# HG changeset patch
# User public-health-bioinformatics
# Date 1578079822 18000
# Node ID 22247b1a59d511ce01da94d024576a7a2af57dd0
# Parent  2262e531c50b4729260ac5a3014fa29ef6b95b31
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"

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)
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[
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
@@ -0,0 +1,63 @@
+#FILE	SEQUENCE	START	END	STRAND	GENE	COVERAGE	COVERAGE_MAP	GAPS	%COVERAGE	%IDENTITY	DATABASE	ACCESSION	PRODUCT	RESISTANCE
+SAMN11840202	contig00001	43895	45142	+	mdtA	1-1248/1248	===============	0/0	100.00	98.00	card	U00096:2154016-2155264	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	antibacterial_free_fatty_acids/aminoglycoside/diaminopyrimidine/carbapenem/aminocoumarin/phenicol/glycylcycline/monobactam/penam/fluoroquinolone/macrolide/acridine_dye/triclosan/tetracycline
+SAMN11840202	contig00001	45142	48264	+	mdtB	1-3123/3123	===============	0/0	100.00	99.84	card	U00096:2155263-2158386	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin/aminoglycoside/diaminopyrimidine/carbapenem/antibacterial_free_fatty_acids/acridine_dye/tetracycline/triclosan/penam/fluoroquinolone/macrolide/phenicol/glycylcycline/monobactam
+SAMN11840202	contig00001	48265	51342	+	mdtC	1-3078/3078	===============	0/0	100.00	99.84	card	U00096:2158386-2161464	MdtC 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.	diaminopyrimidine/carbapenem/aminoglycoside/antibacterial_free_fatty_acids/aminocoumarin/glycylcycline/monobactam/phenicol/acridine_dye/triclosan/tetracycline/macrolide/fluoroquinolone/penam
+SAMN11840202	contig00001	52755	54158	+	baeS	1-1404/1404	===============	0/0	100.00	99.93	card	AP009048:2165013-2166417	BaeS 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.	aminocoumarin/carbapenem/diaminopyrimidine/aminoglycoside/antibacterial_free_fatty_acids/tetracycline/triclosan/acridine_dye/macrolide/fluoroquinolone/penam/monobactam/glycylcycline/phenicol
+SAMN11840202	contig00001	54155	54877	+	baeR	1-723/723	===============	0/0	100.00	99.45	card	AP009048.1:2166413-2167136	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	phenicol/monobactam/glycylcycline/tetracycline/triclosan/acridine_dye/penam/fluoroquinolone/macrolide/aminoglycoside/carbapenem/diaminopyrimidine/antibacterial_free_fatty_acids/aminocoumarin
+SAMN11840202	contig00001	197758	199401	-	yojI	1-1644/1644	===============	0/0	100.00	97.51	card	U00096.3:2306972-2308616	YojI 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.	peptide/nitroimidazole/rifamycin/pleuromutilin/penam/fluoroquinolone/cephalosporin/macrolide/tetracycline/acridine_dye
+SAMN11840202	contig00001	257738	258706	+	pmrF	1-969/969	===============	0/0	100.00	100.00	card	U00096:2367071-2368040	PmrF 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.	peptide
+SAMN11840202	contig00002	125167	126915	-	msbA	1-1749/1749	===============	0/0	100.00	100.00	card	U00096.3:966621-968370	MsbA 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). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	peptide/rifamycin/pleuromutilin/nitroimidazole/tetracycline/acridine_dye/cephalosporin/macrolide/penam/fluoroquinolone
+SAMN11840202	contig00002	208622	209854	-	Escherichia_coli_mdfA	1-1233/1233	===============	0/0	100.00	98.38	card	JQ394987:1-1234	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	antibacterial_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
+SAMN11840202	contig00003	180544	180902	+	Klebsiella_pneumoniae_KpnE	5-363/363	========/======	2/2	98.62	75.83	card	AP006725.1:2483890-2484253	KpnE 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	diaminopyrimidine/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
+SAMN11840202	contig00003	180894	181218	+	Klebsiella_pneumoniae_KpnF	6-330/330	===============	0/0	98.48	75.39	card	AP006725.1:2484239-2484569	KpnF 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.	fosfomycin/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
+SAMN11840202	contig00003	213611	213994	-	marA	1-384/384	===============	0/0	100.00	100.00	card	AP009048.1:1621288-1621672	In 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.	antibacterial_free_fatty_acids/penem/diaminopyrimidine/macrolide/penam/rifamycin/cephamycin/aminocoumarin/carbapenem/aminoglycoside/cephalosporin/fluoroquinolone/tetracycline/triclosan/acridine_dye/monobactam/glycylcycline/phenicol
+SAMN11840202	contig00004	202570	203978	-	mdtK	1-1409/1425	========/======	2/4	98.74	75.34	card	CP014358.1:2161326-2162751	A multidrug and toxic compound extrusions (MATE) transporter conferring resistance to norfloxacin doxorubicin and acriflavine.	glycylcycline/fluoroquinolone/tetracycline/acridine_dye
+SAMN11840202	contig00007	134424	135056	-	CRP	1-633/633	===============	0/0	100.00	99.68	card	AP009048.1:4153664-4154297	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	tetracycline/triclosan/acridine_dye/fluoroquinolone/penam/macrolide/phenicol/monobactam/glycylcycline/aminocoumarin/aminoglycoside/carbapenem/diaminopyrimidine/antibacterial_free_fatty_acids
+SAMN11840202	contig00008	37607	38800	+	Escherichia_coli_acrA	1-1194/1194	===============	0/0	100.00	100.00	card	U00096.3:484426-485620	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	rifamycin/macrolide/penam/diaminopyrimidine/antibacterial_free_fatty_acids/glycylcycline/monobactam/phenicol/acridine_dye/tetracycline/triclosan/cephalosporin/fluoroquinolone/carbapenem/aminoglycoside/aminocoumarin
+SAMN11840202	contig00008	38823	41972	+	acrB	1-3150/3150	===============	0/0	100.00	100.00	card	U00096.3:481254-484404	Protein 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.	antibacterial_free_fatty_acids/diaminopyrimidine/rifamycin/penam/macrolide/aminoglycoside/carbapenem/aminocoumarin/phenicol/monobactam/glycylcycline/fluoroquinolone/cephalosporin/tetracycline/triclosan/acridine_dye
+SAMN11840202	contig00008	126851	128008	+	Escherichia_coli_ampH	1-1158/1158	===============	0/0	100.00	100.00	card	AP012030.1:395554-396712	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin/penam
+SAMN11840202	contig00010	97802	99268	-	mdtP	1-1467/1467	===============	0/0	100.00	100.00	card	AP009048.1:4303043-4304510	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	benzalkonium_chloride/isoniazid/lincosamide/antibacterial_free_fatty_acids/bicyclomycin/diaminopyrimidine/penam/macrolide/nitroimidazole/rifamycin/nucleoside/rhodamine/peptide/fluoroquinolone/cephalosporin/tetracycline/acridine_dye/oxazolidinone/fosfomycin/phenicol/glycylcycline
+SAMN11840202	contig00010	99265	101316	-	mdtO	1-2052/2052	===============	0/0	100.00	99.95	card	AP009048.1:4304506-4306558	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	nucleoside/rifamycin/nitroimidazole/macrolide/penam/diaminopyrimidine/bicyclomycin/antibacterial_free_fatty_acids/isoniazid/lincosamide/benzalkonium_chloride/glycylcycline/phenicol/fosfomycin/oxazolidinone/acridine_dye/tetracycline/cephalosporin/fluoroquinolone/peptide/rhodamine
