| Previous changeset 3:2262e531c50b (2020-01-02) |
|
Commit message:
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb" |
|
modified:
screen_abricate_report.py screen_abricate_report.xml |
|
added:
test-data/SAMN11840202-abricate_report_full.tsv test-data/SAMN11840202-abricate_report_screened.tsv test-data/SAMN11840202-gene_detection_status.tsv test-data/SAMN11840203-abricate_report_full.tsv test-data/SAMN11840203-abricate_report_screened.tsv test-data/SAMN11840203-gene_detection_status.tsv test-data/SAMN13042171-abricate_report_full.tsv test-data/SAMN13042171-abricate_report_screened.tsv test-data/SAMN13042171-gene_detection_status.tsv |
|
removed:
test-data/SAMN13042171_abricate_report.tsv test-data/SAMN13042171_abricate_report_screened.tsv test-data/SAMN13042171_gene_detection_status.tsv |
| b |
| diff -r 2262e531c50b -r 22247b1a59d5 screen_abricate_report.py --- a/screen_abricate_report.py Thu Jan 02 17:14:34 2020 -0500 +++ b/screen_abricate_report.py Fri Jan 03 14:30:22 2020 -0500 |
| [ |
| @@ -57,7 +57,7 @@ def main(args): screen = parse_screen_file(args.screening_file) - gene_detection_status_fieldnames = ['gene_name', 'detected'] + gene_detection_status_fieldnames = ['gene_name', 'detected', 'alleles'] with open(args.abricate_report, 'r') as f1, \ open(args.screened_report, 'w') as f2, \ open(args.gene_detection_status, 'w') as f3: @@ -72,11 +72,19 @@ for gene in screen: gene_detection_status = { 'gene_name': gene['gene_name'], - 'detected': False + 'detected': False, + 'alleles': None, } for abricate_report_row in abricate_report_reader: if detect_gene(abricate_report_row, gene['regex'], args.min_coverage, args.min_identity): gene_detection_status['detected'] = True + if not gene_detection_status['alleles']: + gene_detection_status['alleles'] = abricate_report_row['GENE'] + else: + gene_detection_status['alleles'] = ",".join([ + gene_detection_status['alleles'], + abricate_report_row['GENE'], + ]) screened_report_writer.writerow(abricate_report_row) gene_detection_status_writer.writerow(gene_detection_status) f1.seek(0) # return file pointer to start of abricate report @@ -92,8 +100,11 @@ parser.add_argument("--gene_detection_status", help=("Output: detection status for all genes listed in the screening file (tsv)")) parser.add_argument("--min_coverage", type=float, default=90.0, - choices=Range(0.0, 100.0), help=("Minimum percent coverage")) + choices=Range(0.0, 100.0), + help=("Minimum percent coverage (default 90.0)")) parser.add_argument("--min_identity", type=float, default=90.0, - choices=Range(0.0, 100.0), help=("Minimum percent identity")) + choices=Range(0.0, 100.0), + help=("Minimum percent identity (default 90.0)")) + parser.add_argument("-v", "--version", action='version', version='%(prog)s 0.4.0') args = parser.parse_args() main(args) |
| b |
| diff -r 2262e531c50b -r 22247b1a59d5 screen_abricate_report.xml --- a/screen_abricate_report.xml Thu Jan 02 17:14:34 2020 -0500 +++ b/screen_abricate_report.xml Fri Jan 03 14:30:22 2020 -0500 |
| [ |
| @@ -1,7 +1,8 @@ -<tool id="screen_abricate_report" name="Screen Abricate Report" version="0.3.0"> +<tool id="screen_abricate_report" name="Screen Abricate Report" version="0.4.0+galaxy0"> <description>Screens an abricate report for genes of interest</description> <requirements> </requirements> + <version_command><![CDATA[screen_abricate_report.py --version]]></version_command> <command detect_errors="exit_code"><![CDATA[ '${__tool_directory__}/screen_abricate_report.py' '${abricate_report}' @@ -48,16 +49,30 @@ <test> <param name="screening_file_source.screening_file_source_selector" value="tool_data_table" /> <param name="screening_file_source.screening_file" value="test_entry"/> - <param name="abricate_report" value="SAMN13042171_abricate_report.tsv"/> - <output name="screened_report" file="SAMN13042171_abricate_report_screened.tsv" ftype="tabular"/> - <output name="gene_detection_status" file="SAMN13042171_gene_detection_status.tsv" ftype="tabular"/> + <param name="abricate_report" value="SAMN13042171-abricate_report_full.tsv"/> + <output name="screened_report" file="SAMN13042171-abricate_report_screened.tsv" ftype="tabular"/> + <output name="gene_detection_status" file="SAMN13042171-gene_detection_status.tsv" ftype="tabular"/> </test> <test> <param name="screening_file_source.screening_file_source_selector" value="history" /> <param name="screening_file_source.screening_file" value="screening_file.tsv"/> - <param name="abricate_report" value="SAMN13042171_abricate_report.tsv"/> - <output name="screened_report" file="SAMN13042171_abricate_report_screened.tsv" ftype="tabular"/> - <output name="gene_detection_status" file="SAMN13042171_gene_detection_status.tsv" ftype="tabular"/> + <param name="abricate_report" value="SAMN13042171-abricate_report_full.tsv"/> + <output name="screened_report" file="SAMN13042171-abricate_report_screened.tsv" ftype="tabular"/> + <output