/KANAMYCIN WP_063841495.1 NG_047419.1 No AAK62562.1 AF330699.1 + 1562 2356 + 101 895 11600397 aph(3')-III aph(3')-IIIa 2024-05-02.2 + aph(3')-IIIa aminoglycoside O-phosphotransferase APH(3')-IIIa core AMR AMR AMINOGLYCOSIDE AMIKACIN/KANAMYCIN WP_063841507.1 NG_047420.1 No CAD36021.1 AJ490186.1 + 1993 2787 + 101 895 aph(3')-III aph(3')-IIIa 2024-05-02.2 + catA type A-7 chloramphenicol O-acetyltransferase core AMR AMR PHENICOL CHLORAMPHENICOL WP_063843211.1 NG_047572.1 No AAA26615.1 M64281.1 + 208 855 + 101 748 1713259 catA7 2024-05-02.2 + erm(B) 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B) core AMR AMR LINCOSAMIDE/MACROLIDE/STREPTOGRAMIN CLINDAMYCIN/ERYTHROMYCIN/STREPTOGRAMIN B WP_063844601.1 NG_047793.1 No CAA57314.1 X81655.1 + 300 1037 + 101 838 7486927 erm(AM),erm(TE) erm(B) 2024-05-02.2 + mupB mupirocin-resistant isoleucine--tRNA ligase MupB core AMR AMR MUPIROCIN MUPIROCIN WP_063854488.1 NG_048009.1 No AEY83581.1 JQ231224.1 + 91 3192 + 91 3192 22252810 mupB 2024-05-02.2 + optrA ABC-F type ribosomal protection protein OptrA core AMR AMR PHENICOL/OXAZOLIDINONE FLORFENICOL/OXAZOLIDINONE WP_063854496.1 NG_048023.1 No AKA86814.1 KP399637.1 + 31477 33444 + 101 2068 25977397 optrA 2024-05-02.2 + sat4 streptothricin N-acetyltransferase Sat4 core AMR AMR STREPTOTHRICIN STREPTOTHRICIN WP_063854934.1 NG_048070.1 No AAB53445.1 U01945.1 + 374 916 + 101 643 8056285 sat4A sat4 2024-05-02.2 + sul2 sulfonamide-resistant dihydropteroate synthase Sul2 core AMR AMR SULFONAMIDE SULFONAMIDE WP_063855540.1 NG_048108.1 No CAC81945.1 AJ289135.1 + 3990 4805 + 101 916 sul2 2024-05-02.2 + tet(L) tetracycline efflux MFS transporter Tet(L) core AMR AMR TETRACYCLINE TETRACYCLINE WP_063856080.1 NG_048201.1 No AAA22851.1 M11036.1 + 189 1565 + 101 1477 2996983 tetL tet(L) 2024-05-02.2 + tet(M) tetracycline resistance ribosomal protection protein Tet(M) core AMR AMR TETRACYCLINE TETRACYCLINE WP_063856395.1 NG_048234.1 No ABB70053.1 DQ223247.1 + 1 1920 + 1 1920 16565159 tet(M) 2024-05-02.2 + tetA(46) tetracycline efflux ABC transporter Tet(46) subunit A core AMR AMR TETRACYCLINE TETRACYCLINE WP_063856469.1 NG_048312.1 No AET10444.1 HQ652506.1 + 374 2098 + 101 1825 22941900 tetA(46) 2024-05-02.2 + vanG D-alanine--D-serine ligase VanG core AMR AMR GLYCOPEPTIDE VANCOMYCIN WP_063856695.1 NG_048368.1 No AAF71281.1 AF253562.2 + 3715 4764 + 101 1150 11036060 vanA-G,vanG-G vanG 2024-05-02.2 +blaOXA-484 blaOXA OXA-48 family carbapenem-hydrolyzing class D beta-lactamase OXA-484 core AMR AMR BETA-LACTAM CARBAPENEM WP_063864110.1 NG_049766.1 No ALI16502.1 KR401105.1 + 1 798 + 1 798 blaOXA-484 2024-05-02.2 |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/amrfinderplus-db/ReferenceGeneHierarchy.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amrfinderplus-db/ReferenceGeneHierarchy.txt Wed Jun 05 14:22:02 2024 +0000 |
| b |
| b'@@ -0,0 +1,7043 @@\n+node_id\tparent_node_id\tsymbol\tnum_prots\thmm_acc\tprot_acc\tscope\ttype\tsubtype\tclass\tsubclass\tname\tsynonyms\tdisplay_parent\tallele\tdb_version\n+HEAT\tSTRESS\t\t10\t\t\tnon-reported\tSTRESS\tHEAT\t\t\t\t\t0\t0\t2024-05-02.2\n+HTH_5\tMETAL\t\t13\t\t\tnon-reported\tSTRESS\tMETAL\t\t\tArsR/SmtB family metalloregulatory transcriptional repressor\t\t0\t0\t2024-05-02.2\n+IONOPHORE\tAMR\t\t2\t\t\tnon-reported\tAMR\tAMR\t\t\t\t\t0\t0\t2024-05-02.2\n+LHR_hdeD\tHEAT\thdeD-GI\t1\t\t\tplus\tSTRESS\tHEAT\t\t\theat resistance membrane protein HdeD-GI\t\t0\t0\t2024-05-02.2\n+LHR_hsp20A\tHEAT\thsp20\t1\t\t\tplus\tSTRESS\tHEAT\t\t\tsmall heat shock protein sHSP20\t\t0\t0\t2024-05-02.2\n+LHR_hsp20B\tHEAT\tshsP\t1\t\t\tplus\tSTRESS\tHEAT\t\t\tsmall heat shock protein sHSP20-GI\t\t0\t0\t2024-05-02.2\n+LHR_kefB\tHEAT\tkefB-GI\t1\t\t\tplus\tSTRESS\tHEAT\t\t\theat resistance system K+/H+ antiporter KefB-GI\t\t0\t0\t2024-05-02.2\n+LHR_psiE\tHEAT\tpsi-GI\t1\t\t\tplus\tSTRESS\tHEAT\t\t\theat resistance protein PsiE-GI\t\t0\t0\t2024-05-02.2\n+LHR_trx\tHEAT\ttrxLHR\t1\t\t\tplus\tSTRESS\tHEAT\t\t\theat resistance system thioredoxin Trx-GI\t\t0\t0\t2024-05-02.2\n+LHR_yfdX1\tHEAT\tyfdX1\t1\t\t\tplus\tSTRESS\tHEAT\t\t\theat resistance protein YfdX1\t\t0\t0\t2024-05-02.2\n+LHR_yfdX2\tHEAT\tyfdX2\t1\t\t\tplus\tSTRESS\tHEAT\t\t\theat resistance protein YfdX2\t\t0\t0\t2024-05-02.2\n+MATE_efflux\tEFFLUX\t\t8\t\t\tnon-reported\tAMR\tAMR\t\t\tmultidrug efflux MATE transporter\t\t0\t0\t2024-05-02.2\n+METAL\tSTRESS\t\t180\t\t\tnon-reported\tSTRESS\tMETAL\t\t\tMetal Resistance\t\t0\t0\t2024-05-02.2\n+METAL-RND-IM\tMETAL\t\t2\t\t\tnon-reported\tSTRESS\tMETAL\t\t\tcation efflux RND transporter permease subunit\t\t0\t0\t2024-05-02.2\n+MFS_efflux\tEFFLUX\t\t199\t\t\tnon-reported\tAMR\tAMR\t\t\tmultidrug efflux MFS transporter\t\t0\t0\t2024-05-02.2\n+MFS_efflux_CHL\tMFS_efflux\tcml\t48\t\t\tcore\tAMR\tAMR\tPHENICOL\tCHLORAMPHENICOL\tchloramphenicol efflux MFS transporter\t\t0\t0\t2024-05-02.2\n+ACID\tSTRESS\t\t3\t\t\tnon-reported\tSTRESS\tACID\t\t\t\t\t0\t0\t2024-05-02.2\n+ALL\t\t\t8180\t\t\tnon-reported\tROOT\tROOT\t\t\t\t\t0\t0\t2024-05-02.2\n+AME\tAMR\t\t676\t\t\tnon-reported\tAMR\tAMR\t\t\taminoglycoside modifying enzymes\t\t0\t0\t2024-05-02.2\n+AMR\tALL\t\t6990\t\t\tnon-reported\tAMR\tAMR\t\t\t\t\t0\t0\t2024-05-02.2\n+AMR-SUSCEPTIBLE\tAMR\t\t26\t\t\tnon-reported\tAMR\tAMR-SUSCEPTIBLE\t\t\tFamilies