| Next changeset 1:ec82fac4eb4b (2021-10-23) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e" |
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added:
hamronize_tool.xml macros.xml test-data/abricate/report.tsv test-data/ariba/report.tsv test-data/hamronized_abricate.json test-data/hamronized_abricate.tsv test-data/hamronized_ariba.json test-data/hamronized_ariba.tsv test-data/hamronized_rgi.json test-data/hamronized_rgi.tsv test-data/rgi/rgi.json test-data/rgi/rgi.txt test-data/summary.json test-data/summary.tsv |
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| diff -r 000000000000 -r d2590ecc4189 hamronize_tool.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hamronize_tool.xml Tue Mar 16 12:38:42 2021 +0000 |
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| b'@@ -0,0 +1,200 @@\n+<tool id="hamronize_tool" name="hamronize" version="@VERSION@+galaxy0">\n+ <description> parse multiple Antimicrobial Resistance Analysis Reports into a common data structure</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+\n+ <expand macro="requirements" />\n+ <expand macro="version_command" />\n+\n+ <command detect_errors="exit_code"><![CDATA[\n+ #set $extra_2_params = str("ariba,srax,csstar,groot").split(",")\n+ #set $extra_1_param = $extra_2_params + str("amrfinderplus,rgi,resfinder4,deeparg,kmerresistance,srst2,amrplusplus,resfarms").split(",")\n+ \n+ hamronize \n+ ${select_tool.tool}\n+ --analysis_software_version \'${analysis_software_version}\'\n+ --reference_database_version \'${reference_database_version}\'\n+ --format ${output_format}\n+ #if $output_format == "tsv" \n+ --output hamronized.tsv\n+ #else\n+ --output hamronized.json\n+ #end if \n+ \n+ #if $select_tool.tool in $extra_1_param\n+ --input_file_name $select_tool.input_file_name\n+ #end if\n+ \n+ #if $select_tool.tool in $extra_2_params\n+ --reference_database_id $select_tool.reference_database_id\n+ #end if\n+ \n+ $report\n+ ]]> </command>\n+\n+ <inputs>\n+ <param name="report" type="data" format="txt,tabular,tsv" label="Report file"/>\n+ <conditional name="select_tool">\n+ <param name="tool" type="select" label="Tool">\n+ <option value="abricate" selected="true">abricate</option>\n+ <option value="amrfinderplus">amrfinderplus</option>\n+ <option value="ariba">ariba</option>\n+ <option value="rgi">rgi</option>\n+ <option value="resfinder">resfinder</option>\n+ <option value="resfinder4">resfinder4</option>\n+ <option value="srax">srax</option>\n+ <option value="deeparg">deeparg</option>\n+ <option value="kmerresistance">kmerresistance</option>\n+ <option value="srst2">srst2</option>\n+ <option value="staramr">staramr</option>\n+ <option value="csstar">csstar</option>\n+ <option value="amrplusplus">amrplusplus</option>\n+ <option value="resfams">resfams</option>\n+ <option value="groot">groot</option>\n+ </param>\n+ <when value="abricate" />\n+ <when value="resfinder" />\n+ <when value="staramr" />\n+ <when value="amrfinderplus">\n+ <expand macro="input_file_name"/>\n+ </when>\n+\n+ <when value="ariba">\n+ <expand macro="input_file_name"/>\n+ <expand macro="reference_database_id"/>\n+ </when>\n+\n+ <when value="rgi">\n+ <expand macro="input_file_name"/>\n+ </when>\n+\n+ <when value="resfinder4">\n+ <expand macro="input_file_name"/>\n+ </when>\n+\n+ <when value="srax">\n+ <expand macro="input_file_name"/>\n+ <expand macro="reference_database_id"/>\n+ </when>\n+\n+ <when value="deeparg">\n+ <expand macro="input_file_name"/>\n+ </when>\n+\n+ <when value="kmerresistance">\n+ <expand macro="input_file_name"/>\n+ </when>\n+\n+ <when value="srst2">\n+ <expand macro="input_file_name"/>\n+ </when>\n+\n+ <when value="csstar">\n+ <expand macro="input_file_name"/>\n+ <expand macro="reference_database_id"/>\n+ </when>\n+\n+ <when value="amrplusplus">\n+ <expand macro="input_file_name"/>\n+ </when>\n+\n+ <when value="resfams">\n+ <expand macro="input_file_name"/>\n+ </when>\n+\n+ <when v'..b'puts>\n+ <tests>\n+ <!-- abricate -->\n+ <test expect_num_outputs="1">\n+ <param name="report" value="abricate/report.tsv" ftype="tsv" />\n+ <param name="tool" value="abricate" />\n+ <param name="output_format" value="tsv" />\n+ <param name="reference_database_version" value="db_v_1" />\n+ <param name="analysis_software_version" value="tool_v_1" />\n+ <output name="output_tsv" ftype="tsv" file="hamronized_abricate.tsv" />\n+ </test>\n+ <test expect_num_outputs="1">\n+ <param name="report" value="abricate/report.tsv" ftype="tsv" />\n+ <param name="tool" value="abricate" />\n+ <param name="output_format" value="json" />\n+ <param name="reference_database_version" value="db_v_1" />\n+ <param name="analysis_software_version" value="tool_v_1" />\n+ <output name="output_json" ftype="json" file="hamronized_abricate.json" />\n+ </test>\n+ <!-- ariba -->\n+ <test expect_num_outputs="1">\n+ <param name="report" value="ariba/report.tsv" ftype="tsv" />\n+ <param name="tool" value="ariba" />\n+ <param name="output_format" value="tsv" />\n+ <param name="reference_database_version" value="db_v_1" />\n+ <param name="analysis_software_version" value="ariba_v1" />\n+ <param name="input_file_name" value="ariba_report" />\n+ <param name="reference_database_id" value="dbname" />\n+ <output name="output_tsv" ftype="tsv" file="hamronized_ariba.tsv" />\n+ </test>\n+ <!-- rgi -->\n+ <test expect_num_outputs="1">\n+ <param name="report" value="rgi/rgi.txt" ftype="txt" />\n+ <param name="tool" value="rgi" />\n+ <param name="output_format" value="tsv" />\n+ <param name="reference_database_version" value="card_v1" />\n+ <param name="analysis_software_version" value="rgi_v1" />\n+ <param name="input_file_name" value="rgi_report" />\n+ <output name="output_tsv" ftype="tsv" file="hamronized_rgi.tsv" />\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+ **What it does**\n+ Hamronize parse multiple Antimicrobial Resistance Analysis Reports into a common data structure\n+\n+ **Inputs**\n+ \n+ ::\n+\n+ Tools with hAMRonizable reports:\n+ {abricate,amrfinderplus,ariba,rgi,resfinder,resfinder4,srax,deeparg,kmerresistance,srst2,staramr,csstar,amrplusplus,resfams,groot}\n+ abricate hAMRonize abricate\'s output report i.e., OUTPUT.tsv\n+ amrfinderplus hAMRonize amrfinderplus\'s output report i.e., OUTPUT.tsv\n+ ariba hAMRonize ariba\'s output report i.e., OUTDIR/OUTPUT.tsv\n+ rgi hAMRonize rgi\'s output report i.e., OUTPUT.txt or OUTPUT_bwtoutput.gene_mapping_data.txt\n+ resfinder hAMRonize resfinder\'s output report i.e., data_resfinder.json\n+ resfinder4 hAMRonize resfinder4\'s tabular output report i.e., ResFinder_results_tab.txt\n+ srax hAMRonize srax\'s output report i.e., sraX_detected_ARGs.tsv\n+ deeparg hAMRonize deeparg\'s output report i.e., OUTDIR/OUTPUT.mapping.ARG\n+ kmerresistance hAMRonize kmerresistance\'s output report i.e., OUTPUT.KmerRes\n+ srst2 hAMRonize srst2\'s output report i.e., OUTPUT_srst2_report.tsv\n+ staramr hAMRonize staramr\'s output report i.e., resfinder.tsv\n+ csstar hAMRonize csstar\'s output report i.e., OUTPUT.tsv\n+ amrplusplus hAMRonize amrplusplus\'s output report i.e., gene.tsv\n+ resfams hAMRonize resfams\'s output report i.e., resfams.tblout\n+ groot hAMRonize groot\'s output report i.e., OUTPUT.tsv (from `groot report`)\n+ \n+\n+\n+ ::\n+ \n+ More: https://github.com/pha4ge/hAMRonization/#usage\n+\n+ ]]> </help>\n+</tool>\n' |
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| diff -r 000000000000 -r d2590ecc4189 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Mar 16 12:38:42 2021 +0000 |
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| @@ -0,0 +1,29 @@ +<macros> + <token name="@VERSION@">1.0.3</token> + + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">hamronization</requirement> + </requirements> + </xml> + + <xml name="input_file_name"> + <param name="input_file_name" type="text" label="Input file name" help="Sample name which was scanned with the tool"></param> + </xml> + + <xml name="reference_database_id"> + <param name="reference_database_id" type="text" label="Reference database ID" help="String containing the reference_database_id of this tool"></param> + </xml> + + <xml name="reference_database_version"> + <param name="reference_database_version" type="text" label="Reference database version"></param> + </xml> + + <xml name="analysis_software_version"> + <param name="analysis_software_version" type="text" label="Analysis software version"></param> + </xml> + + <xml name="version_command"> + <version_command>hamronize --version</version_command> + </xml> +</macros> \ No newline at end of file |
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| diff -r 000000000000 -r d2590ecc4189 test-data/abricate/report.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abricate/report.tsv Tue Mar 16 12:38:42 2021 +0000 |