+SAMN11840202	contig00010	101316	102347	-	mdtN	1-1032/1032	===============	0/0	100.00	100.00	card	AP009048.1:4306557-4307589	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	tetracycline/oxazolidinone/acridine_dye/cephalosporin/fluoroquinolone/glycylcycline/phenicol/fosfomycin/peptide/rhodamine/macrolide/penam/nucleoside/rifamycin/nitroimidazole/isoniazid/lincosamide/benzalkonium_chloride/diaminopyrimidine/antibacterial_free_fatty_acids/bicyclomycin
+SAMN11840202	contig00012	85775	87262	+	tolC	1-1488/1488	===============	0/0	100.00	100.00	card	FJ768952:1-1489	TolC 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.	rifamycin/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
+SAMN11840202	contig00013	50531	51007	-	mphB	1-477/477	===============	0/0	100.00	98.32	card	AE005174.2:3397371-3397848	The mphB gene encodes for MPH(2')-II. This enzymes phosphorylates 14-membered and 16-membered macrolides.  It phosphorylates macrolides in GTP- dependent manner at 2'-OH hydroxyl of desosamine sugar of macrolides.	macrolide
+SAMN11840202	contig00013	71693	74806	-	acrD	1-3114/3114	===============	0/0	100.00	100.00	card	AP009048.1:2586251-2589365	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminocoumarin/aminoglycoside/carbapenem/diaminopyrimidine/antibacterial_free_fatty_acids/tetracycline/triclosan/acridine_dye/fluoroquinolone/penam/macrolide/phenicol/monobactam/glycylcycline
+SAMN11840202	contig00017	52034	53572	-	emrY	1-1539/1539	===============	0/0	100.00	98.83	card	D78168:1592-3131	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	oxazolidinone/acridine_dye/tetracycline/cephalosporin/fluoroquinolone/glycylcycline/phenicol/fosfomycin/peptide/rhodamine/macrolide/penam/nucleoside/rifamycin/nitroimidazole/lincosamide/isoniazid/benzalkonium_chloride/diaminopyrimidine/bicyclomycin/antibacterial_free_fatty_acids
+SAMN11840202	contig00017	53572	54627	-	emrK	1-1056/1056	===============	0/0	100.00	99.72	card	D78168:537-1593	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	macrolide/penam/rifamycin/nitroimidazole/nucleoside/isoniazid/lincosamide/benzalkonium_chloride/bicyclomycin/antibacterial_free_fatty_acids/diaminopyrimidine/cephalosporin/fluoroquinolone/acridine_dye/oxazolidinone/tetracycline/fosfomycin/glycylcycline/phenicol/rhodamine/peptide
+SAMN11840202	contig00017	55151	55765	+	evgA	1-615/615	===============	0/0	100.00	99.02	card	BA000007.3:3212026-3212641	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	diaminopyrimidine/antibacterial_free_fatty_acids/bicyclomycin/benzalkonium_chloride/isoniazid/lincosamide/nucleoside/nitroimidazole/rifamycin/penam/macrolide/aminoglycoside/carbapenem/aminocoumarin/peptide/rhodamine/phenicol/monobactam/glycylcycline/fosfomycin/triclosan/tetracycline/oxazolidinone/acridine_dye/fluoroquinolone/cephalosporin
+SAMN11840202	contig00017	55770	59363	+	evgS	1-3594/3594	===============	0/0	100.00	99.11	card	U00096:2484374-2487968	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	triclosan/tetracycline/acridine_dye/oxazolidinone/fluoroquinolone/cephalosporin/phenicol/monobactam/glycylcycline/fosfomycin/aminocoumarin/peptide/rhodamine/aminoglycoside/carbapenem/penam/macrolide/nucleoside/nitroimidazole/rifamycin/benzalkonium_chloride/isoniazid/lincosamide/diaminopyrimidine/antibacterial_free_fatty_acids/bicyclomycin
+SAMN11840202	contig00018	15251	16072	-	bacA	1-822/822	===============	0/0	100.00	100.00	card	U00096.3:3203310-3204132	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
+SAMN11840202	contig00023	7667	9310	-	eptA	1-1644/1644	===============	0/0	100.00	99.94	card	AP009048:4338625-4340269	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
+SAMN11840202	contig00023	51538	52671	-	Escherichia_coli_ampC	1-1134/1134	===============	0/0	100.00	97.27	card	NC_000913.3:4377811-4378945	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin/penam
+SAMN11840202	contig00024	3696	5234	-	emrB	1-1539/1539	===============	0/0	100.00	100.00	card	U00096:2812616-2814155	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	rhodamine/peptide/fosfomycin/glycylcycline/phenicol/cephalosporin/fluoroquinolone/tetracycline/acridine_dye/oxazolidinone/antibacterial_free_fatty_acids/bicyclomycin/diaminopyrimidine/lincosamide/isoniazid/benzalkonium_chloride/rifamycin/nitroimidazole/nucleoside/macrolide/penam
+SAMN11840202	contig00024	5251	6423	-	emrA	1-1173/1173	===============	0/0	100.00	99.92	card	AP009048:2810083-2811256	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	benzalkonium_chloride/isoniazid/lincosamide/diaminopyrimidine/bicyclomycin/antibacterial_free_fatty_acids/penam/macrolide/nucleoside/nitroimidazole/rifamycin/peptide/rhodamine/acridine_dye/oxazolidinone/tetracycline/fluoroquinolone/cephalosporin/phenicol/glycylcycline/fosfomycin
+SAMN11840202	contig00024	6550	7080	-	emrR	1-531/531	===============	0/0	100.00	99.81	card	U00096.3:2810770-2811301	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	rifamycin/nitroimidazole/nucleoside/macrolide/penam/bicyclomycin/antibacterial_free_fatty_acids/diaminopyrimidine/lincosamide/isoniazid/benzalkonium_chloride/fosfomycin/glycylcycline/phenicol/cephalosporin/fluoroquinolone/oxazolidinone/acridine_dye/tetracycline/rhodamine/peptide
+SAMN11840202	contig00033	19630	20838	+	mdtH	1-1209/1209	===============	0/0	100.00	99.92	card	U00096:1124118-1125327	Multidrug resistance protein MdtH	nitroimidazole/rifamycin/nucleoside/penam/macrolide/antibacterial_free_fatty_acids/bicyclomycin/diaminopyrimidine/benzalkonium_chloride/isoniazid/lincosamide/fosfomycin/phenicol/glycylcycline/fluoroquinolone/cephalosporin/tetracycline/acridine_dye/oxazolidinone/rhodamine/peptide
+SAMN11840202	contig00033	29467	30693	+	mdtG	1-1227/1227	===============	0/0	100.00	99.43	card	CP000800.1:1191728-1192955	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	macrolide/penam/rifamycin/nitroimidazole/nucleoside/isoniazid/lincosamide/benzalkonium_chloride/bicyclomycin/antibacterial_free_fatty_acids/diaminopyrimidine/cephalosporin/fluoroquinolone/acridine_dye/oxazolidinone/tetracycline/fosfomycin/glycylcycline/phenicol/rhodamine/peptide
+SAMN11840202	contig00035	41010	41423	+	H-NS	1-414/414	===============	0/0	100.00	99.28	card	BA000007.3:1737691-1738105	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	bicyclomycin/antibacterial_free_fatty_acids/diaminopyrimidine/benzalkonium_chloride/isoniazid/lincosamide/nitroimidazole/rifamycin/nucleoside/penam/macrolide/aminoglycoside/carbapenem/rhodamine/cephamycin/aminocoumarin/peptide/fosfomycin/phenicol/glycylcycline/monobactam/fluoroquinolone/cephalosporin/acridine_dye/oxazolidinone/triclosan/tetracycline