implicated in adaptive resistance by mutation\t\t0\t0\t2024-05-02.2\n+BIOCIDE\tSTRESS\t\t64\t\t\tnon-reported\tSTRESS\tBIOCIDE\t\t\t\t\t0\t0\t2024-05-02.2\n+CDF_efflux\tMETAL\t\t2\t\t\tnon-reported\tSTRESS\tMETAL\t\t\tCDF family cation efflux transporter\t\t0\t0\t2024-05-02.2\n+EFFLUX\tAMR\t\t295\t\t\tnon-reported\tAMR\tAMR\t\t\tefflux\t\t0\t0\t2024-05-02.2\n+OM_sidero\tVIRULENCE_Ecoli\t\t27\t\t\tnon-reported\tVIRULENCE\tVIRULENCE\t\t\tTonB-dependent siderophore receptor\t\t0\t0\t2024-05-02.2\n+P-type_ATPase\tMETAL\t\t8\t\t\tnon-reported\tSTRESS\tMETAL\t\t\tmetal-translocating P-type ATPase\t\t0\t0\t2024-05-02.2\n+PERI-SENSOR\tMETAL\t\t1\t\t\tnon-reported\tSTRESS\tMETAL\t\t\tperiplasmic heavy metal sensor\t\t0\t0\t2024-05-02.2\n+RESPONSE_REG\tAMR\t\t30\t\t\tnon-reported\tAMR\tAMR\t\t\tDNA-binding response regulator\t\t0\t0\t2024-05-02.2\n+RND-OM\tEFFLUX\t\t10\t\t\tnon-reported\tAMR\tAMR\t\t\tmultidrug efflux transporter outer membrane subunit\t\t0\t0\t2024-05-02.2\n+RND-peri\tEFFLUX\t\t27\t\t\tnon-reported\tAMR\tAMR\t\t\tmultidrug efflux RND transporter periplasmic adaptor subunit\t\t0\t0\t2024-05-02.2\n+SMR_efflux\tBIOCIDE\tqac\t38\t\t\tcore\tSTRESS\tBIOCIDE\tQUATERNARY AMMONIUM\tQUATERNARY AMMONIUM\tSMR family small multidrug resistance efflux protein\t\t0\t0\t2024-05-02.2\n+STRESS\tALL\t\t257\t\t\tnon-reported\tSTRESS\tSTRESS\t\t\t\t\t0\t0\t2024-05-02.2\n+VIRULENCE\tALL\t\t933\t\t\tnon-reported\tVIRULENCE\tVIRULENCE\t\t\t\t\t0\t0\t2024-05-02.2\n+VIRULENCE_Bcer\tVIRULENCE\t\t62\t\t\tnon-reported\tVIRULENCE\tVIRULENCE\t\t\t\t\t0\t0\t2024-05-02.2\n+VIRULENCE_Burk\tVIRULENCE\t\t2\t\t\tnon-reported\tVIRULENCE\tVIRULENCE\t\t\t\t\t0\t0\t2024-05-02.2\n+VIRULENCE_Cbot\tVIRULENCE\t\t46\t\t\tnon-reported\tVIRULENCE\tVIRULENCE\t\t\t\t\t0\t0\t2024-05-02.2\n+VIRULENCE_Cdiff\tVIRULENCE\t\t7\t\t\tnon-reported\tVIRULENCE\tVIRULENCE\t\t\t\t\t0\t0\t2024-05-02.2\n+VIRULENCE_Cperf\tVIRULENCE\t\t16\t\t\tnon-reported\tVIRULENCE\tVIRULENCE\t\t\t\t\t0\t0\t2024-05-02.2\n+VIRULENCE_Ecoli\tVIRULENCE\t\t629\t\t\tnon-reported\tVIRULENCE\tVIRULENCE\t\t\t\t\t0\t0\t2024-05-02.2\n+VIRULENCE_Lmon\tVIRULENCE\t\t18\t\t\tnon-reported\tVIRULENCE\tVIRULENCE\t\t\t\t\t0\t0\t2024-05-02.2\n+VIRULENCE_Salmo\tVIRULENCE\t\t8\t\t\tnon-re'..b'repeat protein QnrVC3\t\t0\t1\t2024-05-02.2\n+qnrVC4\tqnrVC\tqnrVC4\t1\t\tWP_000361704.1\tcore\tAMR\tAMR\tQUINOLONE\tQUINOLONE\tquinolone resistance pentapeptide repeat protein QnrVC4\t\t0\t1\t2024-05-02.2\n+qnrVC5\tqnrVC\tqnrVC5\t1\t\tWP_000361705.1\tcore\tAMR\tAMR\tQUINOLONE\tQUINOLONE\tquinolone resistance pentapeptide repeat protein QnrVC5\t\t0\t1\t2024-05-02.2\n+qnrVC6\tqnrVC\tqnrVC6\t1\t\tWP_032495607.1\tcore\tAMR\tAMR\tQUINOLONE\tQUINOLONE\tquinolone resistance pentapeptide repeat protein QnrVC6\t\t0\t1\t2024-05-02.2\n+qnrVC7\tqnrVC\tqnrVC7\t1\t\tWP_063866460.1\tcore\tAMR\tAMR\tQUINOLONE\tQUINOLONE\tquinolone resistance pentapeptide repeat protein QnrVC7\t\t0\t1\t2024-05-02.2\n+qnrVC8\tqnrVC\tqnrVC8\t1\t\tWP_206627591.1\tcore\tAMR\tAMR\tQUINOLONE\tQUINOLONE\tquinolone resistance pentapeptide repeat protein QnrVC8\t\t0\t1\t2024-05-02.2\n+qnrVC9\tqnrVC\tqnrVC9\t1\t\tWP_148560450.1\tcore\tAMR\tAMR\tQUINOLONE\tQUINOLONE\tquinolone resistance pentapeptide repeat protein QnrVC9\t\t0\t1\t2024-05-02.2\n+rmtB1\trmtB\trmtB1\t1\t\tWP_012372818.1\tcore\tAMR\tAMR\tAMINOGLYCOSIDE\tAMINOGLYCOSIDE\t16S rRNA (guanine(1405)-N(7))-methyltransferase RmtB1\t\t0\t1\t2024-05-02.2\n+rmtB2\trmtB\trmtB2\t1\t\tWP_063854854.1\tcore\tAMR\tAMR\tAMINOGLYCOSIDE\tAMINOGLYCOSIDE\t16S rRNA (guanine(1405)-N(7))-methyltransferase RmtB2\t\t0\t1\t2024-05-02.2\n+rmtB3\trmtB\trmtB3\t1\t\tWP_048266647.1\tcore\tAMR\tAMR\tAMINOGLYCOSIDE\tAMINOGLYCOSIDE\t16S rRNA (guanine(1405)-N(7))-methyltransferase RmtB3\t\t0\t1\t2024-05-02.2\n+rmtB4\trmtB\trmtB4\t1\t\tWP_032634099.1\tcore\tAMR\tAMR\tAMINOGLYCOSIDE\tAMINOGLYCOSIDE\t16S rRNA (guanine(1405)-N(7))-methyltransferase RmtB4\t\t0\t1\t2024-05-02.2\n+rmtD1\trmtD\trmtD1\t1\t\tWP_019726361.1\tcore\tAMR\tAMR\tAMINOGLYCOSIDE\tAMINOGLYCOSIDE\t16S rRNA (guanine(1405)-N(7))-methyltransferase RmtD1\t\t0\t1\t2024-05-02.2\n+rmtD2\trmtD\trmtD2\t1\t\tWP_063866469.1\tcore\tAMR\tAMR\tAMINOGLYCOSIDE\tAMINOGLYCOSIDE\t16S rRNA (guanine(1405)-N(7))-methyltransferase RmtD2\t\t0\t1\t2024-05-02.2\n+rmtE1\trmtE\trmtE1\t1\t\tWP_063866478.1\tcore\tAMR\tAMR\tAMINOGLYCOSIDE\tAMINOGLYCOSIDE\t16S rRNA (guanine(1405)-N(7))-methyltransferase RmtE1\t\t0\t1\t2024-05-02.2\n+rmtE2\trmtE\trmtE2\t1\t\tWP_063866490.1\tcore\tAMR\tAMR\tAMINOGLYCOSIDE\tAMINOGLYCOSIDE\t16S rRNA (guanine(1405)-N(7))-methyltransferase RmtE2\t\t0\t1\t2024-05-02.2\n+rmtF1\trmtF\trmtF1\t1\t\tWP_015632396.1\tcore\tAMR\tAMR\tAMINOGLYCOSIDE\tAMINOGLYCOSIDE\t16S rRNA (guanine(1405)-N(7))-methyltransferase RmtF1\t\t0\t1\t2024-05-02.2\n+rmtF2\trmtF\trmtF2\t1\t\tWP_023434793.1\tcore\tAMR\tAMR\tAMINOGLYCOSIDE\tAMINOGLYCOSIDE\t16S rRNA (guanine(1405)-N(7))-methyltransferase RmtF2\t\t0\t1\t2024-05-02.2\n+tmexC1\ttmexC\ttmexC1\t1\t\tWP_118842626.1\tcore\tAMR\tAMR\tTETRACYCLINE\tTIGECYCLINE\tmultidrug efflux RND transporter periplasmic adaptor subunit TMexC1\t\t0\t1\t2024-05-02.2\n+tmexC2\ttmexC\ttmexC2\t1\t\tWP_088903431.1\tcore\tAMR\tAMR\tTETRACYCLINE\tTIGECYCLINE\tmultidrug