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| @@ -0,0 +1,8 @@ +#FILE SEQUENCE START END STRAND GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY DATABASE ACCESSION PRODUCT RESISTANCE +GCF_010120755.1_ASM1012075v1_genomic.fna NZ_CP039729.1 656118 657620 + eat(A) 1-1503/1503 =============== 0/0 100.00 100.00 ncbi NG_047762.1 ABC-F type ribosomal protection protein Eat(A) PLEUROMUTILIN +GCF_010120755.1_ASM1012075v1_genomic.fna NZ_CP039729.1 2163439 2163987 - aacA-ENT1 1-549/549 =============== 0/0 100.00 100.00 ncbi NG_052371.1 aminoglycoside 6'-N-acetyltransferase AMINOGLYCOSIDE +GCF_010120755.1_ASM1012075v1_genomic.fna NZ_CP039729.1 2564038 2565516 - msr(C) 1-1479/1479 =============== 0/0 100.00 98.92 ncbi NG_048003.1 ABC-F type ribosomal protection protein Msr(C) MACROLIDE +GCF_010120755.1_ASM1012075v1_genomic.fna NZ_CP039730.1 43619 44197 - vanX-M 1-579/609 =============== 0/0 95.07 100.00 ncbi NG_048495.1 D-Ala-D-Ala dipeptidase VanX-M VANCOMYCIN +GCF_010120755.1_ASM1012075v1_genomic.fna NZ_CP039730.1 44203 45234 - vanM 1-1032/1032 =============== 0/0 100.00 100.00 ncbi NG_048396.1 D-alanine--(R)-lactate ligase VanM VANCOMYCIN +GCF_010120755.1_ASM1012075v1_genomic.fna NZ_CP039730.1 45227 46207 - vanH-M 1-981/981 =============== 0/0 100.00 100.00 ncbi NG_048388.1 D-lactate dehydrogenase VanH-M VANCOMYCIN +GCF_010120755.1_ASM1012075v1_genomic.fna NZ_CP039730.1 47306 48418 - vanS-M 1-1113/1113 =============== 0/0 100.00 100.00 ncbi NG_048450.1 VanM-type vancomycin resistance histidine kinase VanS VANCOMYCIN |
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| diff -r 000000000000 -r d2590ecc4189 test-data/ariba/report.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ariba/report.tsv Tue Mar 16 12:38:42 2021 +0000 |
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| b'@@ -0,0 +1,257 @@\n+#ariba_ref_name\tref_name\tgene\tvar_only\tflag\treads\tcluster\tref_len\tref_base_assembled\tpc_ident\tctg\tctg_len\tctg_cov\tknown_var\tvar_type\tvar_seq_type\tknown_var_change\thas_known_var\tref_ctg_change\tref_ctg_effect\tref_start\tref_end\tref_nt\tctg_start\tctg_end\tctg_nt\tsmtls_total_depth\tsmtls_nts\tsmtls_nts_depth\tvar_description\tfree_text\n+AAC_3__IId.3004623.EU022314.1.0_861.5344\tAAC_3__IId.3004623.EU022314.1.0_861.5344\t1\t0\t27\t256\tAAC_3__II-\t861\t861\t99.88\tAAC_3__II-.l15.c4.ctg.1\t1547\t37.8\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\tb\'AAC(3)-IId is a plasmid-encoded aminoglycoside acetyltransferase in E. coli\';AAC(3)-IId\n+AAC_6___Ib4.3002577.AF445082.2788_3343.401\tAAC_6___Ib4.3002577.AF445082.2788_3343.401\t1\t0\t667\t510\tAAC_6___Ib+\t555\t555\t99.64\tAAC_6___Ib+.l15.c30.ctg.1\t619\t128.1\t0\t.\tp\t.\t0\tW87R\tNONSYN\t259\t261\tTGG\t264\t266\tCGG\t86;89;90\tC,T,A;G;G\t30,28,1;59;63\t.\tAAC(6\')-Ib4;b"AAC(6\')-Ib4 is an aminoglycoside acetyltransferase in Serratia spp."\n+AAC_6___Ib4.3002577.AF445082.2788_3343.401\tAAC_6___Ib4.3002577.AF445082.2788_3343.401\t1\t0\t667\t510\tAAC_6___Ib+\t555\t555\t99.64\tAAC_6___Ib+.l15.c30.ctg.1\t619\t128.1\t0\t.\tp\t.\t0\tS102L\tNONSYN\t304\t306\tTCA\t309\t311\tTTA\t92;92;92\tT;T;A\t70;70;71\t.\tAAC(6\')-Ib4;b"AAC(6\')-Ib4 is an aminoglycoside acetyltransferase in Serratia spp."\n+AAC_6___Ib4.3002577.AF445082.2788_3343.401\tAAC_6___Ib4.3002577.AF445082.2788_3343.401\t1\t0\t667\t510\tAAC_6___Ib+\t555\t555\t99.64\tAAC_6___Ib+.l15.c30.ctg.1\t619\t128.1\t0\tHET\t.\t.\t.\tG490T\t.\t490\t490\tG\t495\t495\tG\t139\tG,T\t57,46\t.\tAAC(6\')-Ib4;b"AAC(6\')-Ib4 is an aminoglycoside acetyltransferase in Serratia spp."\n+BRP_MBL_.3001205.KC503911.1.9883_10249.5446\tBRP_MBL_.3001205.KC503911.1.9883_10249.5446\t1\t0\t27\t132\tBRP_MBL_\t366\t366\t100.0\tBRP_MBL_.l6.c4.ctg.1\t1085\t27.3\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\tBRP(MBL);b\'A novel bleomycin resistance protein encoded by a metallo-beta-lactamase-associated ble gene. Expression of BRP(MBL) confers resistance to bleomycin and bleomycin-like antibiotics in Enterobacteriaceae and Acinetobacter, where it is co-expressed with an MBL and controlled by the same promoter region.\'\n+CRP.3000518.AP009048.1.4153663_4154296.4752\tCRP.3000518.AP009048.1.4153663_4154296.4752\t1\t0\t528\t58\tCRP\t633\t146\t93.84\tCRP.l15.c4.ctg.1\t477\t24.1\t0\t.\tp\t.\t0\tK29T\tNONSYN\t85\t87\tAAG\t414\t416\tACG\t14;14;13\tA;C;G\t10;10;10\t.\tb\'CRP is a global regulator that represses MdtEF multidrug efflux pump expression.\';CRP\n+CTX_M_15.3001878.AY044436.1435_2311.1430\tCTX_M_15.3001878.AY044436.1435_2311.1430\t1\t0\t27\t274\tCTX_M_-\t876\t876\t100.0\tCTX_M_-.l15.c4.ctg.1\t1793\t36.0\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\tCTX-M-15;b\'CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family\'\n+DHA_7.3002136.HQ456945.0_1140.1865\tDHA_7.3002136.HQ456945.0_1140.1865\t1\t0\t16\t170\tDHA_-\t1140\t796\t100.0\tDHA_-.l15.c4.ctg.1\t1350\t29.8\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\tb\'DHA-7 is a beta-lactamase found in the Enterobacteriaceae family\';DHA-7\n+Escherichia_coli_23S.3004173.AE014075.1.237159_240063.4164\tEscherichia_coli_23S.3004173.AE014075.1.237159_240063.4164\t0\t0\t659\t8302\tEscherichia_coli_23S\t2904\t2792\t97.1\tEscherichia_coli_23S.l15.c17.ctg.1\t2822\t611.4\t0\t.\tn\t.\t0\tT72A\tSNP\t72\t72\tT\t86\t86\tA\t506\tA\t125\t.\tEscherichia coli 23S rRNA with mutation conferring resistance to oxazolidinone antibiotics\n+Escherichia_coli_23S.3004173.AE014075.1.237159_240063.4164\tEscherichia_coli_23S.3004173.AE014075.1.237159_240063.4164\t0\t0\t659\t8302\tEscherichia_coli_23S\t2904\t2792\t97.1\tEscherichia_coli_23S.l15.c17.ctg.1\t2822\t611.4\t0\t.\tn\t.\t0\tT113G\tSNP\t113\t113\tT\t127\t127\tG\t376\tG\t146\t.\tEscherichia coli 23S rRNA with mutation conferring resistance to oxazolidinone antibiotics\n+Escherichia_coli_23S.3004173.AE014075.1.237159_240063.4164\tEscherichia_coli_23S.3004173.AE014075.1.237159_240063.4164\t0\t0\t659\t8302\tEscherichia_coli_23S\t2904\t2792\t97.1\tEscherichia_coli_23S.l15.c17.ctg.1\t2822\t611.4\t0\t.\tn\t.\t0\tT135C\tSNP\t135\t135\tT\t149\t149\tC\t343\tC,T\t116,40\t.\tEscherichia coli 23S rRNA with mutation conferring resistance to oxazolidinone antibiotics\n+Escherichia_coli_23S.3004173.AE014075.1.237159_240063.416'..b" (rrsD) mutation conferring resistance to spectinomycin\n+rrsD.3003512.AE006468.3570463_3572006.3227\trrsD.3003512.AE006468.3570463_3572006.3227\t0\t0\t659\t6088\trrsB+\t1544\t1544\t97.22\trrsB+.l15.c17.ctg.1\t1693\t765.7\t0\tHET\t.\t.\t.\tT526A\t.\t526\t526\tT\t613\t613\tT\t821\tT,A\t441,136\t.\tSalmonella enterica 16S rRNA (rrsD) mutation conferring resistance to spectinomycin\n+rrsD.3003512.AE006468.3570463_3572006.3227\trrsD.3003512.AE006468.3570463_3572006.3227\t0\t0\t659\t6088\trrsB+\t1544\t1544\t97.22\trrsB+.l15.c17.ctg.1\t1693\t765.7\t0\tHET\t.\t.\t.\tC527G,T,A\t.\t527\t527\tC\t614\t614\tC\t821\tC,G,T,A\t434,138,1,1\t.\tSalmonella enterica 16S rRNA (rrsD) mutation conferring resistance to spectinomycin\n+rrsD.3003512.AE006468.3570463_3572006.3227\trrsD.3003512.AE006468.3570463_3572006.3227\t0\t0\t659\t6088\trrsB+\t1544\t1544\t97.22\trrsB+.l15.c17.ctg.1\t1693\t765.7\t0\tHET\t.\t.\t.\tC559T\t.\t559\t559\tC\t646\t646\tC\t781\tC,T\t510,63\t.\tSalmonella enterica 16S rRNA (rrsD) mutation conferring resistance to spectinomycin\n+rrsD.3003512.AE006468.3570463_3572006.3227\trrsD.3003512.AE006468.3570463_3572006.3227\t0\t0\t659\t6088\trrsB+\t1544\t1544\t97.22\trrsB+.l15.c17.ctg.1\t1693\t765.7\t0\tHET\t.\t.\t.\tC1071A,T,G\t.\t1071\t1071\tC\t1158\t1158\tC\t806\tC,A,T,G\t240,342,1,1\t.\tSalmonella enterica 16S rRNA (rrsD) mutation conferring resistance to spectinomycin\n+rrsD.3003512.AE006468.3570463_3572006.3227\trrsD.3003512.AE006468.3570463_3572006.3227\t0\t0\t659\t6088\trrsB+\t1544\t1544\t97.22\trrsB+.l15.c17.ctg.1\t1693\t765.7\t0\tHET\t.\t.\t.\tC1072T\t.\t1072\t1072\tT\t1159\t1159\tC\t807\tC,T\t310,274\t.\tSalmonella enterica 16S rRNA (rrsD) mutation conferring resistance to spectinomycin\n+rrsD.3003512.AE006468.3570463_3572006.3227\trrsD.3003512.AE006468.3570463_3572006.3227\t0\t0\t659\t6088\trrsB+\t1544\t1544\t97.22\trrsB+.l15.c17.ctg.1\t1693\t765.7\t0\tHET\t.\t.\t.\tA1073G,T\t.\t1073\t1073\tG\t1160\t1160\tA\t807\tA,G,T\t310,269,2\t.\tSalmonella enterica 16S rRNA (rrsD) mutation conferring resistance to spectinomycin\n+rrsD.3003512.AE006468.3570463_3572006.3227\trrsD.3003512.AE006468.3570463_3572006.3227\t0\t0\t659\t6088\trrsB+\t1544\t1544\t97.22\trrsB+.l15.c17.ctg.1\t1693\t765.7\t0\tHET\t.\t.\t.\tG1234A\t.\t1234\t1234\tG\t1321\t1321\tG\t654\tG,A\t418,54\t.\tSalmonella enterica 16S rRNA (rrsD) mutation conferring resistance to spectinomycin\n+rrsD.3003512.AE006468.3570463_3572006.3227\trrsD.3003512.AE006468.3570463_3572006.3227\t0\t0\t659\t6088\trrsB+\t1544\t1544\t97.22\trrsB+.l15.c17.ctg.1\t1693\t765.7\t0\tHET\t.\t.\t.\tG536C\t.\t536\t536\tG\t623\t623\tG\t826\tG,C\t440,134\t.\tSalmonella enterica 16S rRNA (rrsD) mutation conferring resistance to spectinomycin\n+rrsD.3003512.AE006468.3570463_3572006.3227\trrsD.3003512.AE006468.3570463_3572006.3227\t0\t0\t659\t6088\trrsB+\t1544\t1544\t97.22\trrsB+.l15.c17.ctg.1\t1693\t765.7\t0\tHET\t.\t.\t.\tG409T,A,C\t.\t409\t409\tT\t496\t496\tG\t699\tG,T,A,C\t462,72,1,1\t.\tSalmonella enterica 16S rRNA (rrsD) mutation conferring resistance to spectinomycin\n+rrsD.3003512.AE006468.3570463_3572006.3227\trrsD.3003512.AE006468.3570463_3572006.3227\t0\t0\t659\t6088\trrsB+\t1544\t1544\t97.22\trrsB+.l15.c17.ctg.1\t1693\t765.7\t0\tHET\t.\t.\t.\tA537T\t.\t537\t537\tA\t624\t624\tA\t826\tA,T\t444,136\t.\tSalmonella enterica 16S rRNA (rrsD) mutation conferring resistance to spectinomycin\n+rrsD.3003512.AE006468.3570463_3572006.3227\trrsD.3003512.AE006468.3570463_3572006.3227\t0\t0\t659\t6088\trrsB+\t1544\t1544\t97.22\trrsB+.l15.c17.ctg.1\t1693\t765.7\t0\tHET\t.\t.\t.\tG926A,T\t.\t926\t926\tG\t1013\t1013\tG\t698\tG,A,T\t474,65,2\t.\tSalmonella enterica 16S rRNA (rrsD) mutation conferring resistance to spectinomycin\n+rrsD.3003512.AE006468.3570463_3572006.3227\trrsD.3003512.AE006468.3570463_3572006.3227\t0\t0\t659\t6088\trrsB+\t1544\t1544\t97.22\trrsB+.l15.c17.ctg.1\t1693\t765.7\t0\tHET\t.\t.\t.\tA1089C,T,G\t.\t1089\t1089\tA\t1176\t1176\tA\t807\tA,C,T,G\t312,194,74,1\t.\tSalmonella enterica 16S rRNA (rrsD) mutation conferring resistance to spectinomycin\n+sul1.3000410.JF969163.1053_1893.340\tsul1.3000410.JF969163.1053_1893.340\t1\t0\t27\t360\tsul1\t840\t840\t99.88\tsul1.l15.c17.ctg.1\t1783\t43.9\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\tb'Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.';sul1\n" |