+SAMN11840202	contig00043	12125	13429	-	Escherichia_coli_ampC1_beta-lactamase	1-1305/1305	===============	0/0	100.00	100.00	card	FN649414.1:2765051-2766356	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin/penam
+SAMN11840202	contig00044	462	1286	+	gadX	1-825/825	===============	0/0	100.00	100.00	card	AP009048.1:3974605-3975430	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	aminoglycoside/diaminopyrimidine/carbapenem/antibacterial_free_fatty_acids/aminocoumarin/phenicol/glycylcycline/monobactam/acridine_dye/tetracycline/triclosan/penam/fluoroquinolone/macrolide
+SAMN11840202	contig00044	1654	2382	+	gadW	1-729/729	===============	0/0	100.00	94.65	card	CP015085.1:2551712-2552441	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	phenicol/monobactam/glycylcycline/penam/fluoroquinolone/macrolide/triclosan/tetracycline/acridine_dye/antibacterial_free_fatty_acids/aminoglycoside/carbapenem/diaminopyrimidine/aminocoumarin
+SAMN11840202	contig00044	2745	5858	-	mdtF	1-3114/3114	===============	0/0	100.00	99.97	card	U00096:3660414-3663528	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	triclosan/tetracycline/acridine_dye/macrolide/fluoroquinolone/penam/monobactam/glycylcycline/phenicol/aminocoumarin/carbapenem/diaminopyrimidine/aminoglycoside/antibacterial_free_fatty_acids
+SAMN11840202	contig00044	5883	7040	-	mdtE	1-1158/1158	===============	0/0	100.00	100.00	card	AP009048.1:3980026-3981184	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	glycylcycline/monobactam/phenicol/acridine_dye/tetracycline/triclosan/macrolide/fluoroquinolone/penam/diaminopyrimidine/carbapenem/aminoglycoside/antibacterial_free_fatty_acids/aminocoumarin
+SAMN11840202	contig00049	8136	8813	+	kdpE	1-678/678	===============	0/0	100.00	100.00	card	U00096.3:721056-721734	kdpE 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.	aminoglycoside
+SAMN11840202	contig00049	12775	12918	+	kdpE	535-678/678	...........====	0/0	21.24	90.28	card	U00096.3:721056-721734	kdpE 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.	aminoglycoside
+SAMN11840202	contig00050	22680	23032	-	Nocardia_rifampin_resistant_beta-subunit_of_RNA_polymerase_(rpoB2)	2980-3332/3489	......../...===	4/6	10.03	75.56	card	AP006618.1:4835200-4838689	Due 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.	rifamycin
+SAMN11840202	contig00055	17804	19036	-	mdtM	1-1233/1233	===============	0/0	100.00	96.27	card	U00096.3:4567287-4568520	Multidrug resistance protein MdtM	nitroimidazole/rifamycin/nucleoside/penam/macrolide/bicyclomycin/antibacterial_free_fatty_acids/diaminopyrimidine/benzalkonium_chloride/lincosamide/isoniazid/fosfomycin/phenicol/glycylcycline/fluoroquinolone/cephalosporin/oxazolidinone/acridine_dye/tetracycline/rhodamine/peptide
+SAMN11840202	contig00057	2580	3826	+	tet(A)	1-1247/1275	===============	0/0	97.80	100.00	card	AF534183.1:2971-4246	TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.	phenicol/glycylcycline/fosfomycin/tetracycline/oxazolidinone/acridine_dye/fluoroquinolone/cephalosporin/peptide/rhodamine/nucleoside/nitroimidazole/rifamycin/penam/macrolide/diaminopyrimidine/antibacterial_free_fatty_acids/bicyclomycin/benzalkonium_chloride/isoniazid/lincosamide
+SAMN11840202	contig00063	8997	10370	-	cpxA	1-1374/1374	===============	0/0	100.00	98.98	card	BA000007.3:4903689-4905063	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	acridine_dye/tetracycline/triclosan/macrolide/fluoroquinolone/penam/glycylcycline/monobactam/phenicol/aminocoumarin/diaminopyrimidine/carbapenem/aminoglycoside/antibacterial_free_fatty_acids
+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	contig00074	1377	1742	+	determinant_of_bleomycin_resistance	1-366/366	===============	0/0	100.00	100.00	card	KC503911.1:9884-10250	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.	glycopeptide
+SAMN11840202	contig00074	5686	6525	-	sul1	1-840/840	===============	0/0	100.00	100.00	card	JF969163:1054-1894	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
+SAMN11840202	contig00074	7030	7809	-	aadA2	1-780/780	===============	0/0	100.00	99.87	card	AF156486:5013-5793	aadA2 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids and integrons in K. pneumoniae Salmonella spp. Corynebacterium glutamicum C. freundii and Aeromonas spp.	aminoglycoside
+SAMN11840202	contig00074	8229	8726	-	dfrA12	1-498/498	===============	0/0	100.00	100.00	card	GU585907.1:21606-22104	dfrA12 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae	diaminopyrimidine
+SAMN11840202	contig00074	8727	8975	-	AAC(6')-Ib7	1-249/980	====...........	0/0	25.41	98.80	card	Y11946.1:1-981	AAC(6')-Ib7 is a plasmid-encoded aminoglycoside acetyltransferase in E. cloacae and C. freundii	aminoglycoside
+SAMN11840202	contig00077	5190	8294	-	acrF	1-3105/3105	===============	0/0	100.00	99.97	card	U00096:3415033-3418138	AcrF is a inner membrane transporter similar to AcrB.	aminoglycoside/carbapenem/diaminopyrimidine/antibacterial_free_fatty_acids/aminocoumarin/cephamycin/phenicol/monobactam/glycylcycline/tetracycline/triclosan/acridine_dye/fluoroquinolone/penam/cephalosporin/macrolide
+SAMN11840202	contig00077	8306	9272	-	acrE	192-1158/1158	..=============	0/0	83.51	99.90	card	U00096:3413864-3415022	AcrE is a membrane fusion protein similar to AcrA.	aminocoumarin/cephamycin/carbapenem/diaminopyrimidine/aminoglycoside/antibacterial_free_fatty_acids/triclosan/tetracycline/acridine_dye/cephalosporin/macrolide/penam/fluoroquinolone/monobactam/glycylcycline/phenicol
+SAMN11840202	contig00080	1250	2005	-	rmtB	1-756/756	===============	0/0	100.00	100.00	card	AM886293.1:116480-117236	RmtB 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.	aminoglycoside
+SAMN11840202	contig00080	2175	3035	-	TEM-1	1-861/861	===============	0/0	100.00	99.88	card	AL513383:161911-162772	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	penam/cephalosporin/penem/monobactam
+SAMN11840202	contig00080	7165	8067	-	mphA	1-903/906	===============	0/0	99.67	100.00	card	D16251.1:1626-2532	The 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.	macrolide
+SAMN11840202	contig00088	2703	3578	-	CTX-M-15	1-876/876	===============	0/0	100.00	100.00	card	AY044436:1436-2312	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
+SAMN11840202	contig00102	130	779	+	OXA-368	2072-2721/2721	...........====	0/0	23.89	99.08	card	KT736121.1:1-2722	OXA-368 is a beta-lactamase found in Aeromonas sobria. From the Lahey list of OXA beta-lactamases.	cephalosporin/penam
+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
+SAMN11840202	contig00102	1812	2256	+	catB3	1-445/633	===========....	0/0	70.30	99.78	card	JX101693.1:58201-58834	catB3 is a plasmid or chromosome-encoded variant of the cat gene found in Salmonella typhimurium Acinetobacter baumannii and Escherichia coli	phenicol
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
@@ -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
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