efflux RND transporter periplasmic adaptor subunit TMexC2\t\t0\t1\t2024-05-02.2\n+tmexC3\ttmexC\ttmexC3\t1\t\tWP_034039546.1\tcore\tAMR\tAMR\tTETRACYCLINE\tTIGECYCLINE\tmultidrug efflux RND transporter periplasmic adaptor subunit TMexC3\t\t0\t1\t2024-05-02.2\n+tmexD1\ttmexD\ttmexD1\t1\t\tWP_118842627.1\tcore\tAMR\tAMR\tTETRACYCLINE\tTIGECYCLINE\tmultidrug efflux RND transporter permease subunit TMexD1\t\t0\t1\t2024-05-02.2\n+tmexD2\ttmexD\ttmexD2\t1\t\tWP_027591160.1\tcore\tAMR\tAMR\tTETRACYCLINE\tTIGECYCLINE\tmultidrug efflux RND transporter permease subunit TMexD2\t\t0\t1\t2024-05-02.2\n+tmexD3\ttmexD\ttmexD3\t1\t\tWP_034065037.1\tcore\tAMR\tAMR\tTETRACYCLINE\tTIGECYCLINE\tmultidrug efflux RND transporter permease subunit TMexD3\t\t0\t1\t2024-05-02.2\n+toprJ1\ttoprJ\ttoprJ1\t1\t\tWP_003152694.1\tcore\tAMR\tAMR\tTETRACYCLINE\tTIGECYCLINE\tmultidrug efflux transporter outer membrane subunit TOprJ1\t\t0\t1\t2024-05-02.2\n+toprJ2\ttoprJ\ttoprJ2\t1\t\tWP_088903432.1\tcore\tAMR\tAMR\tTETRACYCLINE\tTIGECYCLINE\tmultidrug efflux transporter outer membrane subunit TOprJ2\t\t0\t1\t2024-05-02.2\n+vanS-B-Delta\tvanS-B\tvanS-B-Delta\t1\t\tWP_063856737.1\tcore\tAMR\tAMR\tGLYCOPEPTIDE\tVANCOMYCIN\tVanB-type vancomycin resistance histidine kinase VanS-B-Delta\t\t0\t1\t2024-05-02.2\n+vga(A)-LC\tvga(A)\tvga(A)-LC\t1\t\tWP_002449123.1\tcore\tAMR\tAMR\tLINCOSAMIDE\tLINCOSAMIDE\tABC-F type ribosomal protection protein Vga(A)-LC\t\t0\t1\t2024-05-02.2\n' |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/amrfinderplus-db/amr_targets.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amrfinderplus-db/amr_targets.fa Wed Jun 05 14:22:02 2024 +0000 |
| b |
| b'@@ -0,0 +1,394 @@\n+>NG_048023.1__optrA\n+ttgtccaaagccacctttgcaattgctagtactaacgcaaaggaggatatgaaaatgcaatacaaaataattaatggtgc\n+cgtttactatgatggtaatatggtgttggaaaacatcggtattgaaatcaatgataatgaaaagattgctattgttggta\n+gaaatggatgtggaaaaacaaccttgctaaaagctattataggcgaaattgaattagaagaaggaactggtgaaagtgag\n+tttcaagtaataaagaccggtaacccttatattagctatttaagacagatgccttttgaagatgaaagtatatcaatggt\n+ggatgaagtccgtacggtatttaagacgcttattgatatggaaaacaagatgaaacagctgatagataaaatggagaatc\n+aatatgatgataaaatcatcaatgaatactctgatatcagtgaaaggtatatggctcttggaggtctaacctaccaaaaa\n+gaatatgaaacgatgattcgtagtatgggttttactgaagcagattataaaaaacccatttctgaattttcaggtggtca\n+gcgaactaagatagcttttataaaaatacttttaacaaagccagacattctattacttgatgaacctactaaccaccttg\n+atatagaaacaatacaatggttggagagttatttgagaagttataaatctacattggttattatttcccatgatagaatg\n+tttcttaatcgaattgtggataaggtttatgaaatcgaatggggagagaccaaatgttataaaggtaattattcagcctt\n+tgaggagcaaaaacgagaaaatcatatcaaacagcaaaaagattacgacttgcaacagatagaaattgaaaggattacac\n+gcttgattgaacgttttcgttataaacctacgaaagctaaaatggtgcaatctaaaattaaattattacagcgtatgcaa\n+atattaaatgcaccagaccaatacgatacaaaaacttatatgtctaaatttcaaccgagaatcagtagttcaaggcaagt\n+attaagtgcttcagaacttgtgataggctatgatactcctcttgcaaaggttaatttcaaccttgaaaggggacagaagc\n+ttggaattgttgggagtaatggtattggtaaatccacgttgcttaaaacacttatgggtggtgtggcagcattgtctgga\n+gattttaaattcggatacaatgttgaaattagctattttgaccaacagcttgctcaaatcagtggagatgatacactatt\n+cgaaatttttcaaagcgaataccctgagctaaatgacacagaggtcagaactgctcttggctcatttcagtttagtggag\n+atgatgtttttagaccggtgtcctctttgtcaggtggagaaaaggttagattgacattatgtaaattattatataaacgt\n+actaatgttttaatcttagatgaaccgacaaaccacatggatattattggaaaagagaatttagagaatatcttatgcag\n+ttatcaaggtacaattatttttgtgtcacatgatagatattttactaataagattgctgacagattacttgtttttgata\n+aggatggtgtagagtttgtacaatctacttatggtgagtacgagaaaaaaaggatgaattctgaaaagccatttaataac\n+attaaagttgagcagaaagtagagaaaaataacacagtaaaaggcgatcgtaactccattgagaaggagaaggttaagaa\n+ggagaaacgaattgaaaagcttgaagtgttaataaatcaatatgatgaagaattagaaagattgaataaaatcatttctg\n+aaccaaacaattcttctgattatatagtactgacggaaatacaaaaatcaattgatgatgttaaaaggtgtcagggtaat\n+tattttaatgaatgggaacagttgatgagagaattggaagttatgtaa\n+>NG_047419.1__aph3p-IIIa\n+atggctaaaatgagaatatcaccggaattgaaaaaactgatcgaaaaataccgctgcgtaaaagatacggaaggaatgtc\n+tcctgctaaggtatataagctggtgggagaaaatgaaaacctatatttaaaaatgacggacagccggtataaagggacca\n+cctatgatgtggaacgggaaaaggacatgatgctatggctggaaggaaagctgcctgttccaaaggtcctgcactttgaa\n+cggcatgatggctggagcaatctgctcatgagtgaggccgatggcgtcctttgctcggaagagtatgaagatgaacaaag\n+ccctgaaaagattatcgagctgtatgcggagtgcatcaggctctttcactccatcgacatatcggattgtccctatacga\n+atagcttagacagccgcttagccgaattggattacttactgaataacgatctggccgatgtggattgcgaaaactgggaa\n+gaagacactccatttaaagatccgcgcgagctgtatgattttttaaagacggaaaagcccgaagaggaacttgtcttttc\n+ccacggcgacctgggagacagcaacatctttgtgaaagatggcaaagtaagtggctttattgatcttgggagaagcggca\n+gggcggacaagtggtatgacattgccttctgcatccggtcgatcagggaggatatcggggaagaacagtatgtcgagcta\n+ttttttgacttactggggatcaagcctgattgggagaaaataaaatattatattttactggatgaattgttttag\n+>NG_048070.1__sat4\n+gtgattacagaaatgaaagcagagcacctgaaagatatcgataaacccagcgaaccatttgaggtgataggtaagattat\n+accgaggtatgaaaacgagaattggacctttacagaattactctatgaagcgccatatttaaaaagctaccaagacgaag\n+aggatgaagaggatgaggaggcagattgccttgaatatattgacaatactgataagataatatatctttactaccaagac\n+gataaatgcgtcggaaaagttaaactgcgaaaaaattggaaccggtacgcttatatagaagatatcgccgtatgtaagga\n+tttcagggggcaaggcataggcagcgcgcttatcaatatatctatagaatgggcaaagcataaaaacttgcatggactaa\n+tgcttgaaacccaggacaataaccttatagcttgtaaattctatcataattgtggtttcaaaatcggctccgtcgatact\n+atgttatacgccaactttgaaaacaactttgaaaaagctgttttctggtatttaaggttttag\n+>NG_048214.1__tetM\n+atgaaaattattaatattggagttttagctcatgttgatgcaggaaaaactaccttaacagaaagcttattatataacag\n+tggagcgattacagaattaggaagcgtggacaaaggtacaacgaggacggataatacgcttttagaacgtcagagaggaa\n+ttacaattcagacaggaataacctcttttcagtgggaaaatacgaaggtgaacatcatagacacgccaggacatatggat\n+ttcttagcagaagtatatcgttcattatcagttttagatggggcaattctactgatttctgcaaaagatttcgtacaagc\n+acaaactcgtatattatttcatgcacttaggaaaatggggattcccacaatcttttttatcaataagattgaccaaaatg\n+gaattgatttatcaacggtttatcaggatattaaagagaaactttctgccgaaattgtaatcaaacagaaggtagaactg\n+tatcctaatat'..b'atttagagcagatcgattcggtagagtttaaggattattccttcagttatcctggtgctgagcgaaa\n+gagcctatcaggcattgattggactatccagcgaggacagacggttggaattgttggtcgtaccggtgcaggaaagacta\n+ccctggttcgacaattcttgcggcaatacccagttggtgagggagaattcttggtcaaccagcaaccgatcgtggactac\n+aaccgacactcgattgaagaaaaaattggttatgtttcccaagaacatattttattttctaagtctatccgtgagaatat\n+agcgcttggtaaaaaaggagccagccaagaagacttgatggaagcagtagcccaagctgcttttgcggatgatctcgagc\n+ggatgtctcatggaatggacaccctgatcggtgagaaaggggtctctgtatcaggaggtcaaaaacagcggatctctttg\n+gcgcgtgccttcttaagagatgcagatctcttgttgttagatgattccctttcggcagtggatgcgaagaccgaacaggc\n+cattattgacaccattcaaaaagaacgaaaagacaagacgaccatcattgtttctcatcgcttgtcggctgtccatcagg\n+ctgattggatcatcgtcttggatcaaggacagattgttgaagaaggcagggctagtgatttattagctcaagagggctgg\n+tattatgaacaataccaacggcaacaaaaacaggaaggagaataa\n+>NG_048009.1__mupB\n+ttggaaaacgagaatataatagaagaacaaaaaatcttaaatttttggaaagaagaaaacattttcaaaaagagtattga\n+taatagaaaaaatgataatccatttgttttttacgatggtcctccaactgccaatggcttaccacatacaggtcacgtgt\n+taggaagagtaataaaagatttatttgctcgatataagacaatgcaaggattttatgttgaaagaaaagctgggtgggat\n+acccatggactacctgtagaacttggtgttgaaaaaaaacttggaattaaggataaaaatgaaatagaaaaatatggaat\n+agaaaaatttataaatgaatgtaaaaatagtgtgtttatgtatgaaaaacagtggagagaatttagtgaactaatcggat\n+attgggtagatatggaaaaaccgtacaaaacaatggataatacgtatatagaatcaatctggtatatattgtctgacttt\n+cataaaaaaggtcttttatacaaagggcataaagttaccccgtattgtccaagctgtgaaacttctttaagttctcatga\n+agtagctcagggatataaggaagtaaaagatatctctgtaatcttaaaatttccgattttagacagtgatgagaatttct\n+tagtttggacgacaactccatggagcttaccaggtaatatagctttagccataaatgctgaagaaatatatgttaaagtt\n+aattatgataatgaaatttttattatcatggaaagtttgttgcaaagtgtttttaaagatgaagacaatatagatatagt\n+aagtaaacataaaggaaaagaatttgtaggaaaagaatacctcgctcctttccctaacaagtctcttatgaacaatgaaa\n+actcatataaagttttacctgctgattttgttacaaataaagatggtacgggtatcgtccatattgctccggcttatggg\n+gaagatgattacaaattagttcaagaaaataatataccctttattaatgttattgattctagaggaaaatataatcaaga\n+ttctcctatttttaaaggagagctagctaaagaatcagatattaacattattaaagaacttacacatttaaatctacttt\n+tcaaaaaagaaaaatatgaacatagctatcctttttgttggagatgtgataatccattaatctattatgcaatggaaggt\n+tggtttataaaaacaacggcttataaaaatgaaataaaggaaaacaatcaaaaaatagaatggtatccagaccatattaa\n+aaatggaaggtttggaaatttcttagataatatgattgattggaatattggtagaaaaagatattggggcactccactaa\n+atatatggaaatgctccacgtgttcccatgagttttcacctaaaagcataaatgatctaatacaacattccattgaagat\n+attccttctgatatagaattacatcgaccttatatagataatgtgaaatgtaaatgtcaaaattgtggtggtgacatgtg\n+tagagaagaagaagtcattgatgtatggtttgatagtggatcgatgccttttgcacaaaatcactatccatttagtggtc\n+ccattcaaaactcatacccagctgactttatagctgaaggagttgatcaaactagagggtggttttatagcttattggtg\n+atttcaacaattttcaaaggggaagcaccttataaaaacgcattgtcattaggacatatattagattccaatggacaaaa\n+aatgtcgaaaagtaaagggaatgttatagatcctatatcaatgataaaaacttatggcgctgattctttaagatggacat\n+tagtttctgacagcgttccttggactaacaaaaggttttcagaaaatatggtggcacaatcaaaatcgagagtaattgat\n+actttaaaaaatatatttaacttctataatatgtatcaaaaaattgataattatgactatactagggatactcctaaaca\n+gctgaatttacttgataattgggctatatctcgaatgaattcagttataaaagaggtagagctgcatttagaaaaatata\n+accctacaaatgcatcaagagctattggggagtttatcaatgaaataagtaattggtatattagaagatctagaagtcga\n+ttttggagtagtgaaatgaatgaggataaaaagagtgcgtattttactcttagacttattttgattaatacttgtaaaat\n+aatagctcctttcaccccatttactagcgaggaaatacatctaaatctcaccaaaaaaagtgtacacttagaagatttcc\n+ctcaagccaaggaagaatatataaatttaaaactagaagaagatatgaataaagttttagatattgtcgaaaaatctaga\n+agcataagaaataacataaacatcaaaacaaaacaaccactttcaaacatgtatatatatgacaataataatcttgataa\n+tgaatttctaagaaaatacaaagacatcattaaagatgaaataaatgttaaaaagataaatattgtttctgatttagaca\n+attttttagaatatgatgtaaaaccgaacttttcaactttaggccctaaattaggaaaagatatgaaacaattccaaatt\n+ttatttaaaaatattaaaaaagaagaaatgaataaactaatcaatgatttcgataaacttcaaaaagtttttgactcttt\n+aggtgtaacaattgaggaaaaggattttattattagtaaaatacctaaaaagggattctctctttcaagcaatgactctg\n+atcgtcttatcattttagacactaatttgactcaagaattaattcgcgaagggtttgtcagagaattaattcgtgttatt\n+caacaactaagaaaacaacagaactttaatattgaagaacgtataaatgtagtaatagacatagattccgatggtttact\n+atcaattaaaaataatatcaatatattgaaagaaaatgtactaattaataatctaaaatttgagaaaagagaaactatga\n+aatattttaaaattaatcagaaagaaattggtattcagttaatgtctagctttacaaattaa\n\\ No newline at end of file\n' |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/amrfinderplus-db/bla.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amrfinderplus-db/bla.tsv Wed Jun 05 14:22:02 2024 +0000 |
| b |