| b |
| diff -r 000000000000 -r d2590ecc4189 test-data/hamronized_abricate.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hamronized_abricate.json Tue Mar 16 12:38:42 2021 +0000 |
| [ |
| @@ -0,0 +1,1 @@ +[{"input_file_name": "GCF_010120755.1_ASM1012075v1_genomic", "gene_symbol": "eat(A)", "gene_name": "ABC-F type ribosomal protection protein Eat(A)", "reference_database_id": "ncbi", "reference_database_version": "db_v_1", "reference_accession": "NG_047762.1", "analysis_software_name": "abricate", "analysis_software_version": "tool_v_1", "sequence_identity": "100.0", "input_sequence_id": "NZ_CP039729.1", "input_protein_start": "", "input_protein_stop": "", "input_gene_start": "656118", "input_gene_stop": "657620", "reference_protein_start": "", "reference_protein_stop": "", "reference_gene_start": "", "reference_gene_stop": "", "strand_orientation": "+", "coverage_depth": "", "coverage_percentage": "100.0", "coverage_ratio": "", "reference_gene_length": "", "reference_protein_length": "", "input_gene_length": "", "input_protein_length": "", "drug_class": "PLEUROMUTILIN", "antimicrobial_agent": "", "resistance_mechanism": ""}, {"input_file_name": 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| b |
| diff -r 000000000000 -r d2590ecc4189 test-data/hamronized_abricate.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hamronized_abricate.tsv Tue Mar 16 12:38:42 2021 +0000 |
| b |
| @@ -0,0 +1,8 @@ +input_file_name gene_symbol gene_name reference_database_id reference_database_version reference_accession analysis_software_name analysis_software_version sequence_identity input_sequence_id input_protein_start input_protein_stop input_gene_start input_gene_stop reference_protein_start reference_protein_stop reference_gene_start reference_gene_stop strand_orientation coverage_depth coverage_percentage coverage_ratio reference_gene_length reference_protein_length input_gene_length input_protein_length drug_class antimicrobial_agent resistance_mechanism +GCF_010120755.1_ASM1012075v1_genomic eat(A) ABC-F type ribosomal protection protein Eat(A) ncbi db_v_1 NG_047762.1 abricate tool_v_1 100.0 NZ_CP039729.1 656118 657620 + 100.0 PLEUROMUTILIN +GCF_010120755.1_ASM1012075v1_genomic aacA-ENT1 aminoglycoside 6'-N-acetyltransferase ncbi db_v_1 NG_052371.1 abricate tool_v_1 100.0 NZ_CP039729.1 2163439 2163987 - 100.0 AMINOGLYCOSIDE +GCF_010120755.1_ASM1012075v1_genomic msr(C) ABC-F type ribosomal protection protein Msr(C) ncbi db_v_1 NG_048003.1 abricate tool_v_1 98.92 NZ_CP039729.1 2564038 2565516 - 100.0 MACROLIDE +GCF_010120755.1_ASM1012075v1_genomic vanX-M D-Ala-D-Ala dipeptidase VanX-M ncbi db_v_1 NG_048495.1 abricate tool_v_1 100.0 NZ_CP039730.1 43619 44197 - 95.07 VANCOMYCIN +GCF_010120755.1_ASM1012075v1_genomic vanM D-alanine--(R)-lactate ligase VanM ncbi db_v_1 NG_048396.1 abricate tool_v_1 100.0 NZ_CP039730.1 44203 45234 - 100.0 VANCOMYCIN +GCF_010120755.1_ASM1012075v1_genomic vanH-M D-lactate dehydrogenase VanH-M ncbi db_v_1 NG_048388.1 abricate tool_v_1 100.0 NZ_CP039730.1 45227 46207 - 100.0 VANCOMYCIN +GCF_010120755.1_ASM1012075v1_genomic vanS-M VanM-type vancomycin resistance histidine kinase VanS ncbi db_v_1 NG_048450.1 abricate tool_v_1 100.0 NZ_CP039730.1 47306 48418 - 100.0 VANCOMYCIN |
| b |
| diff -r 000000000000 -r d2590ecc4189 test-data/hamronized_ariba.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hamronized_ariba.json Tue Mar 16 12:38:42 2021 +0000 |
| [ |
| b'@@ -0,0 +1,1 @@\n+[{"input_file_name": "ariba_report", "gene_symbol": "AAC_3__IId", "gene_name": "AAC_3__IId.3004623.EU022314.1.0_861.5344", "reference_database_id": "dbname", "reference_database_version": "db_v_1", "reference_accession": "AAC_3__IId.3004623.EU022314.1.0_861.5344", "analysis_software_name": "ariba", "analysis_software_version": "ariba_v1", "sequence_identity": "99.88", "input_sequence_id": "AAC_3__II-.l15.c4.ctg.1", "input_protein_start": "", "input_protein_stop": "", "input_gene_start": "", "input_gene_stop": "", "reference_protein_start": "", "reference_protein_stop": "", "reference_gene_start": "", "reference_gene_stop": "", "strand_orientation": "", "coverage_depth": "37.8", "coverage_percentage": "", "coverage_ratio": "", "reference_gene_length": "861", "reference_protein_length": "", "input_gene_length": "", "input_protein_length": "", "drug_class": "", "antimicrobial_agent": "", "resistance_mechanism": ""}, {"input_file_name": "ariba_report", "gene_symbol": 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"reference_gene_length": "1544", "reference_protein_length": "", "input_gene_length": "", "input_protein_length": "", "drug_class": "", "antimicrobial_agent": "", "resistance_mechanism": ""}, {"input_file_name": "ariba_report", "gene_symbol": "sul1", "gene_name": "sul1.3000410.JF969163.1053_1893.340", "reference_database_id": "dbname", "reference_database_version": "db_v_1", "reference_accession": "sul1.3000410.JF969163.1053_1893.340", "analysis_software_name": "ariba", "analysis_software_version": "ariba_v1", "sequence_identity": "99.88", "input_sequence_id": "sul1.l15.c17.ctg.1", "input_protein_start": "", "input_protein_stop": "", "input_gene_start": "", "input_gene_stop": "", "reference_protein_start": "", "reference_protein_stop": "", "reference_gene_start": "", "reference_gene_stop": "", "strand_orientation": "", "coverage_depth": "43.9", "coverage_percentage": "", "coverage_ratio": "", "reference_gene_length": "840", "reference_protein_length": "", "input_gene_length": "", "input_protein_length": "", "drug_class": "", "antimicrobial_agent": "", "resistance_mechanism": ""}]\n' |
| b |
| diff -r 000000000000 -r d2590ecc4189 test-data/hamronized_ariba.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hamronized_ariba.tsv Tue Mar 16 12:38:42 2021 +0000 |
| b |
| b'@@ -0,0 +1,257 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|
| b |
| diff -r 000000000000 -r d2590ecc4189 test-data/hamronized_rgi.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hamronized_rgi.json Tue Mar 16 12:38:42 2021 +0000 |
| [ |
| b'@@ -0,0 +1,1 @@\n+[{"input_file_name": "rgi_report", "gene_symbol": "oqxA", "gene_name": "resistance-nodulation-cell division (RND) antibiotic efflux pump", "reference_database_id": "CARD", "reference_database_version": "card_v1", "reference_accession": "3003922", "analysis_software_name": "rgi", "analysis_software_version": "rgi_v1", "sequence_identity": "100.0", "input_sequence_id": "NODE_1_length_803036_cov_42.265_33", "input_protein_start": "", "input_protein_stop": "", "input_gene_start": "30758", "input_gene_stop": "31933", "reference_protein_start": "", "reference_protein_stop": "", "reference_gene_start": "", "reference_gene_stop": "", "strand_orientation": "+", "coverage_depth": "", "coverage_percentage": "100.0", "coverage_ratio": "", "reference_gene_length": "", "reference_protein_length": "", "input_gene_length": "", "input_protein_length": "", "drug_class": "fluoroquinolone antibiotic; glycylcycline; tetracycline antibiotic; diaminopyrimidine antibiotic; nitrofuran antibiotic", "antimicrobial_agent": "", "resistance_mechanism": "antibiotic efflux"}, {"input_file_name": "rgi_report", "gene_symbol": "oqxB", "gene_name": "resistance-nodulation-cell division (RND) antibiotic efflux pump", "reference_database_id": "CARD", "reference_database_version": "card_v1", "reference_accession": "3003923", "analysis_software_name": "rgi", "analysis_software_version": "rgi_v1", "sequence_identity": "99.52", "input_sequence_id": "NODE_1_length_803036_cov_42.265_34", "input_protein_start": "", "input_protein_stop": "", "input_gene_start": "31957", "input_gene_stop": "35109", "reference_protein_start": "", "reference_protein_stop": "", "reference_gene_start": "", "reference_gene_stop": "", "strand_orientation": "+", "coverage_depth": "", "coverage_percentage": "100.0", "coverage_ratio": "", "reference_gene_length": "", "reference_protein_length": "", "input_gene_length": "", "input_protein_length": "", "drug_class": "fluoroquinolone