name="gene_detection_status" file="SAMN13042171-gene_detection_status.tsv" ftype="tabular"/> + </test> + <test> + <param name="screening_file_source.screening_file_source_selector" value="history" /> + <param name="screening_file_source.screening_file" value="screening_file.tsv"/> + <param name="abricate_report" value="SAMN11840202-abricate_report_full.tsv"/> + <output name="screened_report" file="SAMN11840202-abricate_report_screened.tsv" ftype="tabular"/> + <output name="gene_detection_status" file="SAMN11840202-gene_detection_status.tsv" ftype="tabular"/> + </test> + <test> + <param name="screening_file_source.screening_file_source_selector" value="history" /> + <param name="screening_file_source.screening_file" value="screening_file.tsv"/> + <param name="abricate_report" value="SAMN11840203-abricate_report_full.tsv"/> + <output name="screened_report" file="SAMN11840203-abricate_report_screened.tsv" ftype="tabular"/> + <output name="gene_detection_status" file="SAMN11840203-gene_detection_status.tsv" ftype="tabular"/> </test> </tests> <help><![CDATA[ |
| b |
| diff -r 2262e531c50b -r 22247b1a59d5 test-data/SAMN11840202-abricate_report_full.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SAMN11840202-abricate_report_full.tsv Fri Jan 03 14:30:22 2020 -0500 |
| b |
| b'@@ -0,0 +1,63 @@\n+#FILE\tSEQUENCE\tSTART\tEND\tSTRAND\tGENE\tCOVERAGE\tCOVERAGE_MAP\tGAPS\t%COVERAGE\t%IDENTITY\tDATABASE\tACCESSION\tPRODUCT\tRESISTANCE\n+SAMN11840202\tcontig00001\t43895\t45142\t+\tmdtA\t1-1248/1248\t===============\t0/0\t100.00\t98.00\tcard\tU00096:2154016-2155264\tMdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.\tantibacterial_free_fatty_acids/aminoglycoside/diaminopyrimidine/carbapenem/aminocoumarin/phenicol/glycylcycline/monobactam/penam/fluoroquinolone/macrolide/acridine_dye/triclosan/tetracycline\n+SAMN11840202\tcontig00001\t45142\t48264\t+\tmdtB\t1-3123/3123\t===============\t0/0\t100.00\t99.84\tcard\tU00096:2155263-2158386\tMdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.\taminocoumarin/aminoglycoside/diaminopyrimidine/carbapenem/antibacterial_free_fatty_acids/acridine_dye/tetracycline/triclosan/penam/fluoroquinolone/macrolide/phenicol/glycylcycline/monobactam\n+SAMN11840202\tcontig00001\t48265\t51342\t+\tmdtC\t1-3078/3078\t===============\t0/0\t100.00\t99.84\tcard\tU00096:2158386-2161464\tMdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.\tdiaminopyrimidine/carbapenem/aminoglycoside/antibacterial_free_fatty_acids/aminocoumarin/glycylcycline/monobactam/phenicol/acridine_dye/triclosan/tetracycline/macrolide/fluoroquinolone/penam\n+SAMN11840202\tcontig00001\t52755\t54158\t+\tbaeS\t1-1404/1404\t===============\t0/0\t100.00\t99.93\tcard\tAP009048:2165013-2166417\tBaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.\taminocoumarin/carbapenem/diaminopyrimidine/aminoglycoside/antibacterial_free_fatty_acids/tetracycline/triclosan/acridine_dye/macrolide/fluoroquinolone/penam/monobactam/glycylcycline/phenicol\n+SAMN11840202\tcontig00001\t54155\t54877\t+\tbaeR\t1-723/723\t===============\t0/0\t100.00\t99.45\tcard\tAP009048.1:2166413-2167136\tBaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.\tphenicol/monobactam/glycylcycline/tetracycline/triclosan/acridine_dye/penam/fluoroquinolone/macrolide/aminoglycoside/carbapenem/diaminopyrimidine/antibacterial_free_fatty_acids/aminocoumarin\n+SAMN11840202\tcontig00001\t197758\t199401\t-\tyojI\t1-1644/1644\t===============\t0/0\t100.00\t97.51\tcard\tU00096.3:2306972-2308616\tYojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.\tpeptide/nitroimidazole/rifamycin/pleuromutilin/penam/fluoroquinolone/cephalosporin/macrolide/tetracycline/acridine_dye\n+SAMN11840202\tcontig00001\t257738\t258706\t+\tpmrF\t1-969/969\t===============\t0/0\t100.00\t100.00\tcard\tU00096:2367071-2368040\tPmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.\tpeptide\n+SAMN11840202\tcontig00002\t125167\t126915\t-\tmsbA\t1-1749/1749\t===============\t0/0\t100.00\t100.00\tcard\tU00096.3:966621-968370\tMsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). Ms'..b"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.\tglycopeptide\n+SAMN11840202\tcontig00074\t5686\t6525\t-\tsul1\t1-840/840\t===============\t0/0\t100.00\t100.00\tcard\tJF969163:1054-1894\tSul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.\tsulfonamide\n+SAMN11840202\tcontig00074\t7030\t7809\t-\taadA2\t1-780/780\t===============\t0/0\t100.00\t99.87\tcard\tAF156486:5013-5793\taadA2 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids and integrons in K. pneumoniae Salmonella spp. Corynebacterium glutamicum C. freundii and Aeromonas spp.\taminoglycoside\n+SAMN11840202\tcontig00074\t8229\t8726\t-\tdfrA12\t1-498/498\t===============\t0/0\t100.00\t100.00\tcard\tGU585907.1:21606-22104\tdfrA12 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae\tdiaminopyrimidine\n+SAMN11840202\tcontig00074\t8727\t8975\t-\tAAC(6')-Ib7\t1-249/980\t====...........\t0/0\t25.41\t98.80\tcard\tY11946.1:1-981\tAAC(6')-Ib7 is a plasmid-encoded aminoglycoside acetyltransferase in E. cloacae and C. freundii\taminoglycoside\n+SAMN11840202\tcontig00077\t5190\t8294\t-\tacrF\t1-3105/3105\t===============\t0/0\t100.00\t99.97\tcard\tU00096:3415033-3418138\tAcrF is a inner membrane transporter similar to AcrB.\taminoglycoside/carbapenem/diaminopyrimidine/antibacterial_free_fatty_acids/aminocoumarin/cephamycin/phenicol/monobactam/glycylcycline/tetracycline/triclosan/acridine_dye/fluoroquinolone/penam/cephalosporin/macrolide\n+SAMN11840202\tcontig00077\t8306\t9272\t-\tacrE\t192-1158/1158\t..=============\t0/0\t83.51\t99.90\tcard\tU00096:3413864-3415022\tAcrE is a membrane fusion protein similar to AcrA.\taminocoumarin/cephamycin/carbapenem/diaminopyrimidine/aminoglycoside/antibacterial_free_fatty_acids/triclosan/tetracycline/acridine_dye/cephalosporin/macrolide/penam/fluoroquinolone/monobactam/glycylcycline/phenicol\n+SAMN11840202\tcontig00080\t1250\t2005\t-\trmtB\t1-756/756\t===============\t0/0\t100.00\t100.00\tcard\tAM886293.1:116480-117236\tRmtB is a 16S rRNA methyltransferase that targets mature or nearly mature 30S subunits. It transfers a methyl group from S-adenosyl-L-methionine to N7-G1405 of the 16S rRNA an aminoglycoside binding site.\taminoglycoside\n+SAMN11840202\tcontig00080\t2175\t3035\t-\tTEM-1\t1-861/861\t===============\t0/0\t100.00\t99.88\tcard\tAL513383:161911-162772\tTEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.\tpenam/cephalosporin/penem/monobactam\n+SAMN11840202\tcontig00080\t7165\t8067\t-\tmphA\t1-903/906\t===============\t0/0\t99.67\t100.00\tcard\tD16251.1:1626-2532\tThe mphA gene encodes for resistance enzyme MPH(2')-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2'-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.\tmacrolide\n+SAMN11840202\tcontig00088\t2703\t3578\t-\tCTX-M-15\t1-876/876\t===============\t0/0\t100.00\t100.00\tcard\tAY044436:1436-2312\tCTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family\tcephalosporin\n+SAMN11840202\tcontig00102\t130\t779\t+\tOXA-368\t2072-2721/2721\t...........====\t0/0\t23.89\t99.08\tcard\tKT736121.1:1-2722\tOXA-368 is a beta-lactamase found in Aeromonas sobria. From the Lahey list of OXA beta-lactamases.\tcephalosporin/penam\n+SAMN11840202\tcontig00102\t844\t1674\t+\tOXA-1\t1-831/831\t===============\t0/0\t100.00\t100.00\tcard\tJN420336.1:1400-2231\tOXA-1 is a beta-lactamase found in E. coli\tpenam/cephalosporin\n+SAMN11840202\tcontig00102\t1812\t2256\t+\tcatB3\t1-445/633\t===========....\t0/0\t70.30\t99.78\tcard\tJX101693.1:58201-58834\tcatB3 is a plasmid or chromosome-encoded variant of the cat gene found in Salmonella typhimurium Acinetobacter baumannii and Escherichia coli\tphenicol\n" |
| b |
| diff -r 2262e531c50b -r 22247b1a59d5 test-data/SAMN11840202-abricate_report_screened.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SAMN11840202-abricate_report_screened.tsv Fri Jan 03 14:30:22 2020 -0500 |
| b |
| @@ -0,0 +1,3 @@ +#FILE SEQUENCE START END STRAND GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY DATABASE ACCESSION PRODUCT RESISTANCE +SAMN11840202 contig00074 561 1373 + NDM-5 1-813/813 =============== 0/0 100.00 100.00 card JN104597:115-928 New Delhi beta-lactamase NDM-5. cephamycin/penam/cephalosporin/carbapenem +SAMN11840202 contig00102 844 1674 + OXA-1 1-831/831 =============== 0/0 100.00 100.00 card JN420336.1:1400-2231 OXA-1 is a beta-lactamase found in E. coli penam/cephalosporin |
| b |
| diff -r 2262e531c50b -r 22247b1a59d5 test-data/SAMN11840202-gene_detection_status.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SAMN11840202-gene_detection_status.tsv Fri Jan 03 14:30:22 2020 -0500 |
| b |
| @@ -0,0 +1,5 @@ +gene_name detected alleles +KPC False +NDM True NDM-5 +OXA True OXA-1 +rpoB2 False |
| b |
| diff -r 2262e531c50b -r 22247b1a59d5 test-data/SAMN11840203-abricate_report_full.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SAMN11840203-abricate_report_full.tsv Fri Jan 03 14:30:22 2020 -0500 |
| b |
| b'@@ -0,0 +1,61 @@\n+#FILE\tSEQUENCE\tSTART\tEND\tSTRAND\tGENE\tCOVERAGE\tCOVERAGE_MAP\tGAPS\t%COVERAGE\t%IDENTITY\tDATABASE\tACCESSION\tPRODUCT\tRESISTANCE\n+SAMN11840203\tcontig00001\t316814\t317172\t+\tKlebsiella_pneumoniae_KpnE\t5-363/363\t========/======\t2/2\t98.62\t76.67\tcard\tAP006725.1:2483890-2484253\tKpnE subunit of KpnEF resembles EbrAB from E. coli. Mutation in KpnEF resulted in increased susceptibility to cefepime ceftriaxon colistin erythromycin rifampin tetracycline and streptomycin as well as enhanced sensitivity toward sodium dodecyl sulfate deoxycholate dyes benzalkonium chloride chlorhexidine and triclosan\tdiaminopyrimidine/bicyclomycin/antibacterial_free_fatty_acids/benzalkonium_chloride/isoniazid/lincosamide/nucleoside/nitroimidazole/rifamycin/penam/macrolide/aminoglycoside/peptide/rhodamine/phenicol/glycylcycline/fosfomycin/oxazolidinone/acridine_dye/tetracycline/fluoroquinolone/cephalosporin\n+SAMN11840203\tcontig00001\t317164\t317488\t+\tKlebsiella_pneumoniae_KpnF\t6-330/330\t===============\t0/0\t98.48\t75.69\tcard\tAP006725.1:2484239-2484569\tKpnF subunit of KpnEF resembles EbrAB from E. coli. Mutation in KpnEF resulted in increased susceptibility to cefepime ceftriaxon colistin erythromycin rifampin tetracycline and streptomycin as well as enhanced sensitivity toward sodium dodecyl sulfate deoxycholate dyes benzalkonium chloride chlorhexidine and triclosan.