@@ -0,0 +1,5 @@
+gene_name	detected	alleles
+KPC	False	
+NDM	True	NDM-5
+OXA	True	OXA-1
+rpoB2	False	
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
@@ -0,0 +1,61 @@
+#FILE	SEQUENCE	START	END	STRAND	GENE	COVERAGE	COVERAGE_MAP	GAPS	%COVERAGE	%IDENTITY	DATABASE	ACCESSION	PRODUCT	RESISTANCE
+SAMN11840203	contig00001	316814	317172	+	Klebsiella_pneumoniae_KpnE	5-363/363	========/======	2/2	98.62	76.67	card	AP006725.1:2483890-2484253	KpnE 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	diaminopyrimidine/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
+SAMN11840203	contig00001	317164	317488	+	Klebsiella_pneumoniae_KpnF	6-330/330	===============	0/0	98.48	75.69	card	AP006725.1:2484239-2484569	KpnF 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.	fosfomycin/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
+SAMN11840203	contig00001	355656	356039	-	marA	1-384/384	===============	0/0	100.00	99.48	card	AP009048.1:1621288-1621672	In 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.	antibacterial_free_fatty_acids/penem/diaminopyrimidine/macrolide/penam/rifamycin/cephamycin/aminocoumarin/carbapenem/aminoglycoside/cephalosporin/fluoroquinolone/tetracycline/triclosan/acridine_dye/monobactam/glycylcycline/phenicol
+SAMN11840203	contig00002	118693	120180	+	tolC	1-1488/1488	===============	0/0	100.00	98.52	card	FJ768952:1-1489	TolC 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.	rifamycin/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
+SAMN11840203	contig00002	140892	141711	-	bacA	1-820/822	===============	0/0	99.76	96.22	card	U00096.3:3203310-3204132	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
+SAMN11840203	contig00002	340230	340892	-	acrS	1-663/663	===============	0/0	100.00	98.94	card	U00096:3412803-3413466	AcrS 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.	glycylcycline/monobactam/phenicol/acridine_dye/triclosan/tetracycline/cephalosporin/fluoroquinolone/carbapenem/aminoglycoside/aminocoumarin/cephamycin/rifamycin/macrolide/penam/diaminopyrimidine/antibacterial_free_fatty_acids
+SAMN11840203	contig00002	341291	342448	+	acrE	1-1158/1158	===============	0/0	100.00	98.36	card	U00096:3413864-3415022	AcrE is a membrane fusion protein similar to AcrA.	aminocoumarin/cephamycin/carbapenem/diaminopyrimidine/aminoglycoside/antibacterial_free_fatty_acids/triclosan/tetracycline/acridine_dye/cephalosporin/macrolide/penam/fluoroquinolone/monobactam/glycylcycline/phenicol
+SAMN11840203	contig00002	342460	345564	+	acrF	1-3105/3105	===============	0/0	100.00	97.78	card	U00096:3415033-3418138	AcrF is a inner membrane transporter similar to AcrB.	aminoglycoside/carbapenem/diaminopyrimidine/antibacterial_free_fatty_acids/aminocoumarin/cephamycin/phenicol/monobactam/glycylcycline/tetracycline/triclosan/acridine_dye/fluoroquinolone/penam/cephalosporin/macrolide
+SAMN11840203	contig00003	31686	35279	-	evgS	1-3594/3594	===============	0/0	100.00	96.83	card	U00096:2484374-2487968	EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	triclosan/tetracycline/acridine_dye/oxazolidinone/fluoroquinolone/cephalosporin/phenicol/monobactam/glycylcycline/fosfomycin/aminocoumarin/peptide/rhodamine/aminoglycoside/carbapenem/penam/macrolide/nucleoside/nitroimidazole/rifamycin/benzalkonium_chloride/isoniazid/lincosamide/diaminopyrimidine/antibacterial_free_fatty_acids/bicyclomycin
+SAMN11840203	contig00003	35284	35898	-	evgA	1-615/615	===============	0/0	100.00	99.02	card	BA000007.3:3212026-3212641	EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed.	diaminopyrimidine/antibacterial_free_fatty_acids/bicyclomycin/benzalkonium_chloride/isoniazid/lincosamide/nucleoside/nitroimidazole/rifamycin/penam/macrolide/aminoglycoside/carbapenem/aminocoumarin/peptide/rhodamine/phenicol/monobactam/glycylcycline/fosfomycin/triclosan/tetracycline/oxazolidinone/acridine_dye/fluoroquinolone/cephalosporin
+SAMN11840203	contig00003	36422	37477	+	emrK	1-1056/1056	===============	0/0	100.00	97.82	card	D78168:537-1593	emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux.	macrolide/penam/rifamycin/nitroimidazole/nucleoside/isoniazid/lincosamide/benzalkonium_chloride/bicyclomycin/antibacterial_free_fatty_acids/diaminopyrimidine/cephalosporin/fluoroquinolone/acridine_dye/oxazolidinone/tetracycline/fosfomycin/glycylcycline/phenicol/rhodamine/peptide
+SAMN11840203	contig00003	37477	39015	+	emrY	1-1539/1539	===============	0/0	100.00	97.47	card	D78168:1592-3131	emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.	oxazolidinone/acridine_dye/tetracycline/cephalosporin/fluoroquinolone/glycylcycline/phenicol/fosfomycin/peptide/rhodamine/macrolide/penam/nucleoside/rifamycin/nitroimidazole/lincosamide/isoniazid/benzalkonium_chloride/diaminopyrimidine/bicyclomycin/antibacterial_free_fatty_acids
+SAMN11840203	contig00003	140616	141584	-	pmrF	1-969/969	===============	0/0	100.00	98.14	card	U00096:2367071-2368040	PmrF 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.	peptide
+SAMN11840203	contig00003	203080	204723	+	yojI	1-1644/1644	===============	0/0	100.00	97.51	card	U00096.3:2306972-2308616	YojI 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.	peptide/nitroimidazole/rifamycin/pleuromutilin/penam/fluoroquinolone/cephalosporin/macrolide/tetracycline/acridine_dye
+SAMN11840203	contig00005	39446	41194	+	msbA	1-1749/1749	===============	0/0	100.00	98.97	card	U00096.3:966621-968370	MsbA 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). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	peptide/rifamycin/pleuromutilin/nitroimidazole/tetracycline/acridine_dye/cephalosporin/macrolide/penam/fluoroquinolone
+SAMN11840203	contig00005	174588	175814	-	mdtG	1-1227/1227	===============	0/0	100.00	98.45	card	CP000800.1:1191728-1192955	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	macrolide/penam/rifamycin/nitroimidazole/nucleoside/isoniazid/lincosamide/benzalkonium_chloride/bicyclomycin/antibacterial_free_fatty_acids/diaminopyrimidine/cephalosporin/fluoroquinolone/acridine_dye/oxazolidinone/tetracycline/fosfomycin/glycylcycline/phenicol/rhodamine/peptide
+SAMN11840203	contig00005	184445	185653	-	mdtH	1-1209/1209	===============	0/0	100.00	97.85	card	U00096:1124118-1125327	Multidrug resistance protein MdtH	nitroimidazole/rifamycin/nucleoside/penam/macrolide/antibacterial_free_fatty_acids/bicyclomycin/diaminopyrimidine/benzalkonium_chloride/isoniazid/lincosamide/fosfomycin/phenicol/glycylcycline/fluoroquinolone/cephalosporin/tetracycline/acridine_dye/oxazolidinone/rhodamine/peptide
+SAMN11840203	contig00006	89461	90927	-	mdtP	1-1467/1467	===============	0/0	100.00	97.48	card	AP009048.1:4303043-4304510	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	benzalkonium_chloride/isoniazid/lincosamide/antibacterial_free_fatty_acids/bicyclomycin/diaminopyrimidine/penam/macrolide/nitroimidazole/rifamycin/nucleoside/rhodamine/peptide/fluoroquinolone/cephalosporin/tetracycline/acridine_dye/oxazolidinone/fosfomycin/phenicol/glycylcycline