antibiotic; glycylcycline; tetracycline antibiotic; diaminopyrimidine antibiotic; nitrofuran antibiotic", "antimicrobial_agent": "", "resistance_mechanism": "antibiotic efflux"}, {"input_file_name": "rgi_report", "gene_symbol": "emrR", "gene_name": "major facilitator superfamily (MFS) antibiotic efflux pump", "reference_database_id": "CARD", "reference_database_version": "card_v1", "reference_accession": "3000516", "analysis_software_name": "rgi", "analysis_software_version": "rgi_v1", "sequence_identity": "92.57", "input_sequence_id": "NODE_1_length_803036_cov_42.265_80", "input_protein_start": "", "input_protein_stop": "", "input_gene_start": "79380", "input_gene_stop": "79910", "reference_protein_start": "", "reference_protein_stop": "", "reference_gene_start": "", "reference_gene_stop": "", "strand_orientation": "+", "coverage_depth": "", "coverage_percentage": "100.0", "coverage_ratio": "", "reference_gene_length": "", "reference_protein_length": "", "input_gene_length": "", "input_protein_length": "", "drug_class": "fluoroquinolone antibiotic", "antimicrobial_agent": "", "resistance_mechanism": "antibiotic efflux"}, {"input_file_name": "rgi_report", "gene_symbol": "Klebsiella pneumoniae KpnG", "gene_name": "major facilitator superfamily (MFS) antibiotic efflux pump", "reference_database_id": "CARD", "reference_database_version": "card_v1", "reference_accession": "3004588", "analysis_software_name": "rgi", "analysis_software_version": "rgi_v1", "sequence_identity": "99.74", "input_sequence_id": "NODE_1_length_803036_cov_42.265_81", "input_protein_start": "", "input_protein_stop": "", "input_gene_start": "80036", "input_gene_stop": "81208", "reference_protein_start": "", "reference_protein_stop": "", "reference_gene_start": "", "reference_gene_stop": "", "strand_orientation": "+", "coverage_depth": "", "coverage_percentage": "100.0", "coverage_ratio": "", "reference_gene_length": "", "reference_protein_length": "", "input_gene_length": "", "input_protein_length": "", "drug_class": "macrolide antibioti'..b'", "coverage_ratio": "", "reference_gene_length": "", "reference_protein_length": "", "input_gene_length": "", "input_protein_length": "", "drug_class": "phenicol antibiotic", "antimicrobial_agent": "", "resistance_mechanism": "antibiotic inactivation"}, {"input_file_name": "rgi_report", "gene_symbol": "AAC(6\')-Ib-cr", "gene_name": "AAC(6\')", "reference_database_id": "CARD", "reference_database_version": "card_v1", "reference_accession": "3002547", "analysis_software_name": "rgi", "analysis_software_version": "rgi_v1", "sequence_identity": "95.45", "input_sequence_id": "NODE_54_length_1272_cov_25.1921_2 ", "input_protein_start": "", "input_protein_stop": "", "input_gene_start": "1130", "input_gene_stop": "1270", "reference_protein_start": "", "reference_protein_stop": "", "reference_gene_start": "", "reference_gene_stop": "", "strand_orientation": "+", "coverage_depth": "", "coverage_percentage": "23.62", "coverage_ratio": "", "reference_gene_length": "", "reference_protein_length": "", "input_gene_length": "", "input_protein_length": "", "drug_class": "fluoroquinolone antibiotic; aminoglycoside antibiotic", "antimicrobial_agent": "", "resistance_mechanism": "antibiotic inactivation"}, {"input_file_name": "rgi_report", "gene_symbol": "sul1", "gene_name": "sulfonamide resistant sul", "reference_database_id": "CARD", "reference_database_version": "card_v1", "reference_accession": "3000410", "analysis_software_name": "rgi", "analysis_software_version": "rgi_v1", "sequence_identity": "100.0", "input_sequence_id": "NODE_57_length_1134_cov_34.8908_1", "input_protein_start": "", "input_protein_stop": "", "input_gene_start": "25", "input_gene_stop": "864", "reference_protein_start": "", "reference_protein_stop": "", "reference_gene_start": "", "reference_gene_stop": "", "strand_orientation": "-", "coverage_depth": "", "coverage_percentage": "100.0", "coverage_ratio": "", "reference_gene_length": "", "reference_protein_length": "", "input_gene_length": "", "input_protein_length": "", "drug_class": "sulfonamide antibiotic", "antimicrobial_agent": "", "resistance_mechanism": "antibiotic target replacement"}, {"input_file_name": "rgi_report", "gene_symbol": "AAC(6\')-Ib10", "gene_name": "AAC(6\')", "reference_database_id": "CARD", "reference_database_version": "card_v1", "reference_accession": "3002581", "analysis_software_name": "rgi", "analysis_software_version": "rgi_v1", "sequence_identity": "100.0", "input_sequence_id": "NODE_69_length_625_cov_55.4398_1", "input_protein_start": "", "input_protein_stop": "", "input_gene_start": "63", "input_gene_stop": "623", "reference_protein_start": "", "reference_protein_stop": "", "reference_gene_start": "", "reference_gene_stop": "", "strand_orientation": "-", "coverage_depth": "", "coverage_percentage": "91.63", "coverage_ratio": "", "reference_gene_length": "", "reference_protein_length": "", "input_gene_length": "", "input_protein_length": "", "drug_class": "aminoglycoside antibiotic", "antimicrobial_agent": "", "resistance_mechanism": "antibiotic inactivation"}, {"input_file_name": "rgi_report", "gene_symbol": "AAC(6\')-Ib-cr", "gene_name": "AAC(6\')", "reference_database_id": "CARD", "reference_database_version": "card_v1", "reference_accession": "3002547", "analysis_software_name": "rgi", "analysis_software_version": "rgi_v1", "sequence_identity": "100.0", "input_sequence_id": "NODE_185_length_335_cov_33.8077_1 ", "input_protein_start": "", "input_protein_stop": "", "input_gene_start": "172", "input_gene_stop": "333", "reference_protein_start": "", "reference_protein_stop": "", "reference_gene_start": "", "reference_gene_stop": "", "strand_orientation": "+", "coverage_depth": "", "coverage_percentage": "27.14", "coverage_ratio": "", "reference_gene_length": "", "reference_protein_length": "", "input_gene_length": "", "input_protein_length": "", "drug_class": "fluoroquinolone antibiotic; aminoglycoside antibiotic", "antimicrobial_agent": "", "resistance_mechanism": "antibiotic inactivation"}]\n' |
| b |
| diff -r 000000000000 -r d2590ecc4189 test-data/hamronized_rgi.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hamronized_rgi.tsv Tue Mar 16 12:38:42 2021 +0000 |
| b |
| b'@@ -0,0 +1,35 @@\n+input_file_name\tgene_symbol\tgene_name\treference_database_id\treference_database_version\treference_accession\tanalysis_software_name\tanalysis_software_version\tsequence_identity\tinput_sequence_id\tinput_protein_start\tinput_protein_stop\tinput_gene_start\tinput_gene_stop\treference_protein_start\treference_protein_stop\treference_gene_start\treference_gene_stop\tstrand_orientation\tcoverage_depth\tcoverage_percentage\tcoverage_ratio\treference_gene_length\treference_protein_length\tinput_gene_length\tinput_protein_length\tdrug_class\tantimicrobial_agent\tresistance_mechanism\n+rgi_report\toqxA\tresistance-nodulation-cell division (RND) antibiotic efflux pump\tCARD\tcard_v1\t3003922\trgi\trgi_v1\t100.0\tNODE_1_length_803036_cov_42.265_33\t\t\t30758\t31933\t\t\t\t\t+\t\t100.0\t\t\t\t\t\tfluoroquinolone antibiotic; glycylcycline; tetracycline antibiotic; diaminopyrimidine antibiotic; nitrofuran antibiotic\t\tantibiotic efflux\n+rgi_report\toqxB\tresistance-nodulation-cell division (RND) antibiotic efflux pump\tCARD\tcard_v1\t3003923\trgi\trgi_v1\t99.52\tNODE_1_length_803036_cov_42.265_34\t\t\t31957\t35109\t\t\t\t\t+\t\t100.0\t\t\t\t\t\tfluoroquinolone antibiotic; glycylcycline; tetracycline antibiotic; diaminopyrimidine antibiotic; nitrofuran antibiotic\t\tantibiotic efflux\n+rgi_report\temrR\tmajor facilitator superfamily (MFS) antibiotic efflux pump\tCARD\tcard_v1\t3000516\trgi\trgi_v1\t92.57\tNODE_1_length_803036_cov_42.265_80\t\t\t79380\t79910\t\t\t\t\t+\t\t100.0\t\t\t\t\t\tfluoroquinolone antibiotic\t\tantibiotic efflux\n+rgi_report\tKlebsiella pneumoniae KpnG\tmajor facilitator superfamily (MFS) antibiotic efflux pump\tCARD\tcard_v1\t3004588\trgi\trgi_v1\t99.74\tNODE_1_length_803036_cov_42.265_81\t\t\t80036\t81208\t\t\t\t\t+\t\t100.0\t\t\t\t\t\tmacrolide antibiotic; fluoroquinolone antibiotic; aminoglycoside antibiotic; carbapenem; cephalosporin; penam; peptide antibiotic; penem\t\tantibiotic efflux\n+rgi_report\tKlebsiella pneumoniae KpnH\tmajor facilitator superfamily (MFS) antibiotic efflux pump\tCARD\tcard_v1\t3004597\trgi\trgi_v1\t94.02\tNODE_1_length_803036_cov_42.265_82\t\t\t81224\t82762\t\t\t\t\t+\t\t100.0\t\t\t\t\t\tmacrolide antibiotic; fluoroquinolone antibiotic; aminoglycoside antibiotic; carbapenem; cephalosporin; penam; peptide antibiotic; penem\t\tantibiotic efflux\n+rgi_report\tmdtB\tresistance-nodulation-cell