\tfosfomycin/glycylcycline/phenicol/cephalosporin/fluoroquinolone/acridine_dye/oxazolidinone/tetracycline/aminoglycoside/rhodamine/peptide/rifamycin/nitroimidazole/nucleoside/macrolide/penam/bicyclomycin/antibacterial_free_fatty_acids/diaminopyrimidine/isoniazid/lincosamide/benzalkonium_chloride\n+SAMN11840203\tcontig00001\t355656\t356039\t-\tmarA\t1-384/384\t===============\t0/0\t100.00\t99.48\tcard\tAP009048.1:1621288-1621672\tIn the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF.\tantibacterial_free_fatty_acids/penem/diaminopyrimidine/macrolide/penam/rifamycin/cephamycin/aminocoumarin/carbapenem/aminoglycoside/cephalosporin/fluoroquinolone/tetracycline/triclosan/acridine_dye/monobactam/glycylcycline/phenicol\n+SAMN11840203\tcontig00002\t118693\t120180\t+\ttolC\t1-1488/1488\t===============\t0/0\t100.00\t98.52\tcard\tFJ768952:1-1489\tTolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.\trifamycin/triclosan/tetracycline/glycylcycline/cephamycin/carbapenem/aminoglycoside/macrolide/penam/pleuromutilin/nitroimidazole/nucleoside/isoniazid/lincosamide/benzalkonium_chloride/antibacterial_free_fatty_acids/bicyclomycin/penem/diaminopyrimidine/cephalosporin/fluoroquinolone/oxazolidinone/acridine_dye/fosfomycin/monobactam/phenicol/rhodamine/peptide/aminocoumarin\n+SAMN11840203\tcontig00002\t140892\t141711\t-\tbacA\t1-820/822\t===============\t0/0\t99.76\t96.22\tcard\tU00096.3:3203310-3204132\tThe bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.\tpeptide\n+SAMN11840203\tcontig00002\t340230\t340892\t-\tacrS\t1-663/663\t===============\t0/0\t100.00\t98.94\tcard\tU00096:3412803-3413466\tAcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.\tglycylcycline/monobactam/phenicol/acridine_dye/triclosan/tetracycline/cephalosporin/fluoroquinolone/carbapenem/aminoglycoside/aminocoumarin/cephamycin/rifamycin/macrolide/penam/diaminopyrimidine/antibacterial_free_fatty_acids\n+SAMN11840203\tcontig00002\t341291\t342448\t+\tacrE\t1-1158/1158\t===============\t0/0\t100.00\t98.36\tcard\tU00096:3413864-3415022\tAcrE is a membrane fusion protein similar to AcrA.\taminocoumarin/cephamycin/carbapenem/diaminopyrimidine/aminoglycoside/antibacterial_free_fatty_acids/tricl'..b"bacterial_free_fatty_acids/diaminopyrimidine/lincosamide/isoniazid/benzalkonium_chloride/fosfomycin/glycylcycline/phenicol/cephalosporin/fluoroquinolone/oxazolidinone/acridine_dye/tetracycline/rhodamine/peptide\n+SAMN11840203\tcontig00033\t25605\t26909\t+\tEscherichia_coli_ampC1_beta-lactamase\t1-1305/1305\t===============\t0/0\t100.00\t96.02\tcard\tFN649414.1:2765051-2766356\tAn ampC-like beta-lactamase identified from Escherichia coli.\tcephalosporin/penam\n+SAMN11840203\tcontig00040\t7921\t8598\t+\tkdpE\t1-678/678\t===============\t0/0\t100.00\t95.43\tcard\tU00096.3:721056-721734\tkdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.\taminoglycoside\n+SAMN11840203\tcontig00041\t22681\t23033\t-\tNocardia_rifampin_resistant_beta-subunit_of_RNA_polymerase_(rpoB2)\t2980-3332/3489\t......../...===\t6/10\t9.97\t75.70\tcard\tAP006618.1:4835200-4838689\tDue to gene duplication the genomes of Nocardia species include both rifampin-sensitive beta-subunit of RNA polymerase (rpoB) and rifampin-resistant beta-subunit of RNA polymerase (rpoB2) genes with ~88% similarity between the two gene products. Expression of the rpoB2 variant results in replacement of rifampin sensitivity with rifampin resistance.\trifamycin\n+SAMN11840203\tcontig00046\t459\t1334\t-\tCTX-M-15\t1-876/876\t===============\t0/0\t100.00\t100.00\tcard\tAY044436:1436-2312\tCTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family\tcephalosporin\n+SAMN11840203\tcontig00057\t1194\t2033\t-\tsul1\t1-840/840\t===============\t0/0\t100.00\t100.00\tcard\tJF969163:1054-1894\tSul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.\tsulfonamide\n+SAMN11840203\tcontig00057\t3685\t4341\t-\tQnrA1\t1-657/657\t===============\t0/0\t100.00\t99.85\tcard\tDQ831141:8922-9579\tQnrA1 is a plasmid-mediated quinolone resistance protein found in Klebsiella pneumoniae\tfluoroquinolone\n+SAMN11840203\tcontig00063\t3595\t4455\t-\tSHV-134\t1-861/861\t===============\t0/0\t100.00\t99.88\tcard\tHM559945:1-862\tSHV-134 is an extended-spectrum beta-lactamase.\tcarbapenem/penam/cephalosporin\n+SAMN11840203\tcontig00065\t1\t85\t-\tTEM-101\t1-85/861\t==.............\t0/0\t9.87\t100.00\tcard\tAF495873:1-862\tTEM-101 is an extended-spectrum beta-lactamase found in E. coli.\tmonobactam/penem/cephalosporin/penam\n+SAMN11840203\tcontig00065\t785\t1609\t-\tOXA-9\t1-825/825\t===============\t0/0\t100.00\t100.00\tcard\tM55547:1-826\tOXA-9 is a beta-lactamase found in Klebsiella pneumoniae.