| b'@@ -0,0 +1,257 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HW\tCARBAPENEM\tbla-B\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\n+blaSIM\tCARBAPENEM\tbla-B\t1\t1\t1\t1\t1\t2\t2\t2\t2\t2\t2\t2\t2\t2\t2\n+blaSMB\tCARBAPENEM\tbla-B\t0\t1\t1\t1'..b'RIN\tbla-D\t0\t0\t0\t0\t0\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\n+blaOXY-2\tCEPHALOSPORIN\tbla-A\t11\t11\t14\t15\t16\t18\t21\t22\t22\t22\t27\t28\t29\t29\t29\n+blaOXA-2_fam\tCEPHALOSPORIN\tbla-D\t6\t6\t6\t6\t6\t6\t7\t9\t10\t10\t10\t10\t10\t10\t10\n+blaTLA2\tCEPHALOSPORIN\tbla-A\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\n+blaPEDO-3_fam\tCARBAPENEM\tbla-B\t0\t0\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\n+blaCRD3\tCARBAPENEM\tbla-B\t0\t0\t0\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\n+blaOXY-3\tCEPHALOSPORIN\tbla-A\t1\t1\t1\t1\t1\t1\t1\t1\t1\t3\t3\t3\t3\t3\t3\n+blaOXY-4\tCEPHALOSPORIN\tbla-A\t1\t1\t1\t1\t1\t1\t1\t1\t1\t4\t4\t5\t5\t5\t5\n+blaOXA-5_fam\tBETA-LACTAM\tbla-D\t2\t2\t2\t2\t2\t2\t2\t2\t2\t2\t2\t2\t2\t2\t2\n+blaOXY-5\tCEPHALOSPORIN\tbla-A\t2\t2\t2\t3\t3\t4\t4\t4\t5\t5\t10\t10\t11\t11\t11\n+blaALG6\tCARBAPENEM\tbla-B\t0\t0\t0\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\n+blaOXY-6\tCEPHALOSPORIN\tbla-A\t4\t4\t4\t4\t4\t5\t5\t5\t5\t7\t9\t10\t11\t11\t11\n+blaADC-8_fam\tCEPHALOSPORIN\tbla-C\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\n+blaOXA-10_fam\tBETA-LACTAM\tbla-D\t4\t7\t8\t8\t8\t9\t11\t12\t14\t20\t22\t24\t38\t40\t43\n+blaOXA-10_fam\tCARBAPENEM\tbla-D\t0\t0\t0\t0\t1\t1\t1\t1\t2\t2\t2\t2\t2\t2\t2\n+blaOXA-10_fam\tCEPHALOSPORIN\tbla-D\t11\t11\t11\t11\t12\t12\t12\t12\t14\t15\t15\t15\t15\t15\t15\n+blaALG11\tCARBAPENEM\tbla-B\t0\t0\t0\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\n+blaOXA-12_fam\tBETA-LACTAM\tbla-D\t3\t3\t3\t3\t3\t3\t3\t4\t4\t4\t5\t9\t11\t11\t11\n+blaOXA-22_fam\tBETA-LACTAM\tbla-D\t1\t1\t1\t1\t1\t2\t2\t2\t5\t5\t6\t6\t7\t7\t7\n+blaOXA-23_fam\tCARBAPENEM\tbla-D\t14\t15\t16\t17\t20\t25\t25\t26\t27\t40\t41\t45\t47\t49\t51\n+blaGRD23\tCARBAPENEM\tbla-B\t0\t0\t0\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\n+blaOXA-24_fam\tCARBAPENEM\tbla-D\t6\t6\t7\t7\t7\t8\t8\t8\t9\t9\t10\t11\t12\t12\t13\n+blaGRD33\tCARBAPENEM\tbla-B\t0\t0\t0\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\n+blaOXA-46_fam\tBETA-LACTAM\tbla-D\t3\t4\t4\t4\t4\t4\t4\t4\t5\t6\t6\t6\t6\t6\t6\n+blaOXA-48_fam\tBETA-LACTAM\tbla-D\t0\t0\t0\t0\t0\t0\t0\t0\t1\t1\t1\t1\t2\t7\t9\n+blaOXA-48_fam\tCARBAPENEM\tbla-D\t4\t5\t7\t10\t12\t17\t24\t25\t25\t27\t27\t27\t27\t27\t27\n+blaOXA-48_fam\tCEPHALOSPORIN\tbla-D\t0\t0\t0\t1\t2\t2\t2\t5\t5\t7\t15\t18\t23\t25\t25\n+blaOXA-50_fam\tBETA-LACTAM\tbla-D\t4\t4\t4\t6\t7\t7\t7\t7\t7\t13\t24\t44\t58\t60\t60\n+blaOXA-51_fam\tBETA-LACTAM\tbla-D\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t4\t6\n+blaOXA-51_fam\tCARBAPENEM\tbla-D\t66\t80\t87\t100\t141\t156\t172\t185\t273\t322\t326\t339\t374\t375\t375\n+blaOXA-55_fam\tBETA-LACTAM\tbla-D\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t7\t7\t7\t7\n+blaOXA-55_fam\tCARBAPENEM\tbla-D\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\n+blaOXA-58_fam\tCARBAPENEM\tbla-D\t4\t4\t4\t4\t6\t6\t7\t7\t7\t7\t7\t7\t8\t8\t8\n+blaOXA-60_fam\tBETA-LACTAM\tbla-D\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t1\t1\n+blaOXA-60_fam\tCARBAPENEM\tbla-D\t1\t1\t1\t1\t1\t2\t2\t2\t5\t5\t6\t6\t6\t6\t6\n+blaOXA-61_fam\tBETA-LACTAM\tbla-D\t2\t2\t3\t3\t3\t9\t9\t9\t49\t49\t49\t49\t49\t49\t49\n+blaOXA-62_fam\tCARBAPENEM\tbla-D\t1\t1\t1\t1\t2\t10\t10\t10\t10\t10\t10\t10\t12\t12\t14\n+blaOXA-63_fam\tBETA-LACTAM\tbla-D\t4\t5\t5\t5\t5\t14\t14\t14\t14\t14\t14\t14\t23\t23\t23\n+blaSPN79\tCARBAPENEM\tbla-B\t0\t0\t0\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\n+blaOXA-85_fam\tBETA-LACTAM\tbla-D\t0\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\n+blaOXA-114_fam\tBETA-LACTAM\tbla-D\t7\t7\t14\t21\t21\t21\t23\t23\t23\t26\t26\t26\t26\t26\t26\n+blaOXA-134_fam\tCARBAPENEM\tbla-D\t1\t1\t5\t16\t16\t17\t18\t18\t21\t21\t22\t24\t28\t28\t28\n+blaOXA-143_fam\tBETA-LACTAM\tbla-D\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t3\t3\t3\n+blaOXA-143_fam\tCARBAPENEM\tbla-D\t2\t2\t3\t5\t5\t6\t6\t6\t7\t8\t8\t8\t8\t8\t8\n+blaOXA-184_fam\tBETA-LACTAM\tbla-D\t0\t0\t2\t2\t2\t8\t8\t8\t39\t39\t39\t39\t39\t39\t39\n+blaOXA-211_fam\tBETA-LACTAM\tbla-D\t0\t0\t0\t0\t0\t0\t1\t1\t5\t5\t5\t6\t6\t7\t7\n+blaOXA-211_fam\tCARBAPENEM\tbla-D\t0\t2\t2\t7\t8\t9\t10\t10\t11\t11\t11\t11\t11\t11\t11\n+blaOXA-213_fam\tCARBAPENEM\tbla-D\t0\t1\t2\t32\t34\t38\t42\t47\t51\t67\t67\t86\t97\t99\t102\n+blaOXA-214_fam\tBETA-LACTAM\tbla-D\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t2\t2\t2\t2\t2\n+blaOXA-214_fam\tCARBAPENEM\tbla-D\t0\t2\t2\t4\t4\t4\t4\t4\t5\t5\t5\t5\t5\t5\t5\n+blaOXA-229_fam\tCARBAPENEM\tbla-D\t0\t0\t3\t8\t9\t9\t9\t9\t10\t15\t17\t23\t25\t26\t26\n+blaOXA-266_fam\tBETA-LACTAM\tbla-D\t0\t0\t0\t1\t1\t1\t1\t1\t2\t2\t2\t2\t2\t2\t2\n+blaOXA-274_fam\tCARBAPENEM\tbla-D\t0\t0\t0\t2\t4\t5\t5\t5\t5\t5\t5\t6\t6\t6\t6\n+blaOXA-286_fam\tCARBAPENEM\tbla-D\t0\t0\t0\t10\t13\t13\t13\t15\t15\t15\t15\t15\t16\t17\t17\n+blaOXA-364_fam\tBETA-LACTAM\tbla-D\t0\t0\t1\t1\t1\t2\t3\t3\t3\t5\t5\t5\t5\t5\t5\n+blaOXA-372_fam\tCARBAPENEM\tbla-D\t0\t0\t0\t0\t1\t1\t1\t1\t2\t2\t2\t3\t3\t3\t3\n+blaOXA-493_fam\tBETA-LACTAM\tbla-D\t0\t0\t0\t0\t0\t1\t2\t2\t2\t2\t2\t2\t2\t2\t2\n+blaOXA-542_fam\tCARBAPENEM\tbla-D\t0\t0\t0\t0\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\n+blaOXA-548_fam\tBETA-LACTAM\tbla-D\t0\t0\t0\t0\t0\t0\t0\t6\t6\t6\t6\t6\t6\t6\t6\n+blaOXA-576_fam\tBETA-LACTAM\tbla-D\t0\t0\t0\t0\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\n+blaOXA-727_fam\tBETA-LACTAM\tbla-D\t0\t0\t0\t0\t0\t0\t0\t0\t2\t2\t2\t2\t2\t2\t2\n+\n' |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/amrfinderplus-db/database_format_version.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amrfinderplus-db/database_format_version.txt Wed Jun 05 14:22:02 2024 +0000 |