division (RND) antibiotic efflux pump\tCARD\tcard_v1\t3000793\trgi\trgi_v1\t90.1\tNODE_3_length_454317_cov_40.2449_14\t\t\t17656\t20778\t\t\t\t\t+\t\t100.0\t\t\t\t\t\taminocoumarin antibiotic\t\tantibiotic efflux\n+rgi_report\tmdtC\tresistance-nodulation-cell division (RND) antibiotic efflux pump\tCARD\tcard_v1\t3000794\trgi\trgi_v1\t91.41\tNODE_3_length_454317_cov_40.2449_15\t\t\t20779\t23856\t\t\t\t\t+\t\t100.0\t\t\t\t\t\taminocoumarin antibiotic\t\tantibiotic efflux\n+rgi_report\tbaeR\tresistance-nodulation-cell division (RND) antibiotic efflux pump\tCARD\tcard_v1\t3000828\trgi\trgi_v1\t90.83\tNODE_3_length_454317_cov_40.2449_18\t\t\t26745\t27467\t\t\t\t\t+\t\t100.0\t\t\t\t\t\taminoglycoside antibiotic; aminocoumarin antibiotic\t\tantibiotic efflux\n+rgi_report\tacrD\tresistance-nodulation-cell division (RND) antibiotic efflux pump\tCARD\tcard_v1\t3000491\trgi\trgi_v1\t90.94\tNODE_3_length_454317_cov_40.2449_285\t\t\t330238\t333351\t\t\t\t\t+\t\t100.0\t\t\t\t\t\taminoglycoside antibiotic\t\tantibiotic efflux\n+rgi_report\tFosA6\tfosfomycin thiol transferase\tCARD\tcard_v1\t3004111\trgi\trgi_v1\t97.84\tNODE_4_length_367278_cov_42.3139_12\t\t\t14037\t14456\t\t\t\t\t+\t\t100.0\t\t\t\t\t\tfosfomycin\t\tantibiotic inactivation\n+rgi_report\tKlebsiella pneumoniae acrA\tresistance-nodulation-cell division (RND) antibiotic efflux pump\tCARD\tcard_v1\t3004041\trgi\trgi_v1\t95.24\tNODE_6_length_262587_cov_42.4347_106 \t\t\t86156\t87349\t\t\t\t\t+\t\t99.75\t\t\t\t\t\tfluoroquinolone antibiotic; cephalosporin; glycylcycline; penam; tetracycline antibiotic; rifamycin antibiotic; phenicol antibiotic; triclosan\t\tantibiotic efflux\n+rgi_report\tacrB\tresistance-nodulation-cell division (RND) antibiotic efflux pump\tCARD\tcard_v1\t3000216\trgi\trgi_v1\t91.52\tNODE_6_length_262587_cov_42.4347_107\t\t\t87372\t90518\t\t\t\t\t+\t\t99.9\t\t\t\t\t\tfluoroquinolone antibiotic; cephalosporin; glycylcycline; penam; tetracycline antibiotic; rifamycin antibiotic; phen'..b"7\t\t\t\t\t+\t\t97.64\t\t\t\t\t\tfluoroquinolone antibiotic; monobactam; carbapenem; cephalosporin; glycylcycline; cephamycin; penam; tetracycline antibiotic; rifamycin antibiotic; phenicol antibiotic; triclosan; penem\t\tantibiotic efflux; reduced permeability to antibiotic\n+rgi_report\tSHV-11\tSHV beta-lactamase\tCARD\tcard_v1\t3001070\trgi\trgi_v1\t100.0\tNODE_11_length_157792_cov_39.2115_132\t\t\t128890\t129750\t\t\t\t\t+\t\t100.0\t\t\t\t\t\tcarbapenem; cephalosporin; penam\t\tantibiotic inactivation\n+rgi_report\tCBP-1\tCBP beta-lactamase\tCARD\tcard_v1\t3004764\trgi\trgi_v1\t100.0\tNODE_19_length_86672_cov_43.8582_38 \t\t\t39587\t39811\t\t\t\t\t-\t\t24.03\t\t\t\t\t\tpenam\t\tantibiotic inactivation\n+rgi_report\tEscherichia coli mdfA\tmajor facilitator superfamily (MFS) antibiotic efflux pump\tCARD\tcard_v1\t3001328\trgi\trgi_v1\t85.61\tNODE_21_length_66123_cov_41.3566_52\t\t\t60858\t62090\t\t\t\t\t+\t\t100.0\t\t\t\t\t\ttetracycline antibiotic; benzalkonium chloride; rhodamine\t\tantibiotic efflux\n+rgi_report\tKlebsiella pneumoniae KpnE\tmajor facilitator superfamily (MFS) antibiotic efflux pump\tCARD\tcard_v1\t3004580\trgi\trgi_v1\t99.17\tNODE_27_length_37761_cov_37.6839_21\t\t\t25311\t25673\t\t\t\t\t+\t\t100.0\t\t\t\t\t\tmacrolide antibiotic; aminoglycoside antibiotic; cephalosporin; tetracycline antibiotic; peptide antibiotic; rifamycin antibiotic\t\tantibiotic efflux\n+rgi_report\tKlebsiella pneumoniae KpnF\tmajor facilitator superfamily (MFS) antibiotic efflux pump\tCARD\tcard_v1\t3004583\trgi\trgi_v1\t100.0\tNODE_27_length_37761_cov_37.6839_22\t\t\t25660\t25989\t\t\t\t\t+\t\t100.0\t\t\t\t\t\tmacrolide antibiotic; aminoglycoside antibiotic; cephalosporin; tetracycline antibiotic; peptide antibiotic; rifamycin antibiotic\t\tantibiotic efflux\n+rgi_report\tAAC(3)-IId\tAAC(3)\tCARD\tcard_v1\t3004623\trgi\trgi_v1\t100.0\tNODE_39_length_11164_cov_23.0187_6\t\t\t4569\t5429\t\t\t\t\t+\t\t100.0\t\t\t\t\t\taminoglycoside antibiotic\t\tantibiotic inactivation\n+rgi_report\trmtC\t16S rRNA methyltransferase (G1405)\tCARD\tcard_v1\t3000861\trgi\trgi_v1\t100.0\tNODE_40_length_7360_cov_24.8738_6\t\t\t6358\t7203\t\t\t\t\t-\t\t100.0\t\t\t\t\t\taminoglycoside antibiotic\t\tantibiotic target alteration\n+rgi_report\tNDM-1\tNDM beta-lactamase\tCARD\tcard_v1\t3000589\trgi\trgi_v1\t100.0\tNODE_44_length_4295_cov_23.2123_1\t\t\t301\t1113\t\t\t\t\t+\t\t100.0\t\t\t\t\t\tcarbapenem; cephalosporin; cephamycin; penam\t\tantibiotic inactivation\n+rgi_report\tBRP(MBL)\tBleomycin resistant protein\tCARD\tcard_v1\t3001205\trgi\trgi_v1\t100.0\tNODE_44_length_4295_cov_23.2123_2 \t\t\t1222\t1482\t\t\t\t\t+\t\t71.07\t\t\t\t\t\tglycopeptide antibiotic\t\tantibiotic inactivation\n+rgi_report\tDHA-7\tDHA beta-lactamase\tCARD\tcard_v1\t3002136\trgi\trgi_v1\t100.0\tNODE_44_length_4295_cov_23.2123_3 \t\t\t1846\t2862\t\t\t\t\t-\t\t89.18\t\t\t\t\t\tcephalosporin; cephamycin\t\tantibiotic inactivation\n+rgi_report\tCTX-M-15\tCTX-M beta-lactamase\tCARD\tcard_v1\t3001878\trgi\trgi_v1\t100.0\tNODE_47_length_3813_cov_27.9457_4\t\t\t2763\t3638\t\t\t\t\t-\t\t100.0\t\t\t\t\t\tcephalosporin\t\tantibiotic inactivation\n+rgi_report\tOXA-1\tOXA beta-lactamase\tCARD\tcard_v1\t3001396\trgi\trgi_v1\t100.0\tNODE_51_length_1731_cov_22.5767_1\t\t\t196\t1026\t\t\t\t\t+\t\t100.0\t\t\t\t\t\tcephalosporin; penam\t\tantibiotic inactivation\n+rgi_report\tcatB3\tchloramphenicol acetyltransferase (CAT)\tCARD\tcard_v1\t3002676\trgi\trgi_v1\t100.0\tNODE_51_length_1731_cov_22.5767_2 \t\t\t1164\t1712\t\t\t\t\t+\t\t86.67\t\t\t\t\t\tphenicol antibiotic\t\tantibiotic inactivation\n+rgi_report\tAAC(6')-Ib-cr\tAAC(6')\tCARD\tcard_v1\t3002547\trgi\trgi_v1\t95.45\tNODE_54_length_1272_cov_25.1921_2 \t\t\t1130\t1270\t\t\t\t\t+\t\t23.62\t\t\t\t\t\tfluoroquinolone antibiotic; aminoglycoside antibiotic\t\tantibiotic inactivation\n+rgi_report\tsul1\tsulfonamide resistant sul\tCARD\tcard_v1\t3000410\trgi\trgi_v1\t100.0\tNODE_57_length_1134_cov_34.8908_1\t\t\t25\t864\t\t\t\t\t-\t\t100.0\t\t\t\t\t\tsulfonamide antibiotic\t\tantibiotic target replacement\n+rgi_report\tAAC(6')-Ib10\tAAC(6')\tCARD\tcard_v1\t3002581\trgi\trgi_v1\t100.0\tNODE_69_length_625_cov_55.4398_1\t\t\t63\t623\t\t\t\t\t-\t\t91.63\t\t\t\t\t\taminoglycoside antibiotic\t\tantibiotic inactivation\n+rgi_report\tAAC(6')-Ib-cr\tAAC(6')\tCARD\tcard_v1\t3002547\trgi\trgi_v1\t100.0\tNODE_185_length_335_cov_33.8077_1 \t\t\t172\t333\t\t\t\t\t+\t\t27.14\t\t\t\t\t\tfluoroquinolone antibiotic; aminoglycoside antibiotic\t\tantibiotic inactivation\n" |
| b |
| diff -r 000000000000 -r d2590ecc4189 test-data/rgi/rgi.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgi/rgi.json Tue Mar 16 12:38:42 2021 +0000 |
| b |
| b'@@ -0,0 +1,1 @@\n+{"NODE_1_length_803036_cov_42.265_33 # 30758 # 31933 # 1 # ID=1_33;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.599": {"gnl|BL_ORD_ID|2216|hsp_num:0": {"type_match": "Perfect", "model_id": "2399", "orf_strand": "+", "orf_start": 30758, "orf_end": 31933, "orf_from": "NODE_1_length_803036_cov_42.265_33", "model_name": "oqxA", "model_type": "protein homolog model", "model_type_id": 40292, "pass_evalue": "n/a", "pass_bitscore": "670", "ARO_accession": "3003922", "ARO_name": "oqxA", "ARO_category": {"36005": {"category_aro_accession": "0010004", "category_aro_cvterm_id": "36005", "category_aro_name": "resistance-nodulation-cell division (RND) antibiotic efflux pump", "category_aro_description": "Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding/hydrolysis but by proton movement down the transmembrane electrochemical gradient.", "category_aro_class_name": "AMR Gene Family"}, "35949": {"category_aro_accession": "0000030", "category_aro_cvterm_id": "35949", "category_aro_name": "tigecycline", "category_aro_description": "Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.", "category_aro_class_name": "Antibiotic"}, "35954": {"category_aro_accession": "0000036", "category_aro_cvterm_id": "35954", "category_aro_name": "ciprofloxacin", "category_aro_description": "Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.", "category_aro_class_name": "Antibiotic"}, "35992": {"category_aro_accession": "0000075", "category_aro_cvterm_id": "35992", "category_aro_name": "nitrofurantoin", "category_aro_description": "Nitrofurantoin is an antibiotic used to treat urinary tract infections. It inhibits enzyme synthesis by inhibiting essential enzymes involved in the citric acid cycle, as well as those involved in DNA, RNA, and protein synthesis. It is marketed under the following brand names: Furadantin, Macrobid, Macrodantin, Nitro Macro and Urantoin.", "category_aro_class_name": "Antibiotic"}, "36327": {"category_aro_accession": "3000188", "category_aro_cvterm_id": "36327", "category_aro_name": "trimethoprim", "category_aro_description": "Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.", "category_aro_class_name": "Antibiotic"}, "35920": {"category_aro_accession": "0000001", "category_aro_cvterm_id": "35920", "category_aro_name": "fluoroquinolone