\tcephalosporin/penam\n+SAMN11840203\tcontig00065\t1669\t2470\t-\tANT(3'')-IIa\t168-972/972\t..======/======\t1/3\t82.51\t99.25\tcard\tX02340.1:223-1195\tANT(3'')-IIa is a aminoglycoside nucleotidyltransferase identified in Acinetobacter spp. via horizontal gene transfer mechanisms.\taminoglycoside\n+SAMN11840203\tcontig00065\t2363\t3113\t-\tAAC(6')-Ib7\t234-980/980\t...=====/======\t2/4\t76.22\t96.67\tcard\tY11946.1:1-981\tAAC(6')-Ib7 is a plasmid-encoded aminoglycoside acetyltransferase in E. cloacae and C. freundii\taminoglycoside\n+SAMN11840203\tcontig00081\t26\t823\t+\tOXA-48\t1-798/798\t===============\t0/0\t100.00\t100.00\tcard\tAY236073:2188-2986\tOXA-48 is a beta-lactamase found in Klebsiella pneumoniae\tpenam/cephalosporin\n+SAMN11840203\tcontig00104\t1\t843\t+\tTEM-1\t19-861/861\t===============\t0/0\t97.91\t99.88\tcard\tAL513383:161911-162772\tTEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.\tpenam/cephalosporin/penem/monobactam\n+SAMN11840203\tcontig00192\t1\t85\t-\tTEM-1\t1-85/861\t==.............\t0/0\t9.87\t100.00\tcard\tAL513383:161911-162772\tTEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.\tpenam/cephalosporin/penem/monobactam\n" |
| b |
| diff -r 2262e531c50b -r 22247b1a59d5 test-data/SAMN11840203-abricate_report_screened.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SAMN11840203-abricate_report_screened.tsv Fri Jan 03 14:30:22 2020 -0500 |
| b |
| @@ -0,0 +1,3 @@ +#FILE SEQUENCE START END STRAND GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY DATABASE ACCESSION PRODUCT RESISTANCE +SAMN11840203 contig00065 785 1609 - OXA-9 1-825/825 =============== 0/0 100.00 100.00 card M55547:1-826 OXA-9 is a beta-lactamase found in Klebsiella pneumoniae. cephalosporin/penam +SAMN11840203 contig00081 26 823 + OXA-48 1-798/798 =============== 0/0 100.00 100.00 card AY236073:2188-2986 OXA-48 is a beta-lactamase found in Klebsiella pneumoniae penam/cephalosporin |
| b |
| diff -r 2262e531c50b -r 22247b1a59d5 test-data/SAMN11840203-gene_detection_status.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SAMN11840203-gene_detection_status.tsv Fri Jan 03 14:30:22 2020 -0500 |
| b |
| @@ -0,0 +1,5 @@ +gene_name detected alleles +KPC False +NDM False +OXA True OXA-9,OXA-48 +rpoB2 False |
| b |
| diff -r 2262e531c50b -r 22247b1a59d5 test-data/SAMN13042171-abricate_report_full.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SAMN13042171-abricate_report_full.tsv Fri Jan 03 14:30:22 2020 -0500 |
| b |
| b'@@ -0,0 +1,47 @@\n+#FILE\tSEQUENCE\tSTART\tEND\tSTRAND\tGENE\tCOVERAGE\tCOVERAGE_MAP\tGAPS\t%COVERAGE\t%IDENTITY\tDATABASE\tACCESSION\tPRODUCT\tRESISTANCE\n+SAMN13042171.fasta\tcontig00001\t181303\t181975\t+\tkdpE\t1-673/678\t===============\t0/0\t99.26\t76.08\tcard\tU00096.3:721056-721734\tkdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.\taminoglycoside\n+SAMN13042171.fasta\tcontig00001\t362878\t363231\t-\tramA\t21-375/375\t========/======\t1/1\t94.40\t80.56\tcard\tJQ727668:1-376\tRamA (resistance antibiotic multiple) is a positive regulator of AcrAB-TolC and leads to high level multidrug resistance in Klebsiella pneumoniae Salmonella enterica and Enterobacter aerugenes increasing the expression of both the mar operon as well as AcrAB. RamA also decreases OmpF expression.\tcephamycin/aminocoumarin/aminoglycoside/carbapenem/fluoroquinolone/cephalosporin/triclosan/tetracycline/acridine_dye/phenicol/monobactam/glycylcycline/antibacterial_free_fatty_acids/penem/diaminopyrimidine/penam/macrolide/rifamycin\n+SAMN13042171.fasta\tcontig00001\t568102\t569295\t+\tKlebsiella_pneumoniae_acrA\t1-1197/1197\t========/======\t2/3\t99.75\t95.07\tcard\tAJ318073.1:794-1991\tAcrA is a subunit of the AcrAB multidrug efflux system that in K. pneumoniae which is encoded by the acrRAB operon.\taminocoumarin/carbapenem/aminoglycoside/triclosan/tetracycline/acridine_dye/cephalosporin/fluoroquinolone/monobactam/glycylcycline/phenicol/diaminopyrimidine/antibacterial_free_fatty_acids/macrolide/penam/rifamycin\n+SAMN13042171.fasta\tcontig00001\t569318\t572462\t+\tacrB\t1-3148/3150\t========/======\t1/3\t99.84\t83.74\tcard\tU00096.3:481254-484404\tProtein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.\tantibacterial_free_fatty_acids/diaminopyrimidine/rifamycin/penam/macrolide/aminoglycoside/carbapenem/aminocoumarin/phenicol/monobactam/glycylcycline/fluoroquinolone/cephalosporin/tetracycline/triclosan/acridine_dye\n+SAMN13042171.fasta\tcontig00001\t698224\t699350\t+\tEscherichia_coli_ampH\t1-1127/1158\t===============\t0/0\t97.32\t77.46\tcard\tAP012030.1:395554-396712\tAmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.\tcephalosporin/penam\n+SAMN13042171.fasta\tcontig00002\t345289\t346827\t-\tKlebsiella_pneumoniae_KpnH\t1-1539/1539\t===============\t0/0\t100.00\t84.41\tcard\tASTU01000063.1:61249-62788\tKpnH consists of ~511 residues resembles EmrB of E. coli and is probably a translocase in the KpnGH-TolC efflux protein in K. pneumoniae. Disruption of the pump components KpnG-KpnH signficantly decrease resistance to azithromycin ceftazidime ciprofloxacin ertapenem erythromycin gentamicin imipenem ticarcillin norfloxacin polymyxin-B piperacillin spectinomycin tobramycin and streptomycin.