| b |
| @@ -0,0 +1,1 @@ +3.12.1 |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/amrfinderplus-db/fam.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amrfinderplus-db/fam.tab Wed Jun 05 14:22:02 2024 +0000 |
| b |
| b'@@ -0,0 +1,2089 @@\n+#node_id\tparent_node_id\tgene_symbol\thmm_id\thmm_tc1\thmm_tc2\tblastrule_complete_ident\tblastrule_complete_wp_coverage\tblastrule_complete_br_coverage\tblastrule_partial_ident\tblastrule_partial_wp_coverage\tblastrule_partial_br_coverage\treportable\ttype\tsubtype\tclass\tsubclass\tfamily_name\n+ACID\tSTRESS\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tACID\t\t\t\n+ALL\t\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\t\t\t\t\t\n+AME\tAMR\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\taminoglycoside modifying enzymes\n+AMR\tALL\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\t\n+BIOCIDE\tSTRESS\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tBIOCIDE\t\t\t\n+BcII\tbla-B1\tbla2\tNF033095.1\t500.00\t500.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tBETA-LACTAM\tCARBAPENEM\tBcII family subclass B1 metallo-beta-lactamase\n+CDF_efflux\tMETAL\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tMETAL\t\t\tCDF family cation efflux transporter\n+CMY2-MIR-ACT-EC\tbla-C\tampC\tNF012173.1\t680.00\t680.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tBETA-LACTAM\tBETA-LACTAM\tCMY2/MIR/ACT/EC family class C beta-lactamase\n+EFFLUX\tAMR\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\tefflux\n+HARLDQ_not_B3\tbla-B3\t-\tNF000405.1\t350.00\t350.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\tHARLDQ motif MBL-fold protein\n+HEAT\tSTRESS\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tHEAT\t\t\t\n+HTH_5\tMETAL\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tMETAL\t\t\tArsR/SmtB family metalloregulatory transcriptional repressor\n+IONOPHORE\tAMR\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\t\n+LHR_hdeD\tHEAT\thdeD-GI\t-\t0.00\t0.00\t90.00\t90.00\t90.00\t93.00\t90.00\t25.00\t1\tSTRESS\tHEAT\t\t\theat resistance membrane protein HdeD-GI\n+LHR_hsp20A\tHEAT\thsp20\t-\t0.00\t0.00\t94.00\t90.00\t90.00\t96.00\t90.00\t25.00\t1\tSTRESS\tHEAT\t\t\tsmall heat shock protein sHSP20\n+LHR_hsp20B\tHEAT\tshsP\t-\t0.00\t0.00\t93.00\t90.00\t90.00\t94.00\t90.00\t25.00\t1\tSTRESS\tHEAT\t\t\tsmall heat shock protein sHSP20-GI\n+LHR_kefB\tHEAT\tkefB-GI\t-\t0.00\t0.00\t86.00\t90.00\t90.00\t90.00\t90.00\t25.00\t1\tSTRESS\tHEAT\t\t\theat resistance system K+/H+ antiporter KefB-GI\n+LHR_psiE\tHEAT\tpsi-GI\t-\t0.00\t0.00\t88.00\t90.00\t90.00\t90.00\t90.00\t25.00\t1\tSTRESS\tHEAT\t\t\theat resistance protein PsiE-GI\n+LHR_trx\tHEAT\ttrxLHR\t-\t0.00\t0.00\t85.00\t90.00\t90.00\t90.00\t90.00\t25.00\t1\tSTRESS\tHEAT\t\t\theat resistance system thioredoxin Trx-GI\n+LHR_yfdX1\tHEAT\tyfdX1\t-\t0.00\t0.00\t88.00\t90.00\t90.00\t90.00\t90.00\t25.00\t1\tSTRESS\tHEAT\t\t\theat resistance protein YfdX1\n+LHR_yfdX2\tHEAT\tyfdX2\t-\t0.00\t0.00\t90.00\t90.00\t90.00\t90.00\t90.00\t25.00\t1\tSTRESS\tHEAT\t\t\theat resistance protein YfdX2\n+MATE_efflux\tEFFLUX\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\tmultidrug efflux MATE transporter\n+METAL-RND-IM\tMETAL\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tMETAL\t\t\tcation efflux RND transporter permease subunit\n+METAL\tSTRESS\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tMETAL\t\t\tMetal Resistance\n+MFS_efflux_CHL\tMFS_efflux\tcml\t-\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tPHENICOL\tCHLORAMPHENICOL\tchloramphenicol efflux MFS transporter\n+MFS_efflux_qac\tBIOCIDE\tqac\tNF000089.1\t900.00\t900.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tSTRESS\tBIOCIDE\tQUATERNARY AMMONIUM\tQUATERNARY AMMONIUM\tQacA/B family quaternary ammonium compound efflux MFS transporter\n+MFS_efflux\tEFFLUX\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\tmultidrug efflux MFS transporter\n+MerP_Gneg\tmerP\tmerP\tTIGR02052.1\t92.55\t92.55\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t1\tSTRESS\tMETAL\tMERCURY\tMERCURY\tmercury resistance system periplasmic binding protein MerP\n+OM_sidero\tVIRULENCE_Ecoli\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tVIRULENCE\tVIRULENCE\t\t\tTonB-dependent siderophore receptor\n+P-type_ATPase\tMETAL\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tMETAL\t\t\tmetal-translocating P-type ATPase\n+PERI-SENSOR\tMETAL\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tMETAL\t\t\tperiplasmic heavy metal sensor\n+RESPONSE_REG\tAMR\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\tDNA-binding response regulator\n+RND-IM\tEFFLUX\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\tmultidrug efflux RND transporter permease subunit\n+RND-OM\t'..b'MIN\tstreptogramin B lyase Vgb(A)\n+vgb(B)\tvgb\tvgb(B)\tNF000096.1\t600.00\t600.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin B lyase Vgb(B)\n+vgb(C)\tvgb\tvgbC\t-\t0.00\t0.00\t84.00\t90.00\t90.00\t88.00\t90.00\t25.