antibiotic", "category_aro_description": "The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.", "category_aro_class_name": "Drug Class"}, "35960": {"category_aro_accession": "0000042", "category_aro_cvterm_id": "35960", "category_aro_name": "glycylcycline", "category_aro_description": "Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inh'..b'ng the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.", "category_aro_class_name": "Drug Class"}, "36526": {"category_aro_accession": "3000387", "category_aro_cvterm_id": "36526", "category_aro_name": "phenicol antibiotic", "category_aro_description": "Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.", "category_aro_class_name": "Drug Class"}, "37250": {"category_aro_accession": "3000870", "category_aro_cvterm_id": "37250", "category_aro_name": "triclosan", "category_aro_description": "Triclosan is a common antibacterial agent added to many consumer products as a biocide. It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).", "category_aro_class_name": "Drug Class"}, "36298": {"category_aro_accession": "3000159", "category_aro_cvterm_id": "36298", "category_aro_name": "efflux pump complex or subunit conferring antibiotic resistance", "category_aro_description": "Efflux proteins that pump antibiotic out of a cell to confer resistance.", "category_aro_class_name": "Efflux Component"}, "36590": {"category_aro_accession": "3000451", "category_aro_cvterm_id": "36590", "category_aro_name": "protein(s) and two-component regulatory system modulating antibiotic efflux", "category_aro_description": "Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.", "category_aro_class_name": "Efflux Regulator"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}, "36001": {"category_aro_accession": "0010000", "category_aro_cvterm_id": "36001", "category_aro_name": "antibiotic efflux", "category_aro_description": "Antibiotic resistance via the transport of antibiotics out of the cell.", "category_aro_class_name": "Resistance Mechanism"}}, "evalue": 2.11739, "max_identities": 14, "bit_score": 23.483, "cvterm_id": "36849", "query": "TLKELAEAAGVSKATLHRFCGTRDNLVQMLEDHGETVLNQIIQACDLEH-----AEPLEALQRLI", "match": "+L E+A+AAGV++ ++ + +L + + E+ + ++ +LE+ +PL L+ ++", "sequence_from_db": "SLGEIAKAAGVTRGAIYWHFKDKSDLFSEIWELSESNIGEL----ELEYQAKFPGDPLSVLREIL", "sequence_from_broadstreet": "MARKTKQEAQETRQHILDVALRLFSQQGVSSTSLGEIAKAAGVTRGAIYWHFKDKSDLFSEIWELSESNIGELELEYQAKFPGDPLSVLREILIHVLESTVTEERRRLLMEIIFHKCEFVGEMAVVQQAQRNLCLESYDRIEQTLKHCIEAKMLPADLMTRRAAIIMRGYISGLMENWLFAPQSFDLKKEARDYVAILLEMYLLCPTLRNPATNE", "dna_sequence_from_broadstreet": "ATGGCACGAAAAACCAAACAAGAAGCGCAAGAAACGCGCCAACACATCCTCGATGTGGCTCTACGTCTTTTCTCACAGCAGGGGGTATCATCCACCTCGCTGGGCGAGATTGCAAAAGCAGCTGGCGTTACGCGCGGTGCAATCTACTGGCATTTTAAAGACAAGTCGGATTTGTTCAGTGAGATCTGGGAACTGTCAGAATCCAATATTGGTGAACTAGAGCTTGAGTATCAGGCAAAATTCCCTGGCGATCCACTCTCAGTATTAAGAGAGATATTAATTCATGTTCTTGAATCCACGGTGACAGAAGAACGGCGTCGATTATTGATGGAGATTATATTCCACAAATGCGAATTTGTCGGAGAAATGGCTGTTGTGCAACAGGCACAACGTAATCTCTGTCTGGAAAGTTATGACCGTATAGAACAAACGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATATTTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCTTACTGGAGATGTATCTCCTGTGCCCCACGCTTCGTAATCCTGCCACTAACGAATAA", "partial": "0", "query_start": 73, "query_end": 252, "orf_dna_sequence": "ATGACCCTGATTTCCCATGACGAGCGACTCATCAAGGCGCTGGCAGTCGCTATCGTCGACCGCCCACGAGCGACGCTGAAGGAACTGGCCGAGGCGGCCGGCGTAAGCAAGGCCACCCTGCACCGCTTCTGCGGCACGCGGGACAACCTGGTGCAGATGCTCGAGGACCACGGAGAGACCGTACTGAACCAGATCATCCAGGCCTGCGACCTGGAGCATGCCGAGCCTCTGGAGGCGTTGCAGCGCCTGATCAAGGAACACCTCACCCAC", "orf_prot_sequence": "MTLISHDERLIKALAVAIVDRPRATLKELAEAAGVSKATLHRFCGTRDNLVQMLEDHGETVLNQIIQACDLEHAEPLEALQRLIKEHLTH", "perc_identity": 21.54}}}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r d2590ecc4189 test-data/rgi/rgi.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgi/rgi.txt Tue Mar 16 12:38:42 2021 +0000 |
| b |
| b'@@ -0,0 +1,42 @@\n+ORF_ID\tContig\tStart\tStop\tOrientation\tCut_Off\tPass_Bitscore\tBest_Hit_Bitscore\tBest_Hit_ARO\tBest_Identities\tARO\tModel_type\tSNPs_in_Best_Hit_ARO\tOther_SNPs\tDrug Class\tResistance Mechanism\tAMR Gene Family\tPredicted_DNA\tPredicted_Protein\tCARD_Protein_Sequence\tPercentage Length of Reference Sequence\tID\tModel_ID\tNudged\tNote\r\n+NODE_1_length_803036_cov_42.265_33 # 30758 # 31933 # 1 # ID=1_33;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.599\tNODE_1_length_803036_cov_42.265_33\t30758\t31933\t+\tPerfect\t670\t798.119\toqxA\t100.0\t3003922\tprotein homolog model\tn/a\tn/a\tfluoroquinolone antibiotic; glycylcycline; tetracycline antibiotic; diaminopyrimidine antibiotic; nitrofuran antibiotic\tantibiotic efflux\tresistance-nodulation-cell division (RND) antibiotic efflux pump\tATGAGCCTGCAAAAAACCTGGGGAAACATTCACCTGACCGCGCTCGGCGCGATGATGCTCTCCTTTCTGCTCGTCGGCTGCGACGACAGCGTCGCGCAGAATGCTGCGCCTCCCGCCCCGACGGTCAGCGCCGCTAAGGTGCTGGTGAAGTCGATCAGTCAGTGGGATAGTTTTAACGGTCGCATTGAAGCGGTGGAGAGCGTTCAGCTTCGCCCTCGCGTCTCGGGATACATTGATAAAGTGAATTACACCGACGGCCAGGAGGTGAAAAAGGGCCAGGTGCTGTTCACGATAGATGACAGAACCTATCGCGCCGCGCTGGAGCAGGCGCAGGCGGCGTTGGCAAGAGCCAAAACGCAGGCCAGCCTGGCGCAAAGCGAGGCGAACCGCACCGATAAATTAGTCCATACCAACCTCGTCTCCCGTGAAGAGTGGGAGCAGCGCCGGTCAGCCGCGGTTCAGGCGCAGGCCGACATTCGCGCCGCGCAGGCGGCGGTGGATGCCGCGCAGCTTAACCTCGACTTCACCAAAGTGACCGCCCCTATTGACGGCCGCGCCAGCCGGGCGCTGATCACCAGCGGTAACCTGGTCACCGCGGGCGACACCGCCAGCGTGCTCACCACCCTGGTCTCGCAGAAGACGGTGTACGTCTACTTTGACGTCGACGAGTCAACCTACCTCCACTATCAAAACCTCGCCCGCCGCGGGCAAGGCGCGTCCAGCGATAATCAGGCGCTCCCGGTGGAGATTGGCCTGGTTGGCGAGGAAGGTTACCCCCACCAGGGCAAAGTGGATTTTCTCGATAATCAGTTAACGCCGAGTACCGGCACCATCCGCATGCGTGCGCTGCTGGATAACTCGCAGCGTCTGTTCACACCGGGGCTGTTTGCCCGCGTGCGTCTGCCGGGCAGCGCAGAGTTCAAAGCCACGCTGATCGACGACAAAGCGGTACTGACCGATCAGGATCGTAAATACGTCTATATCGTTGATAAAGATGGTAAAGCACAGCGCCGCGACATTACCCCAGGGCGGCTGGCTGACGGTTTACGCATCGTTCAGAAGGGGTTGAATCCTGGGGATAGCGTCATCGTCGACGGCTTACAAAAAGTGTTTATGCCGGGTATGCCGGTTAACGCCAAAACTGTTGCCATGACCTCCAGCGCCACCCTTAACTGA\tMSLQKTWGNIHLTALGAMMLSFLLVGCDDSVAQNAAPPAPTVSAAKVLVKSISQWDSFNGRIEAVESVQLRPRVSGYIDKVNYTDGQEVKKGQVLFTIDDRTYRAALEQAQAALARAKTQASLAQSEANRTDKLVHTNLVSREEWEQRRSAAVQAQADIRAAQAAVDAAQLNLDFTKVTAPIDGRASRALITSGNLVTAGDTASVLTTLVSQKTVYVYFDVDESTYLHYQNLARRGQGASSDNQALPVEIGLVGEEGYPHQGKVDFLDNQLTPSTGTIRMRALLDNSQRLFTPGLFARVRLPGSAEFKATLIDDKAVLTDQDRKYVYIVDKDGKAQRRDITPGRLADGLRIVQKGLNPGDSVIVDGLQKVFMPGMPVNAKTVAMTSSATLN\tMSLQKTWGNIHLTALGAMMLSFLLVGCDDSVAQNAAPPAPTVSAAKVLVKSISQWDSFNGRIEAVESVQLRPRVSGYIDKVNYTDGQEVKKGQVLFTIDDRTYRAALEQAQAALARAKTQASLAQSEANRTDKLVHTNLVSREEWEQRRSAAVQAQADIRAAQAAVDAAQLNLDFTKVTAPIDGRASRALITSGNLVTAGDTASVLTTLVSQKTVYVYFDVDESTYLHYQNLARRGQGASSDNQALPVEIGLVGEEGYPHQGKVDFLDNQLTPSTGTIRMRALLDNSQRLFTPGLFARVRLPGSAEFKATLIDDKAVLTDQDRKYVYIVDKDGKAQRRDITPGRLADGLRIVQKGLNPGDSVIVDGLQKVFMPGMPVNAKTVAMTSSATLN\t100.00\tgnl|BL_ORD_ID|2216|hsp_num:0\t2399\t\t\r\n+NODE_1_length_803036_cov_42.265_34 # 31957 # 35109 # 1 # ID=1_34;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.612\tNODE_1_length_803036_cov_42.265_34\t31957\t35109\t+\tStrict\t2000\t2107.8\toqxB\t99.52\t3003923\tprotein homolog model\tn/a\tn/a\tfluoroquinolone antibiotic; glycylcycline; tetracycline antibiotic; diaminopyrimidine antibiotic; nitrofuran antibiotic\tantibiotic efflux\tresistance-nodulation-cell division (RND) antibiotic efflux pump\tATGGACTTTTCCCGCTTTTTTATCGACAGGCCGATTTTCGCCGCGGTGCTGTCGATTTTAATTTTTATCACCGGGTTAATCGCTATCCCACTGCTGCCGGTGAGCGAATATCCGGATGTCGTCCCGCCGAGCGTCCAGGTGCGCGCGGAGTATCCCGGCGCCAACCCGAAAGTGATTGCCGAGACCGTGGCGACGCCGCTGGAGGAAGCGATCAACGGCGTTGAAAACATGATGTACATGAAATCGGTCGCCGGCTCCGACGGCGTGCTGGTCACCACCGTCACCTTCCGCCCGGGTACCGACCCGGATCAGGCGCAGGTTCAGGTGCAGAACCGCGTCGCGCAGGCCGAAGCGCGTCTGCCGGAGGATGTACGCCGTCTGGGGATCACCACCCAGAAGCAGTCTCCGACGCTGACCCTGGTGGTGCATCTGTTTTCGCCAAACGGTAAGTACGACTCGCTGTATATGCGCAACTACGCCACGCTGAAAGTGAAGGATGAGCTGGCGCGCCTGCCCGGCGTCGGCCAGATCCAGATTTTTGGCTCCGGTGAATATGCGATGCGCGTCTGGCTGGATCCCAATAAGGTCGCGGCCCGCGGTCTGACGGCCTCGGATGTGGTGACGGCGATGCAGGAGCAAAACGTCCAGGTGTCTGCCGGACAGCTTGGCGCCGAGCCGCTGCCGCAGGAGAGCGATTTCCTGATCTCCATTAACGCCCAGGGC'..b'GGAAGCGAAAATCATCGAACTGGCTGGCCACCTGGATACCTATATCCCGGAACCAGAGCGTGCGATTGACAAGCCGTTCCTGCTGCCGATCGAAGACGTATTCTCCATCTCTGGTCGTGGTACCGTTGTTACCGGTCGTGTAGAGCGCGGTATCATCAAAGTAGGTGAAGAAGTTGAAATCGTTGGTATCAAAGAAACCGCGAAAACCACCTGTACTGGCGTTGAAATGTTCCGCAAACTGCTGGACGAAGGCCGTGCTGGTGAGAACGTAGGTGTTCTGCTGCGTGGTATCAAACGTGAAGAAATCGAACGTGGTCAGGTACTGGCTAAGCCGGGCACCATCAACCCGCACACCAAGTTCGAATCTGAAGTGTACATCCTGTCCAAAGATGAAGGCGGCCGTCACACTCCGTTCTTCAAAGGCTACCGTCCGCAGTTCTACTTCCGTACTACTGACGTGACTGGCACCATCGAACTGCCGGAAGGCGTAGAGATGGTAATGCCGGGCGACAACATCAAAATGGTTGTTACCCTGATCCACCCGATCGCGATGGACGACGGTCTGCGTTTCGCAATCCGTGAAGGC\tARAFDQIDNAPEEKARGITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALEGDAEWEAKIIELAGHLDTYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIKETAKTTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTINPHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMVVTLIHPIAMDDGLRFAIREG\tMLSPEGESTIVRNIAVSKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARGITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALEGDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKPHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMVVTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLG\t82.40\tgnl|BL_ORD_ID|2022|hsp_num:0\t2158\tTrue\tloose