\tisoniazid/lincosamide/benzalkonium_chloride/diaminopyrimidine/penem/bicyclomycin/antibacterial_free_fatty_acids/macrolide/penam/nucleoside/nitroimidazole/peptide/rhodamine/acridine_dye/oxazolidinone/cephalosporin/fluoroquinolone/phenicol/fosfomycin/rifamycin/carbapenem/aminoglycoside/tetracycline/glycylcycline\n+SAMN13042171.fasta\tcontig00002\t346843\t348015\t-\tKlebsiella_pneumoniae_KpnG\t1-1173/1173\t===============\t0/0\t100.00\t94.54\tcard\tACWO01000051.1:22093-23266\tKpnG consists of ~390 residues and resembles EmrA of E. coli. Disruption of the pump components KpnG-KpnH signficantly decrease resistance to azithromycin ceftazidime ciprofloxacin ertapenem erythromycin gentamicin imipenem ticarcillin norfloxacin polymyxin-B piperacillin spectinomycin tobramycin and streptomycin\tpenam/macrolide/nitroimidazole/nucleoside/benzalkonium_chloride/l'..b"tibacterial_free_fatty_acids/penem/diaminopyrimidine/macrolide/penam/rifamycin/cephamycin/aminocoumarin/carbapenem/aminoglycoside/cephalosporin/fluoroquinolone/tetracycline/triclosan/acridine_dye/monobactam/glycylcycline/phenicol\n+SAMN13042171.fasta\tcontig00028\t4483\t5688\t+\tEscherichia_coli_mdfA\t1-1206/1233\t========/======\t2/2\t97.73\t78.21\tcard\tJQ394987:1-1234\tMultidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.\tantibacterial_free_fatty_acids/bicyclomycin/diaminopyrimidine/isoniazid/lincosamide/benzalkonium_chloride/rifamycin/nitroimidazole/nucleoside/macrolide/penam/rhodamine/peptide/fosfomycin/glycylcycline/phenicol/cephalosporin/fluoroquinolone/tetracycline/acridine_dye/oxazolidinone\n+SAMN13042171.fasta\tcontig00030\t26098\t26477\t-\tNocardia_rifampin_resistant_beta-subunit_of_RNA_polymerase_(rpoB2)\t2980-3359/3489\t......../...===\t2/2\t10.86\t76.11\tcard\tAP006618.1:4835200-4838689\tDue to gene duplication the genomes of Nocardia species include both rifampin-sensitive beta-subunit of RNA polymerase (rpoB) and rifampin-resistant beta-subunit of RNA polymerase (rpoB2) genes with ~88% similarity between the two gene products. Expression of the rpoB2 variant results in replacement of rifampin sensitivity with rifampin resistance.\trifamycin\n+SAMN13042171.fasta\tcontig00030\t26758\t26924\t-\tNocardia_rifampin_resistant_beta-subunit_of_RNA_polymerase_(rpoB2)\t2605-2771/3489\t...........=...\t0/0\t4.79\t75.45\tcard\tAP006618.1:4835200-4838689\tDue to gene duplication the genomes of Nocardia species include both rifampin-sensitive beta-subunit of RNA polymerase (rpoB) and rifampin-resistant beta-subunit of RNA polymerase (rpoB2) genes with ~88% similarity between the two gene products. Expression of the rpoB2 variant results in replacement of rifampin sensitivity with rifampin resistance.\trifamycin\n+SAMN13042171.fasta\tcontig00035\t7853\t8713\t-\tTEM-150\t1-861/861\t===============\t0/0\t100.00\t99.88\tcard\tAM183304:209-1070\tTEM-150 is a beta-lactamase found in Enterobacter spp. E. coli and Klebsiella pneumoniae.\tpenem/monobactam/cephalosporin/penam\n+SAMN13042171.fasta\tcontig00035\t9413\t10237\t-\tOXA-9\t1-825/825\t===============\t0/0\t100.00\t100.00\tcard\tM55547:1-826\tOXA-9 is a beta-lactamase found in Klebsiella pneumoniae.\tcephalosporin/penam\n+SAMN13042171.fasta\tcontig00035\t10297\t11098\t-\tANT(3'')-IIa\t168-972/972\t..======/======\t1/3\t82.51\t99.25\tcard\tX02340.1:223-1195\tANT(3'')-IIa is a aminoglycoside nucleotidyltransferase identified in Acinetobacter spp. via horizontal gene transfer mechanisms.\taminoglycoside\n+SAMN13042171.fasta\tcontig00035\t10991\t11741\t-\tAAC(6')-Ib7\t234-980/980\t...=====/======\t2/4\t76.22\t96.67\tcard\tY11946.1:1-981\tAAC(6')-Ib7 is a plasmid-encoded aminoglycoside acetyltransferase in E. cloacae and C. freundii\taminoglycoside\n+SAMN13042171.fasta\tcontig00035\t14582\t15457\t+\tCTX-M-15\t1-876/876\t===============\t0/0\t100.00\t100.00\tcard\tAY044436:1436-2312\tCTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family\tcephalosporin\n+SAMN13042171.fasta\tcontig00035\t20098\t20754\t+\tQnrS1\t1-657/657\t===============\t0/0\t100.00\t100.00\tcard\tDQ485529.1:1-658\tQnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri\tfluoroquinolone\n+SAMN13042171.fasta\tcontig00063\t2129\t2494\t-\tdeterminant_of_bleomycin_resistance\t1-366/366\t===============\t0/0\t100.00\t100.00\tcard\tKC503911.1:9884-10250\tA 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.\tglycopeptide\n+SAMN13042171.fasta\tcontig00063\t2498\t3310\t-\tNDM-1\t1-813/813\t===============\t0/0\t100.00\t100.00\tcard\tFN396876:2407-3220\tNDM-1 is a metallo-beta-lactamase isolated from Klebsiella pneumoniae with nearly complete resistance to all beta-lactam antibiotics.\tcephalosporin/penam/carbapenem/cephamycin\n" |