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin B lyase Vgb(C)\n+vgb\tAMR\tvgb\t-\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin B lyase\n+vip\tVIRULENCE_Lmon\tvip\tNF033201.1\t600.00\t400.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t1\tVIRULENCE\tVIRULENCE\t\t\tcell invasion LPXTG protein Vip\n+virF_Yersin\tVIRULENCE_Yersi\tvirF\t-\t0.00\t0.00\t90.00\t90.00\t90.00\t93.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\tvirulence regulon transcriptional activator VirF\n+virF\tVIRULENCE_Ecoli\tvirF\t-\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t1\tVIRULENCE\tVIRULENCE\t\t\tAraC family invasion system transcriptional regulator VirF\n+vmlR\tabc-f\tvmlR\t-\t0.00\t0.00\t90.00\t90.00\t90.00\t96.00\t90.00\t25.00\t2\tAMR\tAMR\tLINCOSAMIDE/PLEUROMUTILIN/STREPTOGRAMIN\tLINCOMYCIN/TIAMULIN/VIRGINIAMYCIN M\tABC-F type ribosomal protection protein VmlR\n+vph\tAMR\tvph\tNF000088.1\t400.00\t400.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tTUBERACTINOMYCIN\tVIOMYCIN\tviomycin phosphotransferase\n+yadA\tVIRULENCE_Yersi\tyadA\tNF033478.1\t750.00\t425.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t1\tVIRULENCE\tVIRULENCE\t\t\ttrimeric autotransporter adhesin YadA\n+ybtP\tVIRULENCE\tybtP\t-\t0.00\t0.00\t85.00\t90.00\t90.00\t96.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\tyersiniabactin ABC transporter ATP-binding/permease protein YbtP\n+ybtQ\tVIRULENCE\tybtQ\t-\t0.00\t0.00\t85.00\t90.00\t90.00\t96.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\tyersiniabactin ABC transporter ATP-binding/permease protein YbtQ\n+yfeA\tVIRULENCE\tyfeA\t-\t0.00\t0.00\t83.00\t90.00\t90.00\t88.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\tiron/manganese ABC transporter substrate-binding protein YfeA\n+yfeB\tVIRULENCE\tyfeB\t-\t0.00\t0.00\t86.00\t90.00\t90.00\t96.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\tiron/manganese ABC transporter ATP-binding protein YfeB\n+yfeD\tVIRULENCE\tyfeD\t-\t0.00\t0.00\t88.00\t90.00\t90.00\t92.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\tiron/manganese ABC transporter permease subunit YfeD\n+ymoA\tVIRULENCE_Yersi\tymoA\t-\t0.00\t0.00\t94.00\t90.00\t90.00\t96.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\texpression modulating protein YmoA\n+yopB\tVIRULENCE_Yersi\tyopB\t-\t0.00\t0.00\t90.00\t90.00\t90.00\t93.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\ttype III secretion system translocon subunit YopB\n+yopD\tVIRULENCE_Yersi\tyopD\t-\t0.00\t0.00\t90.00\t90.00\t90.00\t93.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\ttype III secretion system translocon subunit YopD\n+yopE\tVIRULENCE_Yersi\tyopE\t-\t0.00\t0.00\t92.00\t90.00\t90.00\t96.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\ttype III secretion system effector GTPase activator YopE\n+yopH\tVIRULENCE_Yersi\tyopH\t-\t0.00\t0.00\t94.00\t90.00\t90.00\t96.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\tT3SS effector protein-tyrosine-phosphatase YopH\n+yopJ_gen\tVIRULENCE_Yersi\tyopJ\tNF040632.1\t610.00\t610.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t1\tVIRULENCE\tVIRULENCE\t\t\tYopJ/YopP family T3SS effector serine/threonine acetyltransferase\n+yopM\tVIRULENCE_Yersi\tyopM\t-\t0.00\t0.00\t85.00\t90.00\t90.00\t90.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\ttype III secretion system effector YopM\n+yopO\tVIRULENCE_Yersi\tyopO\t-\t0.00\t0.00\t94.00\t90.00\t90.00\t96.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\ttype III secretion system effector protein kinase YopO/YpkA\n+yopT\tVIRULENCE_Yersi\tyopT\t-\t0.00\t0.00\t92.00\t90.00\t90.00\t96.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\tT3SS effector cysteine protease YopT\n+ystA\tVIRULENCE_Yersi\tystA\t-\t0.00\t0.00\t94.00\t90.00\t90.00\t96.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\tST-I family heat-stable enterotoxin YstA\n+ystB\tVIRULENCE_Yersi\tystB\t-\t0.00\t0.00\t94.00\t90.00\t90.00\t96.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\tST-I family heat-stable enterotoxin YstB\n+ystC\tVIRULENCE_Yersi\tystC\t-\t0.00\t0.00\t94.00\t90.00\t90.00\t96.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\tST-I family heat-stable enterotoxin YstC\n+zbmA\tble\tzbmA\tNF000479.1\t280.00\t280.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tBLEOMYCIN\tZORBAMYCIN\tzorbamycin binding protein ZbmA\n' |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/amrfinderplus-db/mcr.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amrfinderplus-db/mcr.tsv Wed Jun 05 14:22:02 2024 +0000 |
| b |
| @@ -0,0 +1,11 @@ +Family Subclass Ambler_class 2010 2011 2012 2013 2014 2015 2016 2017 2018 2019 2020 2021 2022 2023 2024 +mcr-1 COLISTIN 0 0 0 0 0 1 5 14 18 23 31 34 35 37 37 +mcr-2 COLISTIN 0 0 0 0 0 0 1 3 3 3 7 8 8 8 8 +mcr-3 COLISTIN 0 0 0 0 0 0 2 16 28 29 40 40 41 41 41 +mcr-4 COLISTIN 0 0 0 0 0 0 0 2 6 6 6 7 7 8 9 +mcr-5 COLISTIN 0 0 0 0 0 1 1 1 3 4 4 4 4 5 5 +mcr-6 COLISTIN 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 +mcr-7 COLISTIN 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 +mcr-8 COLISTIN 0 0 0 0 0 0 1 1 4 4 4 4 4 4 4 +mcr-10 COLISTIN 0 0 0 0 0 0 0 0 0 1 1 4 5 5 5 + |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/amrfinderplus-db/qnr.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amrfinderplus-db/qnr.tsv Wed Jun 05 14:22:02 2024 +0000 |