+SAMN11840203	contig00006	90924	92975	-	mdtO	1-2052/2052	===============	0/0	100.00	96.34	card	AP009048.1:4304506-4306558	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride	nucleoside/rifamycin/nitroimidazole/macrolide/penam/diaminopyrimidine/bicyclomycin/antibacterial_free_fatty_acids/isoniazid/lincosamide/benzalkonium_chloride/glycylcycline/phenicol/fosfomycin/oxazolidinone/acridine_dye/tetracycline/cephalosporin/fluoroquinolone/peptide/rhodamine
+SAMN11840203	contig00006	92975	94006	-	mdtN	1-1032/1032	===============	0/0	100.00	96.42	card	AP009048.1:4306557-4307589	Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride.	tetracycline/oxazolidinone/acridine_dye/cephalosporin/fluoroquinolone/glycylcycline/phenicol/fosfomycin/peptide/rhodamine/macrolide/penam/nucleoside/rifamycin/nitroimidazole/isoniazid/lincosamide/benzalkonium_chloride/diaminopyrimidine/antibacterial_free_fatty_acids/bicyclomycin
+SAMN11840203	contig00006	116674	118317	-	eptA	1-1644/1644	===============	0/0	100.00	98.17	card	AP009048:4338625-4340269	PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B.	peptide
+SAMN11840203	contig00006	160236	161369	-	Escherichia_coli_ampC	1-1134/1134	===============	0/0	100.00	97.62	card	NC_000913.3:4377811-4378945	A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.	cephalosporin/penam
+SAMN11840203	contig00007	24627	25784	+	Escherichia_coli_ampH	1-1158/1158	===============	0/0	100.00	96.89	card	AP012030.1:395554-396712	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin/penam
+SAMN11840203	contig00008	19475	22588	+	acrD	1-3114/3114	===============	0/0	100.00	98.75	card	AP009048.1:2586251-2589365	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminocoumarin/aminoglycoside/carbapenem/diaminopyrimidine/antibacterial_free_fatty_acids/tetracycline/triclosan/acridine_dye/fluoroquinolone/penam/macrolide/phenicol/monobactam/glycylcycline
+SAMN11840203	contig00008	43295	43769	+	mphB	3-477/477	===============	0/0	99.58	96.63	card	AE005174.2:3397371-3397848	The mphB gene encodes for MPH(2')-II. This enzymes phosphorylates 14-membered and 16-membered macrolides.  It phosphorylates macrolides in GTP- dependent manner at 2'-OH hydroxyl of desosamine sugar of macrolides.	macrolide
+SAMN11840203	contig00009	22558	22971	-	H-NS	1-414/414	===============	0/0	100.00	99.52	card	BA000007.3:1737691-1738105	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	bicyclomycin/antibacterial_free_fatty_acids/diaminopyrimidine/benzalkonium_chloride/isoniazid/lincosamide/nitroimidazole/rifamycin/nucleoside/penam/macrolide/aminoglycoside/carbapenem/rhodamine/cephamycin/aminocoumarin/peptide/fosfomycin/phenicol/glycylcycline/monobactam/fluoroquinolone/cephalosporin/acridine_dye/oxazolidinone/triclosan/tetracycline
+SAMN11840203	contig00010	109634	110866	+	Escherichia_coli_mdfA	1-1233/1233	===============	0/0	100.00	96.59	card	JQ394987:1-1234	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	antibacterial_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
+SAMN11840203	contig00011	134538	135170	-	CRP	1-633/633	===============	0/0	100.00	99.05	card	AP009048.1:4153664-4154297	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	tetracycline/triclosan/acridine_dye/fluoroquinolone/penam/macrolide/phenicol/monobactam/glycylcycline/aminocoumarin/aminoglycoside/carbapenem/diaminopyrimidine/antibacterial_free_fatty_acids
+SAMN11840203	contig00012	66296	67462	-	ugd	1-1167/1167	===============	0/0	100.00	96.57	card	U00096:2098447-2099614	PmrE 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	peptide
+SAMN11840203	contig00012	123856	125103	+	mdtA	1-1248/1248	===============	0/0	100.00	96.88	card	U00096:2154016-2155264	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	antibacterial_free_fatty_acids/aminoglycoside/diaminopyrimidine/carbapenem/aminocoumarin/phenicol/glycylcycline/monobactam/penam/fluoroquinolone/macrolide/acridine_dye/triclosan/tetracycline
+SAMN11840203	contig00012	125103	128225	+	mdtB	1-3123/3123	===============	0/0	100.00	96.67	card	U00096:2155263-2158386	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin/aminoglycoside/diaminopyrimidine/carbapenem/antibacterial_free_fatty_acids/acridine_dye/tetracycline/triclosan/penam/fluoroquinolone/macrolide/phenicol/glycylcycline/monobactam
+SAMN11840203	contig00012	128226	131303	+	mdtC	1-3078/3078	===============	0/0	100.00	96.82	card	U00096:2158386-2161464	MdtC 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.	diaminopyrimidine/carbapenem/aminoglycoside/antibacterial_free_fatty_acids/aminocoumarin/glycylcycline/monobactam/phenicol/acridine_dye/triclosan/tetracycline/macrolide/fluoroquinolone/penam
+SAMN11840203	contig00012	132716	134119	+	baeS	1-1404/1404	===============	0/0	100.00	97.65	card	AP009048:2165013-2166417	BaeS 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.	aminocoumarin/carbapenem/diaminopyrimidine/aminoglycoside/antibacterial_free_fatty_acids/tetracycline/triclosan/acridine_dye/macrolide/fluoroquinolone/penam/monobactam/glycylcycline/phenicol
+SAMN11840203	contig00012	134116	134837	+	baeR	1-722/723	===============	0/0	99.86	98.20	card	AP009048.1:2166413-2167136	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	phenicol/monobactam/glycylcycline/tetracycline/triclosan/acridine_dye/penam/fluoroquinolone/macrolide/aminoglycoside/carbapenem/diaminopyrimidine/antibacterial_free_fatty_acids/aminocoumarin
+SAMN11840203	contig00014	128967	129623	-	QnrS1	1-657/657	===============	0/0	100.00	100.00	card	DQ485529.1:1-658	QnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri	fluoroquinolone
+SAMN11840203	contig00015	102091	103284	+	Escherichia_coli_acrA	1-1194/1194	===============	0/0	100.00	99.25	card	U00096.3:484426-485620	AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.	rifamycin/macrolide/penam/diaminopyrimidine/antibacterial_free_fatty_acids/glycylcycline/monobactam/phenicol/acridine_dye/tetracycline/triclosan/cephalosporin/fluoroquinolone/carbapenem/aminoglycoside/aminocoumarin
+SAMN11840203	contig00015	103307	106456	+	acrB	1-3150/3150	===============	0/0	100.00	99.05	card	U00096.3:481254-484404	Protein 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.	antibacterial_free_fatty_acids/diaminopyrimidine/rifamycin/penam/macrolide/aminoglycoside/carbapenem/aminocoumarin/phenicol/monobactam/glycylcycline/fluoroquinolone/cephalosporin/tetracycline/triclosan/acridine_dye
+SAMN11840203	contig00018	22463	23836	+	cpxA	1-1374/1374	===============	0/0	100.00	98.62	card	BA000007.3:4903689-4905063	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	acridine_dye/tetracycline/triclosan/macrolide/fluoroquinolone/penam/glycylcycline/monobactam/phenicol/aminocoumarin/diaminopyrimidine/carbapenem/aminoglycoside/antibacterial_free_fatty_acids