| b |
| diff -r 2262e531c50b -r 22247b1a59d5 test-data/SAMN13042171-abricate_report_screened.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SAMN13042171-abricate_report_screened.tsv Fri Jan 03 14:30:22 2020 -0500 |
| b |
| @@ -0,0 +1,3 @@ +#FILE SEQUENCE START END STRAND GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY DATABASE ACCESSION PRODUCT RESISTANCE +SAMN13042171.fasta contig00063 2498 3310 - NDM-1 1-813/813 =============== 0/0 100.00 100.00 card FN396876:2407-3220 NDM-1 is a metallo-beta-lactamase isolated from Klebsiella pneumoniae with nearly complete resistance to all beta-lactam antibiotics. cephalosporin/penam/carbapenem/cephamycin +SAMN13042171.fasta contig00035 9413 10237 - OXA-9 1-825/825 =============== 0/0 100.00 100.00 card M55547:1-826 OXA-9 is a beta-lactamase found in Klebsiella pneumoniae. cephalosporin/penam |
| b |
| diff -r 2262e531c50b -r 22247b1a59d5 test-data/SAMN13042171-gene_detection_status.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SAMN13042171-gene_detection_status.tsv Fri Jan 03 14:30:22 2020 -0500 |
| b |
| @@ -0,0 +1,5 @@ +gene_name detected alleles +KPC False +NDM True NDM-1 +OXA True OXA-9 +rpoB2 False |
| b |
| diff -r 2262e531c50b -r 22247b1a59d5 test-data/SAMN13042171_abricate_report.tsv --- a/test-data/SAMN13042171_abricate_report.tsv Thu Jan 02 17:14:34 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,47 +0,0 @@\n-#FILE\tSEQUENCE\tSTART\tEND\tSTRAND\tGENE\tCOVERAGE\tCOVERAGE_MAP\tGAPS\t%COVERAGE\t%IDENTITY\tDATABASE\tACCESSION\tPRODUCT\tRESISTANCE\n-SAMN13042171.fasta\tcontig00001\t181303\t181975\t+\tkdpE\t1-673/678\t===============\t0/0\t99.26\t76.08\tcard\tU00096.3:721056-721734\tkdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.\taminoglycoside\n-SAMN13042171.fasta\tcontig00001\t362878\t363231\t-\tramA\t21-375/375\t========/======\t1/1\t94.40\t80.56\tcard\tJQ727668:1-376\tRamA (resistance antibiotic multiple) is a positive regulator of AcrAB-TolC and leads to high level multidrug resistance in Klebsiella pneumoniae Salmonella enterica and Enterobacter aerugenes increasing the expression of both the mar operon as well as AcrAB. RamA also decreases OmpF expression.\tcephamycin/aminocoumarin/aminoglycoside/carbapenem/fluoroquinolone/cephalosporin/triclosan/tetracycline/acridine_dye/phenicol/monobactam/glycylcycline/antibacterial_free_fatty_acids/penem/diaminopyrimidine/penam/macrolide/rifamycin\n-SAMN13042171.fasta\tcontig00001\t568102\t569295\t+\tKlebsiella_pneumoniae_acrA\t1-1197/1197\t========/======\t2/3\t99.75\t95.07\tcard\tAJ318073.1:794-1991\tAcrA is a subunit of the AcrAB multidrug efflux system that in K. pneumoniae which is encoded by the acrRAB operon.\taminocoumarin/carbapenem/aminoglycoside/triclosan/tetracycline/acridine_dye/cephalosporin/fluoroquinolone/monobactam/glycylcycline/phenicol/diaminopyrimidine/antibacterial_free_fatty_acids/macrolide/penam/rifamycin\n-SAMN13042171.fasta\tcontig00001\t569318\t572462\t+\tacrB\t1-3148/3150\t========/======\t1/3\t99.84\t83.74\tcard\tU00096.3:481254-484404\tProtein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.\tantibacterial_free_fatty_acids/diaminopyrimidine/rifamycin/penam/macrolide/aminoglycoside/carbapenem/aminocoumarin/phenicol/monobactam/glycylcycline/fluoroquinolone/cephalosporin/tetracycline/triclosan/acridine_dye\n-SAMN13042171.fasta\tcontig00001\t698224\t699350\t+\tEscherichia_coli_ampH\t1-1127/1158\t===============\t0/0\t97.32\t77.46\tcard\tAP012030.1:395554-396712\tAmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.\tcephalosporin/penam\n-SAMN13042171.fasta\tcontig00002\t345289\t346827\t-\tKlebsiella_pneumoniae_KpnH\t1-1539/1539\t===============\t0/0\t100.00\t84.41\tcard\tASTU01000063.1:61249-62788\tKpnH consists of ~511 residues resembles EmrB of E. coli and is probably a translocase in the KpnGH-TolC efflux protein in K. pneumoniae. Disruption of the pump components KpnG-KpnH signficantly decrease resistance to azithromycin ceftazidime ciprofloxacin ertapenem erythromycin gentamicin imipenem ticarcillin norfloxacin polymyxin-B piperacillin spectinomycin tobramycin and streptomycin.\tisoniazid/lincosamide/benzalkonium_chloride/diaminopyrimidine/penem/bicyclomycin/antibacterial_free_fatty_acids/macrolide/penam/nucleoside/nitroimidazole/peptide/rhodamine/acridine_dye/oxazolidinone/cephalosporin/fluoroquinolone/phenicol/fosfomycin/rifamycin/carbapenem/aminoglycoside/tetracycline/glycylcycline\n-SAMN13042171.fasta\tcontig00002\t346843\t348015\t-\tKlebsiella_pneumoniae_KpnG\t1-1173/1173\t===============\t0/0\t100.00\t94.54\tcard\tACWO01000051.1:22093-23266\tKpnG consists of ~390 residues and resembles EmrA of E. coli. Disruption of the pump components KpnG-KpnH signficantly decrease resistance to azithromycin ceftazidime ciprofloxacin ertapenem erythromycin gentamicin imipenem ticarcillin norfloxacin polymyxin-B piperacillin spectinomycin tobramycin and streptomycin\tpenam/macrolide/nitroimidazole/nucleoside/benzalkonium_chloride/l'..b"tibacterial_free_fatty_acids/penem/diaminopyrimidine/macrolide/penam/rifamycin/cephamycin/aminocoumarin/carbapenem/aminoglycoside/cephalosporin/fluoroquinolone/tetracycline/triclosan/acridine_dye/monobactam/glycylcycline/phenicol\n-SAMN13042171.fasta\tcontig00028\t4483\t5688\t+\tEscherichia_coli_mdfA\t1-1206/1233\t========/======\t2/2\t97.73\t78.21\tcard\tJQ394987:1-1234\tMultidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.