| b |
| @@ -0,0 +1,8 @@ +Family Subclass Ambler_class 2010 2011 2012 2013 2014 2015 2016 2017 2018 2019 2020 2021 2022 2023 2024 +qnrA QUINOLONE 7 7 7 7 7 7 7 8 9 9 11 12 12 12 12 +qnrB QUINOLONE 16 27 30 45 49 54 78 79 81 82 84 85 85 87 87 +qnrD QUINOLONE 1 1 1 1 2 2 3 3 3 3 3 3 3 3 3 +qnrE QUINOLONE 0 0 0 1 1 1 2 3 4 4 4 4 4 4 4 +qnrS QUINOLONE 3 6 7 9 10 10 12 13 14 14 14 14 14 14 14 +qnrVC QUINOLONE 3 4 4 6 7 7 7 7 7 8 8 9 9 9 9 + |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/amrfinderplus-db/taxgroup.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amrfinderplus-db/taxgroup.tab Wed Jun 05 14:22:02 2024 +0000 |
| b |
| @@ -0,0 +1,2 @@ +#taxgroup gpipe_taxgroup number_of_nucl_ref_genes +Escherichia Escherichia_coli_Shigella 6 |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/amrfinderplus-db/version.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amrfinderplus-db/version.txt Wed Jun 05 14:22:02 2024 +0000 |
| b |
| @@ -0,0 +1,1 @@ +2024-05-02.2 |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/amrfinderplus_database.loc --- a/test-data/amrfinderplus_database.loc Sun Feb 11 00:56:12 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,8 +0,0 @@ -# this is a tab separated file describing the location of amrfinderplus database -# -# the columns are: -# value, name, path -# -# for example -amrfinderplus_V3.10_2022-10-11.2 V3.10-2022-10-11.2 ${__HERE__}/amrfinderplus-db/latest -amrfinderplus_V3.6_2020-03-20.1 V3.6-2020-03-20.1 ${__HERE__}/amrfinderplus-db/latest |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/amrfinderplus_versioned_database.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amrfinderplus_versioned_database.loc Wed Jun 05 14:22:02 2024 +0000 |
| b |
| @@ -0,0 +1,7 @@ +# this is a tab separated file describing the location of amrfinderplus database +# +# the columns are: +# value, name, db_version, path +# +# for example +amrfinderplus_V3.12_2024-05-02.2 V3.12-2024-05-02.2 3.12 ${__HERE__}/amrfinderplus-db/ |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 test-data/bakta_database.loc --- a/test-data/bakta_database.loc Sun Feb 11 00:56:12 2024 +0000 +++ b/test-data/bakta_database.loc Wed Jun 05 14:22:02 2024 +0000 |
| b |
| @@ -8,3 +8,4 @@ V0.0_date_test 7190015 1.5 ${__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 +V5.1_light_2024-01-19 10522951 1.7 ${__HERE__}/V5.1_light_2024-01-19 |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 tool-data/amrfinderplus_database.loc.sample --- a/tool-data/amrfinderplus_database.loc.sample Sun Feb 11 00:56:12 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,11 +0,0 @@ -# this is a tab separated file describing the location of amrfinderplus database -# -# the columns are: -# value, name, path -# -# for example -2022-11-10_15:48 2022-10-11.2 ${__HERE__} -amrfinderplus_V3.10_2022-10-11.2 V3.10-2022-10-11.2 /tmp/tmp3as7lw95/galaxy-dev/tool-data/amrfinderplus-db/amrfinderplus_V3.10_2022-10-11.2 -amrfinderplus_V3.6_2020-03-20.1 V3.6-2020-03-20.1 /tmp/tmp3as7lw95/galaxy-dev/tool-data/amrfinderplus-db/amrfinderplus_V3.6_2020-03-20.1 -amrfinderplus_V3.10_2022-10-11.2 V3.10-2022-10-11.2 /tmp/tmpqjc1v8il/galaxy-dev/tool-data/amrfinderplus-db/amrfinderplus_V3.10_2022-10-11.2 -amrfinderplus_V3.6_2020-03-20.1 V3.6-2020-03-20.1 /tmp/tmpqjc1v8il/galaxy-dev/tool-data/amrfinderplus-db/amrfinderplus_V3.6_2020-03-20.1 |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 tool-data/amrfinderplus_versioned_database.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/amrfinderplus_versioned_database.loc.sample Wed Jun 05 14:22:02 2024 +0000 |
| b |
| @@ -0,0 +1,7 @@ +# this is a tab separated file describing the location of amrfinderplus database +# +# the columns are: +# value, name, db_version, path +# +# for example +#amrfinderplus_V3.12_2024-05-02.2 V3.12-2024-05-02.2 3.12 path-to-db |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Sun Feb 11 00:56:12 2024 +0000 +++ b/tool_data_table_conf.xml.sample Wed Jun 05 14:22:02 2024 +0000 |
| b |
| @@ -4,8 +4,8 @@ <columns>value, dbkey, bakta_version, path</columns> <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 name="amrfinderplus_versioned_database" comment_char="#"> + <columns>value, name, db_version, path</columns> + <file path="tool-data/amrfinderplus_versioned_database.loc.sample"/> </table> </tables> |
| b |
| diff -r 92eee5f31117 -r ba6990f72184 tool_data_table_conf.xml.test --- a/tool_data_table_conf.xml.test Sun Feb 11 00:56:12 2024 +0000 +++ b/tool_data_table_conf.xml.test Wed Jun 05 14:22:02 2024 +0000 |
| b |
| @@ -4,8 +4,8 @@ <columns>value, dbkey, bakta_version, path</columns> <file path="${__HERE__}/test-data/bakta_database.loc" /> </table> - <table name="amrfinderplus_database" comment_char="#"> - <columns>value, name, path</columns> - <file path="${__HERE__}/test-data/amrfinderplus_database.loc" /> + <table name="amrfinderplus_versioned_database" comment_char="#"> + <columns>value, name, db_version, path</columns> + <file path="${__HERE__}/test-data/amrfinderplus_versioned_database.loc" /> </table> </tables> |