+SAMN11840203	contig00023	327	1559	+	mdtM	1-1233/1233	===============	0/0	100.00	96.51	card	U00096.3:4567287-4568520	Multidrug resistance protein MdtM	nitroimidazole/rifamycin/nucleoside/penam/macrolide/bicyclomycin/antibacterial_free_fatty_acids/diaminopyrimidine/benzalkonium_chloride/lincosamide/isoniazid/fosfomycin/phenicol/glycylcycline/fluoroquinolone/cephalosporin/oxazolidinone/acridine_dye/tetracycline/rhodamine/peptide
+SAMN11840203	contig00027	49570	50727	+	mdtE	1-1158/1158	===============	0/0	100.00	98.79	card	AP009048.1:3980026-3981184	MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.	glycylcycline/monobactam/phenicol/acridine_dye/tetracycline/triclosan/macrolide/fluoroquinolone/penam/diaminopyrimidine/carbapenem/aminoglycoside/antibacterial_free_fatty_acids/aminocoumarin
+SAMN11840203	contig00027	50752	53865	+	mdtF	1-3114/3114	===============	0/0	100.00	98.49	card	U00096:3660414-3663528	MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.	triclosan/tetracycline/acridine_dye/macrolide/fluoroquinolone/penam/monobactam/glycylcycline/phenicol/aminocoumarin/carbapenem/diaminopyrimidine/aminoglycoside/antibacterial_free_fatty_acids
+SAMN11840203	contig00027	54228	54956	-	gadW	1-729/729	===============	0/0	100.00	95.61	card	CP015085.1:2551712-2552441	GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC.	phenicol/monobactam/glycylcycline/penam/fluoroquinolone/macrolide/triclosan/tetracycline/acridine_dye/antibacterial_free_fatty_acids/aminoglycoside/carbapenem/diaminopyrimidine/aminocoumarin
+SAMN11840203	contig00027	55325	56149	-	gadX	1-825/825	===============	0/0	100.00	94.30	card	AP009048.1:3974605-3975430	GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.	aminoglycoside/diaminopyrimidine/carbapenem/antibacterial_free_fatty_acids/aminocoumarin/phenicol/glycylcycline/monobactam/acridine_dye/tetracycline/triclosan/penam/fluoroquinolone/macrolide
+SAMN11840203	contig00031	3563	5101	-	emrB	1-1539/1539	===============	0/0	100.00	97.99	card	U00096:2812616-2814155	emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.	rhodamine/peptide/fosfomycin/glycylcycline/phenicol/cephalosporin/fluoroquinolone/tetracycline/acridine_dye/oxazolidinone/antibacterial_free_fatty_acids/bicyclomycin/diaminopyrimidine/lincosamide/isoniazid/benzalkonium_chloride/rifamycin/nitroimidazole/nucleoside/macrolide/penam
+SAMN11840203	contig00031	5118	6290	-	emrA	1-1173/1173	===============	0/0	100.00	97.95	card	AP009048:2810083-2811256	EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.	benzalkonium_chloride/isoniazid/lincosamide/diaminopyrimidine/bicyclomycin/antibacterial_free_fatty_acids/penam/macrolide/nucleoside/nitroimidazole/rifamycin/peptide/rhodamine/acridine_dye/oxazolidinone/tetracycline/fluoroquinolone/cephalosporin/phenicol/glycylcycline/fosfomycin
+SAMN11840203	contig00031	6417	6947	-	emrR	1-531/531	===============	0/0	100.00	99.44	card	U00096.3:2810770-2811301	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	rifamycin/nitroimidazole/nucleoside/macrolide/penam/bicyclomycin/antibacterial_free_fatty_acids/diaminopyrimidine/lincosamide/isoniazid/benzalkonium_chloride/fosfomycin/glycylcycline/phenicol/cephalosporin/fluoroquinolone/oxazolidinone/acridine_dye/tetracycline/rhodamine/peptide
+SAMN11840203	contig00033	25605	26909	+	Escherichia_coli_ampC1_beta-lactamase	1-1305/1305	===============	0/0	100.00	96.02	card	FN649414.1:2765051-2766356	An ampC-like beta-lactamase identified from Escherichia coli.	cephalosporin/penam
+SAMN11840203	contig00040	7921	8598	+	kdpE	1-678/678	===============	0/0	100.00	95.43	card	U00096.3:721056-721734	kdpE 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.	aminoglycoside
+SAMN11840203	contig00041	22681	23033	-	Nocardia_rifampin_resistant_beta-subunit_of_RNA_polymerase_(rpoB2)	2980-3332/3489	......../...===	6/10	9.97	75.70	card	AP006618.1:4835200-4838689	Due 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.	rifamycin
+SAMN11840203	contig00046	459	1334	-	CTX-M-15	1-876/876	===============	0/0	100.00	100.00	card	AY044436:1436-2312	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
+SAMN11840203	contig00057	1194	2033	-	sul1	1-840/840	===============	0/0	100.00	100.00	card	JF969163:1054-1894	Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.	sulfonamide
+SAMN11840203	contig00057	3685	4341	-	QnrA1	1-657/657	===============	0/0	100.00	99.85	card	DQ831141:8922-9579	QnrA1 is a plasmid-mediated quinolone resistance protein found in Klebsiella pneumoniae	fluoroquinolone
+SAMN11840203	contig00063	3595	4455	-	SHV-134	1-861/861	===============	0/0	100.00	99.88	card	HM559945:1-862	SHV-134 is an extended-spectrum beta-lactamase.	carbapenem/penam/cephalosporin
+SAMN11840203	contig00065	1	85	-	TEM-101	1-85/861	==.............	0/0	9.87	100.00	card	AF495873:1-862	TEM-101 is an extended-spectrum beta-lactamase found in E. coli.	monobactam/penem/cephalosporin/penam
+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	contig00065	1669	2470	-	ANT(3'')-IIa	168-972/972	..======/======	1/3	82.51	99.25	card	X02340.1:223-1195	ANT(3'')-IIa is a aminoglycoside nucleotidyltransferase identified in Acinetobacter spp. via horizontal gene transfer mechanisms.	aminoglycoside
+SAMN11840203	contig00065	2363	3113	-	AAC(6')-Ib7	234-980/980	...=====/======	2/4	76.22	96.67	card	Y11946.1:1-981	AAC(6')-Ib7 is a plasmid-encoded aminoglycoside acetyltransferase in E. cloacae and C. freundii	aminoglycoside
+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
+SAMN11840203	contig00104	1	843	+	TEM-1	19-861/861	===============	0/0	97.91	99.88	card	AL513383:161911-162772	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	penam/cephalosporin/penem/monobactam
+SAMN11840203	contig00192	1	85	-	TEM-1	1-85/861	==.............	0/0	9.87	100.00	card	AL513383:161911-162772	TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.	penam/cephalosporin/penem/monobactam
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
@@ -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
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
@@ -0,0 +1,5 @@
+gene_name	detected	alleles
+KPC	False	
+NDM	False	
+OXA	True	OXA-9,OXA-48
+rpoB2	False	
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
@@ -0,0 +1,47 @@
+#FILE	SEQUENCE	START	END	STRAND	GENE	COVERAGE	COVERAGE_MAP	GAPS	%COVERAGE	%IDENTITY	DATABASE	ACCESSION	PRODUCT	RESISTANCE
+SAMN13042171.fasta	contig00001	181303	181975	+	kdpE	1-673/678	===============	0/0	99.26	76.08	card	U00096.3:721056-721734	kdpE 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.	aminoglycoside
+SAMN13042171.fasta	contig00001	362878	363231	-	ramA	21-375/375	========/======	1/1	94.40	80.56	card	JQ727668:1-376	RamA (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.	cephamycin/aminocoumarin/aminoglycoside/carbapenem/fluoroquinolone/cephalosporin/triclosan/tetracycline/acridine_dye/phenicol/monobactam/glycylcycline/antibacterial_free_fatty_acids/penem/diaminopyrimidine/penam/macrolide/rifamycin