hit with at least 95 percent identity pushed strict\r\n+NODE_11_length_157792_cov_39.2115_111 # 107958 # 108392 # 1 # ID=11_111;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.545\tNODE_11_length_157792_cov_39.2115_111\t107958\t108392\t+\tStrict\t210\t251.906\tEscherichia coli marR mutant conferring antibiotic resistance\t83.33\t3003378\tprotein overexpression model\tn/a\tn/a\tfluoroquinolone antibiotic; cephalosporin; glycylcycline; penam; tetracycline antibiotic; rifamycin antibiotic; phenicol antibiotic; triclosan\tantibiotic target alteration; antibiotic efflux\tresistance-nodulation-cell division (RND) antibiotic efflux pump\tATGAAAAGTACCAGCGACCTGTTTAATGAAATGATCCCGCTGGGTCGCTTGATCCAGATGGTTAACCAGAAAAAAGATCGCCTGCTCAATGACTACCTCTCACCTATGGATATTACCGCGACCCAGTTTCGCGTGCTCTGCTCCATTCGTTGCGAAGTATGTATTACCCCCGTTGAGCTGAAAACCGTGCTTTCCGTCGACCCGGGCGCAATGACGCGCATGCTCGACCGCCTGGCGTGCAAAGGCTGGATTAAACGGTTACCCAACCCCGCTGACAAGCGCGGCGTGCTGGTGCAGTTGACGCCGGACGGCGCAGCCCTTTGCGAGCAGTGTCATCAGGTTGTGGGTCAGAAGTTACACCAGGAGTTAACGAAAAATCTGTCGGCGGACGAAGTCGCCATGCTTGAGCAACTGCTCAAGAAGGTCCTGCCGTAA\tMKSTSDLFNEMIPLGRLIQMVNQKKDRLLNDYLSPMDITATQFRVLCSIRCEVCITPVELKTVLSVDPGAMTRMLDRLACKGWIKRLPNPADKRGVLVQLTPDGAALCEQCHQVVGQKLHQELTKNLSADEVAMLEQLLKKVLP\tMKSTSDLFNEIIPLGRLIHMVNQKKDRLLNEYLSPLDITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTGGAAICEQCHQLVGQDLHQELTKNLTADEVATLEYLLKKVLP\t100.00\tgnl|BL_ORD_ID|2040|hsp_num:0\t431\t\t\r\n+NODE_152_length_397_cov_0.740741_1 # 1 # 270 # -1 # ID=152_1;partial=10;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.637\tNODE_152_length_397_cov_0.740741_1 \t1\t270\t-\tStrict\t310\t182.956\tType B NfxB\t100.0\t3004060\tprotein overexpression model\tn/a\tn/a\tmacrolide antibiotic; fluoroquinolone antibiotic; aminoglycoside antibiotic; cephalosporin; penam; tetracycline antibiotic; aminocoumarin antibiotic; diaminopyrimidine antibiotic; phenicol antibiotic\tantibiotic efflux\tresistance-nodulation-cell division (RND) antibiotic efflux pump\tATGACCCTGATTTCCCATGACGAGCGACTCATCAAGGCGCTGGCAGTCGCTATCGTCGACCGCCCACGAGCGACGCTGAAGGAACTGGCCGAGGCGGCCGGCGTAAGCAAGGCCACCCTGCACCGCTTCTGCGGCACGCGGGACAACCTGGTGCAGATGCTCGAGGACCACGGAGAGACCGTACTGAACCAGATCATCCAGGCCTGCGACCTGGAGCATGCCGAGCCTCTGGAGGCGTTGCAGCGCCTGATCAAGGAACACCTCACCCAC\tMTLISHDERLIKALAVAIVDRPRATLKELAEAAGVSKATLHRFCGTRDNLVQMLEDHGETVLNQIIQACDLEHAEPLEALQRLIKEHLTH\tMTLISHDERLIKALAVAIVDRPRATLKELAEAAGVSKATLHRFCGTRDNLVQMLEDHGETVLNQIIQACDLEHAEPLEALQRLIKEHLTHRELLVFLVFQYRPDFLDPHGEGARWQSYLEALDAFFLRGQQKGVFRIDITAAVFTELFITLVYGMVDAERRGRAASSNSAHTLEQMFLHGASNPARS\t48.13\tgnl|BL_ORD_ID|2412|hsp_num:0\t2693\tTrue\tloose hit with at least 95 percent identity pushed strict\r\n' |
| b |
| diff -r 000000000000 -r d2590ecc4189 test-data/summary.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary.json Tue Mar 16 12:38:42 2021 +0000 |
| [ |
| b'@@ -0,0 +1,1 @@\n+[{"input_file_name":"GCF_010120755.1_ASM1012075v1_genomic","gene_symbol":"aacA-ENT1","gene_name":"aminoglycoside 6\'-N-acetyltransferase","reference_database_id":"ncbi","reference_database_version":"db_v_1","reference_accession":"NG_052371.1","analysis_software_name":"abricate","analysis_software_version":"tool_v_1","sequence_identity":100.0,"input_sequence_id":"NZ_CP039729.1","input_protein_start":"","input_protein_stop":"","input_gene_start":2163439,"input_gene_stop":2163987,"reference_protein_start":"","reference_protein_stop":"","reference_gene_start":"","reference_gene_stop":"","strand_orientation":"-","coverage_depth":"","coverage_percentage":100.0,"coverage_ratio":"","reference_gene_length":"","reference_protein_length":"","input_gene_length":"","input_protein_length":"","drug_class":"AMINOGLYCOSIDE","antimicrobial_agent":"","resistance_mechanism":""},{"input_file_name":"GCF_010120755.1_ASM1012075v1_genomic","gene_symbol":"aacA-ENT1","gene_name":"aminoglycoside 6\'-N-acetyltransferase","reference_database_id":"ncbi","reference_database_version":"db_v_1","reference_accession":"NG_052371.1","analysis_software_name":"abricate","analysis_software_version":"tool_v_1","sequence_identity":100.0,"input_sequence_id":"NZ_CP039729.1","input_protein_start":null,"input_protein_stop":null,"input_gene_start":2163439,"input_gene_stop":2163987,"reference_protein_start":null,"reference_protein_stop":null,"reference_gene_start":null,"reference_gene_stop":null,"strand_orientation":"-","coverage_depth":null,"coverage_percentage":100.0,"coverage_ratio":null,"reference_gene_length":null,"reference_protein_length":null,"input_gene_length":null,"input_protein_length":null,"drug_class":"AMINOGLYCOSIDE","antimicrobial_agent":null,"resistance_mechanism":null},{"input_file_name":"GCF_010120755.1_ASM1012075v1_genomic","gene_symbol":"eat(A)","gene_name":"ABC-F type ribosomal protection protein Eat(A)","reference_database_id":"ncbi","reference_database_version":"db_v_1","reference_accession":"NG_047762.1","analysis_software_name":"abricate","analysis_software_version":"tool_v_1","sequence_identity":100.0,"input_sequence_id":"NZ_CP039729.1","input_protein_start":"","input_protein_stop":"","input_gene_start":656118,"input_gene_stop":657620,"reference_protein_start":"","reference_protein_stop":"","reference_gene_start":"","reference_gene_stop":"","strand_orientation":"+","coverage_depth":"","coverage_percentage":100.0,"coverage_ratio":"","reference_gene_length":"","reference_protein_length":"","input_gene_length":"","input_protein_length":"","drug_class":"PLEUROMUTILIN","antimicrobial_agent":"","resistance_mechanism":""},{"input_file_name":"GCF_010120755.1_ASM1012075v1_genomic","gene_symbol":"eat(A)","gene_name":"ABC-F type ribosomal protection protein Eat(A)","reference_database_id":"ncbi","reference_database_version":"db_v_1","reference_accession":"NG_047762.1","analysis_software_name":"abricate","analysis_software_version":"tool_v_1","sequence_identity":100.0,"input_sequence_id":"NZ_CP039729.1","input_protein_start":null,"input_protein_stop":null,"input_gene_start":656118,"input_gene_stop":657620,"reference_protein_start":null,"reference_protein_stop":null,"reference_gene_start":null,"reference_gene_stop":null,"strand_orientation":"+","coverage_depth":null,"coverage_percentage":100.0,"coverage_ratio":null,"reference_gene_length":null,"reference_protein_length":null,"input_gene_length":null,"input_protein_length":null,"drug_class":"PLEUROMUTILIN","antimicrobial_agent":null,"resistance_mechanism":null},{"input_file_name":"GCF_010120755.1_ASM1012075v1_genomic","gene_symbol":"msr(C)","gene_name":"ABC-F type ribosomal protection protein Msr(C)","reference_database_id":"ncbi","reference_database_version":"db_v_1","reference_accession":"NG_048003.1","analysis_software_name":"abricate","analysis_software_version":"tool_v_1","sequence_identity":98.92,"input_sequence_id":"NZ_CP039729.1","input_protein_start":"","input_protein_stop":"","input_gen'..b'eference_gene_stop":null,"strand_orientation":"+","coverage_depth":null,"coverage_percentage":100.0,"coverage_ratio":null,"reference_gene_length":null,"reference_protein_length":null,"input_gene_length":null,"input_protein_length":null,"drug_class":"fluoroquinolone antibiotic; glycylcycline; tetracycline antibiotic; diaminopyrimidine antibiotic; nitrofuran antibiotic","antimicrobial_agent":null,"resistance_mechanism":"antibiotic efflux"},{"input_file_name":"rgi_report","gene_symbol":"rmtC","gene_name":"16S rRNA methyltransferase (G1405)","reference_database_id":"CARD","reference_database_version":"card_v1","reference_accession":3000861,"analysis_software_name":"rgi","analysis_software_version":"rgi_v1","sequence_identity":100.0,"input_sequence_id":"NODE_40_length_7360_cov_24.8738_6","input_protein_start":"","input_protein_stop":"","input_gene_start":6358,"input_gene_stop":7203,"reference_protein_start":"","reference_protein_stop":"","reference_gene_start":"","reference_gene_stop":"","strand_orientation":"-","coverage_depth":"","coverage_percentage":100.0,"coverage_ratio":"","reference_gene_length":"","reference_protein_length":"","input_gene_length":"","input_protein_length":"","drug_class":"aminoglycoside antibiotic","antimicrobial_agent":"","resistance_mechanism":"antibiotic target alteration"},{"input_file_name":"rgi_report","gene_symbol":"rmtC","gene_name":"16S rRNA methyltransferase (G1405)","reference_database_id":"CARD","reference_database_version":"card_v1","reference_accession":3000861,"analysis_software_name":"rgi","analysis_software_version":"rgi_v1","sequence_identity":100.0,"input_sequence_id":"NODE_40_length_7360_cov_24.8738_6","input_protein_start":null,"input_protein_stop":null,"input_gene_start":6358,"input_gene_stop":7203,"reference_protein_start":null,"reference_protein_stop":null,"reference_gene_start":null,"reference_gene_stop":null,"strand_orientation":"-","coverage_depth":null,"coverage_percentage":100.0,"coverage_ratio":null,"reference_gene_length":null,"reference_protein_length":null,"input_gene_length":null,"input_protein_length":null,"drug_class":"aminoglycoside