\tantibacterial_free_fatty_acids/bicyclomycin/diaminopyrimidine/isoniazid/lincosamide/benzalkonium_chloride/rifamycin/nitroimidazole/nucleoside/macrolide/penam/rhodamine/peptide/fosfomycin/glycylcycline/phenicol/cephalosporin/fluoroquinolone/tetracycline/acridine_dye/oxazolidinone\n-SAMN13042171.fasta\tcontig00030\t26098\t26477\t-\tNocardia_rifampin_resistant_beta-subunit_of_RNA_polymerase_(rpoB2)\t2980-3359/3489\t......../...===\t2/2\t10.86\t76.11\tcard\tAP006618.1:4835200-4838689\tDue to gene duplication the genomes of Nocardia species include both rifampin-sensitive beta-subunit of RNA polymerase (rpoB) and rifampin-resistant beta-subunit of RNA polymerase (rpoB2) genes with ~88% similarity between the two gene products. Expression of the rpoB2 variant results in replacement of rifampin sensitivity with rifampin resistance.\trifamycin\n-SAMN13042171.fasta\tcontig00030\t26758\t26924\t-\tNocardia_rifampin_resistant_beta-subunit_of_RNA_polymerase_(rpoB2)\t2605-2771/3489\t...........=...\t0/0\t4.79\t75.45\tcard\tAP006618.1:4835200-4838689\tDue to gene duplication the genomes of Nocardia species include both rifampin-sensitive beta-subunit of RNA polymerase (rpoB) and rifampin-resistant beta-subunit of RNA polymerase (rpoB2) genes with ~88% similarity between the two gene products. Expression of the rpoB2 variant results in replacement of rifampin sensitivity with rifampin resistance.\trifamycin\n-SAMN13042171.fasta\tcontig00035\t7853\t8713\t-\tTEM-150\t1-861/861\t===============\t0/0\t100.00\t99.88\tcard\tAM183304:209-1070\tTEM-150 is a beta-lactamase found in Enterobacter spp. E. coli and Klebsiella pneumoniae.\tpenem/monobactam/cephalosporin/penam\n-SAMN13042171.fasta\tcontig00035\t9413\t10237\t-\tOXA-9\t1-825/825\t===============\t0/0\t100.00\t100.00\tcard\tM55547:1-826\tOXA-9 is a beta-lactamase found in Klebsiella pneumoniae.\tcephalosporin/penam\n-SAMN13042171.fasta\tcontig00035\t10297\t11098\t-\tANT(3'')-IIa\t168-972/972\t..======/======\t1/3\t82.51\t99.25\tcard\tX02340.1:223-1195\tANT(3'')-IIa is a aminoglycoside nucleotidyltransferase identified in Acinetobacter spp. via horizontal gene transfer mechanisms.\taminoglycoside\n-SAMN13042171.fasta\tcontig00035\t10991\t11741\t-\tAAC(6')-Ib7\t234-980/980\t...=====/======\t2/4\t76.22\t96.67\tcard\tY11946.1:1-981\tAAC(6')-Ib7 is a plasmid-encoded aminoglycoside acetyltransferase in E. cloacae and C. freundii\taminoglycoside\n-SAMN13042171.fasta\tcontig00035\t14582\t15457\t+\tCTX-M-15\t1-876/876\t===============\t0/0\t100.00\t100.00\tcard\tAY044436:1436-2312\tCTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family\tcephalosporin\n-SAMN13042171.fasta\tcontig00035\t20098\t20754\t+\tQnrS1\t1-657/657\t===============\t0/0\t100.00\t100.00\tcard\tDQ485529.1:1-658\tQnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri\tfluoroquinolone\n-SAMN13042171.fasta\tcontig00063\t2129\t2494\t-\tdeterminant_of_bleomycin_resistance\t1-366/366\t===============\t0/0\t100.00\t100.00\tcard\tKC503911.1:9884-10250\tA 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.\tglycopeptide\n-SAMN13042171.fasta\tcontig00063\t2498\t3310\t-\tNDM-1\t1-813/813\t===============\t0/0\t100.00\t100.00\tcard\tFN396876:2407-3220\tNDM-1 is a metallo-beta-lactamase isolated from Klebsiella pneumoniae with nearly complete resistance to all beta-lactam antibiotics.\tcephalosporin/penam/carbapenem/cephamycin\n" |
| b |
| diff -r 2262e531c50b -r 22247b1a59d5 test-data/SAMN13042171_abricate_report_screened.tsv --- a/test-data/SAMN13042171_abricate_report_screened.tsv Thu Jan 02 17:14:34 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,3 +0,0 @@ -#FILE SEQUENCE START END STRAND GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY DATABASE ACCESSION PRODUCT RESISTANCE -SAMN13042171.fasta contig00063 2498 3310 - NDM-1 1-813/813 =============== 0/0 100.00 100.00 card FN396876:2407-3220 NDM-1 is a metallo-beta-lactamase isolated from Klebsiella pneumoniae with nearly complete resistance to all beta-lactam antibiotics. cephalosporin/penam/carbapenem/cephamycin -SAMN13042171.fasta contig00035 9413 10237 - OXA-9 1-825/825 =============== 0/0 100.00 100.00 card M55547:1-826 OXA-9 is a beta-lactamase found in Klebsiella pneumoniae. cephalosporin/penam |
| b |
| diff -r 2262e531c50b -r 22247b1a59d5 test-data/SAMN13042171_gene_detection_status.tsv --- a/test-data/SAMN13042171_gene_detection_status.tsv Thu Jan 02 17:14:34 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,5 +0,0 @@ -gene_name detected -KPC False -NDM True -OXA True -rpoB2 False |