+SAMN13042171.fasta	contig00001	568102	569295	+	Klebsiella_pneumoniae_acrA	1-1197/1197	========/======	2/3	99.75	95.07	card	AJ318073.1:794-1991	AcrA is a subunit of the AcrAB multidrug efflux system that in K. pneumoniae which is encoded by the acrRAB operon.	aminocoumarin/carbapenem/aminoglycoside/triclosan/tetracycline/acridine_dye/cephalosporin/fluoroquinolone/monobactam/glycylcycline/phenicol/diaminopyrimidine/antibacterial_free_fatty_acids/macrolide/penam/rifamycin
+SAMN13042171.fasta	contig00001	569318	572462	+	acrB	1-3148/3150	========/======	1/3	99.84	83.74	card	U00096.3:481254-484404	Protein 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.	antibacterial_free_fatty_acids/diaminopyrimidine/rifamycin/penam/macrolide/aminoglycoside/carbapenem/aminocoumarin/phenicol/monobactam/glycylcycline/fluoroquinolone/cephalosporin/tetracycline/triclosan/acridine_dye
+SAMN13042171.fasta	contig00001	698224	699350	+	Escherichia_coli_ampH	1-1127/1158	===============	0/0	97.32	77.46	card	AP012030.1:395554-396712	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin/penam
+SAMN13042171.fasta	contig00002	345289	346827	-	Klebsiella_pneumoniae_KpnH	1-1539/1539	===============	0/0	100.00	84.41	card	ASTU01000063.1:61249-62788	KpnH 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.	isoniazid/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
+SAMN13042171.fasta	contig00002	346843	348015	-	Klebsiella_pneumoniae_KpnG	1-1173/1173	===============	0/0	100.00	94.54	card	ACWO01000051.1:22093-23266	KpnG 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	penam/macrolide/nitroimidazole/nucleoside/benzalkonium_chloride/lincosamide/isoniazid/bicyclomycin/antibacterial_free_fatty_acids/diaminopyrimidine/penem/fluoroquinolone/cephalosporin/acridine_dye/oxazolidinone/fosfomycin/phenicol/rhodamine/peptide/rifamycin/tetracycline/glycylcycline/aminoglycoside/carbapenem
+SAMN13042171.fasta	contig00002	348162	348671	-	emrR	1-510/531	===============	0/0	96.05	83.33	card	U00096.3:2810770-2811301	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	rifamycin/nitroimidazole/nucleoside/macrolide/penam/bicyclomycin/antibacterial_free_fatty_acids/diaminopyrimidine/lincosamide/isoniazid/benzalkonium_chloride/fosfomycin/glycylcycline/phenicol/cephalosporin/fluoroquinolone/oxazolidinone/acridine_dye/tetracycline/rhodamine/peptide
+SAMN13042171.fasta	contig00002	389327	392479	-	oqxB	1-3153/3153	===============	0/0	100.00	95.53	card	EU370913.1:47851-51004	RND efflux pump conferring resistance to fluoroquinolone	tetracycline/triclosan/acridine_dye/fluoroquinolone/penam/nitrofuran/macrolide/phenicol/monobactam/glycylcycline/aminocoumarin/aminoglycoside/carbapenem/diaminopyrimidine/antibacterial_free_fatty_acids
+SAMN13042171.fasta	contig00002	392503	393678	-	oqxA	1-1176/1176	===============	0/0	100.00	93.71	card	EU370913.1:46652-47828	RND efflux pump conferring resistance to fluoroquinolone	phenicol/monobactam/glycylcycline/penam/fluoroquinolone/nitrofuran/macrolide/tetracycline/triclosan/acridine_dye/antibacterial_free_fatty_acids/aminoglycoside/carbapenem/diaminopyrimidine/aminocoumarin
+SAMN13042171.fasta	contig00003	27739	29154	-	mdtK	1-1416/1425	========/======	2/2	99.30	76.71	card	CP014358.1:2161326-2162751	A multidrug and toxic compound extrusions (MATE) transporter conferring resistance to norfloxacin doxorubicin and acriflavine.	glycylcycline/fluoroquinolone/tetracycline/acridine_dye
+SAMN13042171.fasta	contig00003	144300	145294	+	mdtA	178-1172/1248	.=======/======	2/2	79.65	78.51	card	U00096:2154016-2155264	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	antibacterial_free_fatty_acids/aminoglycoside/diaminopyrimidine/carbapenem/aminocoumarin/phenicol/glycylcycline/monobactam/penam/fluoroquinolone/macrolide/acridine_dye/triclosan/tetracycline
+SAMN13042171.fasta	contig00003	145364	148486	+	mdtB	1-3123/3123	========/======	2/4	99.94	80.90	card	U00096:2155263-2158386	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin/aminoglycoside/diaminopyrimidine/carbapenem/antibacterial_free_fatty_acids/acridine_dye/tetracycline/triclosan/penam/fluoroquinolone/macrolide/phenicol/glycylcycline/monobactam
+SAMN13042171.fasta	contig00003	148487	151564	+	mdtC	1-3078/3078	===============	0/0	100.00	82.00	card	U00096:2158386-2161464	MdtC 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.	diaminopyrimidine/carbapenem/aminoglycoside/antibacterial_free_fatty_acids/aminocoumarin/glycylcycline/monobactam/phenicol/acridine_dye/triclosan/tetracycline/macrolide/fluoroquinolone/penam
+SAMN13042171.fasta	contig00003	152979	153244	+	baeS	2-267/1404	===............	0/0	18.95	80.45	card	AP009048:2165013-2166417	BaeS 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.	aminocoumarin/carbapenem/diaminopyrimidine/aminoglycoside/antibacterial_free_fatty_acids/tetracycline/triclosan/acridine_dye/macrolide/fluoroquinolone/penam/monobactam/glycylcycline/phenicol
+SAMN13042171.fasta	contig00003	154462	155174	+	baeR	1-713/723	===============	0/0	98.62	82.61	card	AP009048.1:2166413-2167136	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	phenicol/monobactam/glycylcycline/tetracycline/triclosan/acridine_dye/penam/fluoroquinolone/macrolide/aminoglycoside/carbapenem/diaminopyrimidine/antibacterial_free_fatty_acids/aminocoumarin
+SAMN13042171.fasta	contig00003	277916	279555	-	yojI	1-1640/1644	========/======	6/6	99.57	75.65	card	U00096.3:2306972-2308616	YojI 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.	peptide/nitroimidazole/rifamycin/pleuromutilin/penam/fluoroquinolone/cephalosporin/macrolide/tetracycline/acridine_dye
+SAMN13042171.fasta	contig00004	25617	26032	+	FosA5	1-416/420	===============	0/0	99.05	93.51	card	KP143090.1:1200-1620	fosA5 is a fosfomycin resistance gene isolated from clinical strain of Escherichia coli E265. It is susceptible to amikacin tetracycline and imipenem and resistant to sulphonamide cephalosporins gentamicin ciprofloxacin chloramphenicol and streptomycin	fosfomycin
+SAMN13042171.fasta	contig00006	173	577	-	H-NS	1-405/414	===============	0/0	97.83	87.16	card	BA000007.3:1737691-1738105	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	bicyclomycin/antibacterial_free_fatty_acids/diaminopyrimidine/benzalkonium_chloride/isoniazid/lincosamide/nitroimidazole/rifamycin/nucleoside/penam/macrolide/aminoglycoside/carbapenem/rhodamine/cephamycin/aminocoumarin/peptide/fosfomycin/phenicol/glycylcycline/monobactam/fluoroquinolone/cephalosporin/acridine_dye/oxazolidinone/triclosan/tetracycline
+SAMN13042171.fasta	contig00007	21771	22687	-	pmrF	16-932/969	===============	0/0	94.63	76.77	card	U00096:2367071-2368040	PmrF 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.	peptide