antibiotic","antimicrobial_agent":null,"resistance_mechanism":"antibiotic target alteration"},{"input_file_name":"rgi_report","gene_symbol":"sul1","gene_name":"sulfonamide resistant sul","reference_database_id":"CARD","reference_database_version":"card_v1","reference_accession":3000410,"analysis_software_name":"rgi","analysis_software_version":"rgi_v1","sequence_identity":100.0,"input_sequence_id":"NODE_57_length_1134_cov_34.8908_1","input_protein_start":"","input_protein_stop":"","input_gene_start":25,"input_gene_stop":864,"reference_protein_start":"","reference_protein_stop":"","reference_gene_start":"","reference_gene_stop":"","strand_orientation":"-","coverage_depth":"","coverage_percentage":100.0,"coverage_ratio":"","reference_gene_length":"","reference_protein_length":"","input_gene_length":"","input_protein_length":"","drug_class":"sulfonamide antibiotic","antimicrobial_agent":"","resistance_mechanism":"antibiotic target replacement"},{"input_file_name":"rgi_report","gene_symbol":"sul1","gene_name":"sulfonamide resistant sul","reference_database_id":"CARD","reference_database_version":"card_v1","reference_accession":3000410,"analysis_software_name":"rgi","analysis_software_version":"rgi_v1","sequence_identity":100.0,"input_sequence_id":"NODE_57_length_1134_cov_34.8908_1","input_protein_start":null,"input_protein_stop":null,"input_gene_start":25,"input_gene_stop":864,"reference_protein_start":null,"reference_protein_stop":null,"reference_gene_start":null,"reference_gene_stop":null,"strand_orientation":"-","coverage_depth":null,"coverage_percentage":100.0,"coverage_ratio":null,"reference_gene_length":null,"reference_protein_length":null,"input_gene_length":null,"input_protein_length":null,"drug_class":"sulfonamide antibiotic","antimicrobial_agent":null,"resistance_mechanism":"antibiotic target replacement"}]\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r d2590ecc4189 test-data/summary.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary.tsv Tue Mar 16 12:38:42 2021 +0000 |
| b |
| b"@@ -0,0 +1,155 @@\n+input_file_name\tgene_symbol\tgene_name\treference_database_id\treference_database_version\treference_accession\tanalysis_software_name\tanalysis_software_version\tsequence_identity\tinput_sequence_id\tinput_protein_start\tinput_protein_stop\tinput_gene_start\tinput_gene_stop\treference_protein_start\treference_protein_stop\treference_gene_start\treference_gene_stop\tstrand_orientation\tcoverage_depth\tcoverage_percentage\tcoverage_ratio\treference_gene_length\treference_protein_length\tinput_gene_length\tinput_protein_length\tdrug_class\tantimicrobial_agent\tresistance_mechanism\n+GCF_010120755.1_ASM1012075v1_genomic\taacA-ENT1\taminoglycoside 6'-N-acetyltransferase\tncbi\tdb_v_1\tNG_052371.1\tabricate\ttool_v_1\t100.0\tNZ_CP039729.1\t\t\t2163439\t2163987\t\t\t\t\t-\t\t100.0\t\t\t\t\t\tAMINOGLYCOSIDE\t\t\n+GCF_010120755.1_ASM1012075v1_genomic\taacA-ENT1\taminoglycoside 6'-N-acetyltransferase\tncbi\tdb_v_1\tNG_052371.1\tabricate\ttool_v_1\t100.0\tNZ_CP039729.1\t\t\t2163439\t2163987\t\t\t\t\t-\t\t100.0\t\t\t\t\t\tAMINOGLYCOSIDE\t\t\n+GCF_010120755.1_ASM1012075v1_genomic\teat(A)\tABC-F type ribosomal protection protein Eat(A)\tncbi\tdb_v_1\tNG_047762.1\tabricate\ttool_v_1\t100.0\tNZ_CP039729.1\t\t\t656118\t657620\t\t\t\t\t+\t\t100.0\t\t\t\t\t\tPLEUROMUTILIN\t\t\n+GCF_010120755.1_ASM1012075v1_genomic\teat(A)\tABC-F type ribosomal protection protein Eat(A)\tncbi\tdb_v_1\tNG_047762.1\tabricate\ttool_v_1\t100.0\tNZ_CP039729.1\t\t\t656118\t657620\t\t\t\t\t+\t\t100.0\t\t\t\t\t\tPLEUROMUTILIN\t\t\n+GCF_010120755.1_ASM1012075v1_genomic\tmsr(C)\tABC-F type ribosomal protection protein Msr(C)\tncbi\tdb_v_1\tNG_048003.1\tabricate\ttool_v_1\t98.92\tNZ_CP039729.1\t\t\t2564038\t2565516\t\t\t\t\t-\t\t100.0\t\t\t\t\t\tMACROLIDE\t\t\n+GCF_010120755.1_ASM1012075v1_genomic\tmsr(C)\tABC-F type ribosomal protection protein Msr(C)\tncbi\tdb_v_1\tNG_048003.1\tabricate\ttool_v_1\t98.92\tNZ_CP039729.1\t\t\t2564038\t2565516\t\t\t\t\t-\t\t100.0\t\t\t\t\t\tMACROLIDE\t\t\n+GCF_010120755.1_ASM1012075v1_genomic\tvanH-M\tD-lactate dehydrogenase VanH-M\tncbi\tdb_v_1\tNG_048388.1\tabricate\ttool_v_1\t100.0\tNZ_CP039730.1\t\t\t45227\t46207\t\t\t\t\t-\t\t100.0\t\t\t\t\t\tVANCOMYCIN\t\t\n+GCF_010120755.1_ASM1012075v1_genomic\tvanH-M\tD-lactate dehydrogenase VanH-M\tncbi\tdb_v_1\tNG_048388.1\tabricate\ttool_v_1\t100.0\tNZ_CP039730.1\t\t\t45227\t46207\t\t\t\t\t-\t\t100.0\t\t\t\t\t\tVANCOMYCIN\t\t\n+GCF_010120755.1_ASM1012075v1_genomic\tvanM\tD-alanine--(R)-lactate ligase VanM\tncbi\tdb_v_1\tNG_048396.1\tabricate\ttool_v_1\t100.0\tNZ_CP039730.1\t\t\t44203\t45234\t\t\t\t\t-\t\t100.0\t\t\t\t\t\tVANCOMYCIN\t\t\n+GCF_010120755.1_ASM1012075v1_genomic\tvanM\tD-alanine--(R)-lactate ligase VanM\tncbi\tdb_v_1\tNG_048396.1\tabricate\ttool_v_1\t100.0\tNZ_CP039730.1\t\t\t44203\t45234\t\t\t\t\t-\t\t100.0\t\t\t\t\t\tVANCOMYCIN\t\t\n+GCF_010120755.1_ASM1012075v1_genomic\tvanS-M\tVanM-type vancomycin resistance histidine kinase VanS\tncbi\tdb_v_1\tNG_048450.1\tabricate\ttool_v_1\t100.0\tNZ_CP039730.1\t\t\t47306\t48418\t\t\t\t\t-\t\t100.0\t\t\t\t\t\tVANCOMYCIN\t\t\n+GCF_010120755.1_ASM1012075v1_genomic\tvanS-M\tVanM-type vancomycin resistance histidine kinase VanS\tncbi\tdb_v_1\tNG_048450.1\tabricate\ttool_v_1\t100.0\tNZ_CP039730.1\t\t\t47306\t48418\t\t\t\t\t-\t\t100.0\t\t\t\t\t\tVANCOMYCIN\t\t\n+GCF_010120755.1_ASM1012075v1_genomic\tvanX-M\tD-Ala-D-Ala dipeptidase VanX-M\tncbi\tdb_v_1\tNG_048495.1\tabricate\ttool_v_1\t100.0\tNZ_CP039730.1\t\t\t43619\t44197\t\t\t\t\t-\t\t95.07\t\t\t\t\t\tVANCOMYCIN\t\t\n+GCF_010120755.1_ASM1012075v1_genomic\tvanX-M\tD-Ala-D-Ala dipeptidase VanX-M\tncbi\tdb_v_1\tNG_048495.1\tabricate\ttool_v_1\t100.0\tNZ_CP039730.1\t\t\t43619\t44197\t\t\t\t\t-\t\t95.07\t\t\t\t\t\tVANCOMYCIN\t\t\n+ariba_report\tAAC_3__IId\tAAC_3__IId.3004623.EU022314.1.0_861.5344\tdbname\tdb_v_1\tAAC_3__IId.3004623.EU022314.1.0_861.5344\tariba\tariba_v1\t99.88\tAAC_3__II-.l15.c4.ctg.1\t\t\t\t\t\t\t\t\t\t37.8\t\t\t861\t\t\t\t\t\t\n+ariba_report\tAAC_3__IId\tAAC_3__IId.3004623.EU022314.1.0_861.5344\tdbname\tdb_v_1\tAAC_3__IId.3004623.EU022314.1.0_861.5344\tariba\tariba_v1\t99.88\tAAC_3__II-.l15.c4.ctg.1\t\t\t\t\t\t\t\t\t\t37.8\t\t\t861\t\t\t\t\t\t\n+ariba_report\tAAC_6___Ib4\tAAC_6___Ib4.3002577.AF445082.2788_3343.401\tdbname\tdb_v_1\tAAC_6___Ib4.3002577.AF445082.2788_3343.401\tariba\tariba_v1\t99.64\tAAC_6___Ib+.l15.c30.ctg.1\t\t\t\t\t\t\t\t\t\t128.1\t\t\t555\t\t\t\t\t\t\n+ariba_report\tAAC_6___Ib4\tAAC_6___Ib4.3002577.AF445082.2788_3343.401\tdbname\tdb_v_1\tAAC_6___Ib4.3002577.AF4450"..b' to antibiotic\n+rgi_report\tmarA\tresistance-nodulation-cell division (RND) antibiotic efflux pump; 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glycylcycline; tetracycline antibiotic; diaminopyrimidine antibiotic; nitrofuran antibiotic\t\tantibiotic efflux\n+rgi_report\toqxA\tresistance-nodulation-cell division (RND) antibiotic efflux pump\tCARD\tcard_v1\t3003922\trgi\trgi_v1\t100.0\tNODE_1_length_803036_cov_42.265_33\t\t\t30758\t31933\t\t\t\t\t+\t\t100.0\t\t\t\t\t\tfluoroquinolone antibiotic; glycylcycline; tetracycline antibiotic; diaminopyrimidine antibiotic; nitrofuran antibiotic\t\tantibiotic efflux\n+rgi_report\toqxB\tresistance-nodulation-cell division (RND) antibiotic efflux pump\tCARD\tcard_v1\t3003923\trgi\trgi_v1\t99.52\tNODE_1_length_803036_cov_42.265_34\t\t\t31957\t35109\t\t\t\t\t+\t\t100.0\t\t\t\t\t\tfluoroquinolone antibiotic; glycylcycline; tetracycline antibiotic; diaminopyrimidine antibiotic; nitrofuran antibiotic\t\tantibiotic efflux\n+rgi_report\toqxB\tresistance-nodulation-cell division (RND) antibiotic efflux pump\tCARD\tcard_v1\t3003923\trgi\trgi_v1\t99.52\tNODE_1_length_803036_cov_42.265_34\t\t\t31957\t35109\t\t\t\t\t+\t\t100.0\t\t\t\t\t\tfluoroquinolone antibiotic; glycylcycline; tetracycline antibiotic; diaminopyrimidine antibiotic; nitrofuran antibiotic\t\tantibiotic efflux\n+rgi_report\trmtC\t16S rRNA methyltransferase (G1405)\tCARD\tcard_v1\t3000861\trgi\trgi_v1\t100.0\tNODE_40_length_7360_cov_24.8738_6\t\t\t6358\t7203\t\t\t\t\t-\t\t100.0\t\t\t\t\t\taminoglycoside antibiotic\t\tantibiotic target alteration\n+rgi_report\trmtC\t16S rRNA methyltransferase (G1405)\tCARD\tcard_v1\t3000861\trgi\trgi_v1\t100.0\tNODE_40_length_7360_cov_24.8738_6\t\t\t6358\t7203\t\t\t\t\t-\t\t100.0\t\t\t\t\t\taminoglycoside antibiotic\t\tantibiotic target alteration\n+rgi_report\tsul1\tsulfonamide resistant sul\tCARD\tcard_v1\t3000410\trgi\trgi_v1\t100.0\tNODE_57_length_1134_cov_34.8908_1\t\t\t25\t864\t\t\t\t\t-\t\t100.0\t\t\t\t\t\tsulfonamide antibiotic\t\tantibiotic target replacement\n+rgi_report\tsul1\tsulfonamide resistant sul\tCARD\tcard_v1\t3000410\trgi\trgi_v1\t100.0\tNODE_57_length_1134_cov_34.8908_1\t\t\t25\t864\t\t\t\t\t-\t\t100.0\t\t\t\t\t\tsulfonamide antibiotic\t\tantibiotic target replacement\n' |