+SAMN13042171.fasta	contig00008	29896	31020	-	Klebsiella_pneumoniae_OmpK37	1-1125/1125	===============	0/0	100.00	92.71	card	AJ011502.1:301-1426	Klebsiella pneumoniae outer membrane porin protein. Is preferentially detected in porin-deficient strains. Functional characterization of this new porin revealed a narrower pore than those of porins OmpK35 and OmpK36 which did not allow penetration by certain ##-lactams. Also when a resistant strain expresses porin OmpK37 is less susceptible to cefotaxime and cefoxitin than when it is expressing either OmpK36 or OmpK35.	cephalosporin/penam/cephamycin/monobactam/carbapenem/penem
+SAMN13042171.fasta	contig00008	175297	175659	+	Klebsiella_pneumoniae_KpnE	1-363/363	===============	0/0	100.00	88.43	card	AP006725.1:2483890-2484253	KpnE 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	diaminopyrimidine/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
+SAMN13042171.fasta	contig00008	175646	175975	+	Klebsiella_pneumoniae_KpnF	1-330/330	===============	0/0	100.00	92.42	card	AP006725.1:2484239-2484569	KpnF 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.	fosfomycin/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
+SAMN13042171.fasta	contig00008	217869	218728	-	OKP-B-18	1-860/861	===============	0/0	99.88	99.53	card	AM850920:41-902	OKP-B-18 is a beta-lactamase found in Klebsiella pneumoniae	cephalosporin/penam
+SAMN13042171.fasta	contig00009	93196	94580	+	tolC	1-1403/1488	========/======	2/18	93.08	78.40	card	FJ768952:1-1489	TolC 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.	rifamycin/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
+SAMN13042171.fasta	contig00009	108077	108898	-	bacA	1-822/822	===============	0/0	100.00	80.53	card	U00096.3:3203310-3204132	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
+SAMN13042171.fasta	contig00012	114632	116380	-	msbA	1-1749/1749	===============	0/0	100.00	80.96	card	U00096.3:966621-968370	MsbA 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). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	peptide/rifamycin/pleuromutilin/nitroimidazole/tetracycline/acridine_dye/cephalosporin/macrolide/penam/fluoroquinolone
+SAMN13042171.fasta	contig00012	155728	155882	-	macB	1586-1740/1935	............==.	0/0	8.01	76.13	card	AY768532:1-1936	MacB is an ATP-binding cassette (ABC) transporter that exports macrolides with 14- or 15- membered lactones. It forms an antibiotic efflux complex with MacA and TolC. macB corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	macrolide/cephalosporin/fluoroquinolone/penam/acridine_dye/tetracycline/pleuromutilin/rifamycin/nitroimidazole/peptide
+SAMN13042171.fasta	contig00015	140084	143160	+	acrF	1-3080/3105	========/======	7/9	99.00	76.74	card	U00096:3415033-3418138	AcrF is a inner membrane transporter similar to AcrB.	aminoglycoside/carbapenem/diaminopyrimidine/antibacterial_free_fatty_acids/aminocoumarin/cephamycin/phenicol/monobactam/glycylcycline/tetracycline/triclosan/acridine_dye/fluoroquinolone/penam/cephalosporin/macrolide
+SAMN13042171.fasta	contig00016	114383	115015	-	CRP	1-633/633	===============	0/0	100.00	87.36	card	AP009048.1:4153664-4154297	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	tetracycline/triclosan/acridine_dye/fluoroquinolone/penam/macrolide/phenicol/monobactam/glycylcycline/aminocoumarin/aminoglycoside/carbapenem/diaminopyrimidine/antibacterial_free_fatty_acids
+SAMN13042171.fasta	contig00018	59247	60613	-	cpxA	1-1367/1374	===============	0/0	99.49	81.71	card	BA000007.3:4903689-4905063	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	acridine_dye/tetracycline/triclosan/macrolide/fluoroquinolone/penam/glycylcycline/monobactam/phenicol/aminocoumarin/diaminopyrimidine/carbapenem/aminoglycoside/antibacterial_free_fatty_acids
+SAMN13042171.fasta	contig00019	55611	58724	+	acrD	1-3114/3114	========/======	2/2	99.97	80.58	card	AP009048.1:2586251-2589365	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminocoumarin/aminoglycoside/carbapenem/diaminopyrimidine/antibacterial_free_fatty_acids/tetracycline/triclosan/acridine_dye/fluoroquinolone/penam/macrolide/phenicol/monobactam/glycylcycline
+SAMN13042171.fasta	contig00024	52994	54169	+	mdtH	1-1176/1209	===============	0/0	97.27	77.04	card	U00096:1124118-1125327	Multidrug resistance protein MdtH	nitroimidazole/rifamycin/nucleoside/penam/macrolide/antibacterial_free_fatty_acids/bicyclomycin/diaminopyrimidine/benzalkonium_chloride/isoniazid/lincosamide/fosfomycin/phenicol/glycylcycline/fluoroquinolone/cephalosporin/tetracycline/acridine_dye/oxazolidinone/rhodamine/peptide
+SAMN13042171.fasta	contig00024	60718	61881	+	mdtG	18-1181/1227	========/======	3/8	94.54	76.03	card	CP000800.1:1191728-1192955	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	macrolide/penam/rifamycin/nitroimidazole/nucleoside/isoniazid/lincosamide/benzalkonium_chloride/bicyclomycin/antibacterial_free_fatty_acids/diaminopyrimidine/cephalosporin/fluoroquinolone/acridine_dye/oxazolidinone/tetracycline/fosfomycin/glycylcycline/phenicol/rhodamine/peptide
+SAMN13042171.fasta	contig00025	3007	3375	-	marA	1-369/384	===============	0/0	96.09	81.57	card	AP009048.1:1621288-1621672	In 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.	antibacterial_free_fatty_acids/penem/diaminopyrimidine/macrolide/penam/rifamycin/cephamycin/aminocoumarin/carbapenem/aminoglycoside/cephalosporin/fluoroquinolone/tetracycline/triclosan/acridine_dye/monobactam/glycylcycline/phenicol
+SAMN13042171.fasta	contig00028	4483	5688	+	Escherichia_coli_mdfA	1-1206/1233	========/======	2/2	97.73	78.21	card	JQ394987:1-1234	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	antibacterial_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
+SAMN13042171.fasta	contig00030	26098	26477	-	Nocardia_rifampin_resistant_beta-subunit_of_RNA_polymerase_(rpoB2)	2980-3359/3489	......../...===	2/2	10.86	76.11	card	AP006618.1:4835200-4838689	Due 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.	rifamycin
+SAMN13042171.fasta	contig00030	26758	26924	-	Nocardia_rifampin_resistant_beta-subunit_of_RNA_polymerase_(rpoB2)	2605-2771/3489	...........=...	0/0	4.79	75.45	card	AP006618.1:4835200-4838689	Due 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.	rifamycin
+SAMN13042171.fasta	contig00035	7853	8713	-	TEM-150	1-861/861	===============	0/0	100.00	99.88	card	AM183304:209-1070	TEM-150 is a beta-lactamase found in Enterobacter spp. E. coli and Klebsiella pneumoniae.	penem/monobactam/cephalosporin/penam
+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
+SAMN13042171.fasta	contig00035	10297	11098	-	ANT(3'')-IIa	168-972/972	..======/======	1/3	82.51	99.25	card	X02340.1:223-1195	ANT(3'')-IIa is a aminoglycoside nucleotidyltransferase identified in Acinetobacter spp. via horizontal gene transfer mechanisms.	aminoglycoside
+SAMN13042171.fasta	contig00035	10991	11741	-	AAC(6')-Ib7	234-980/980	...=====/======	2/4	76.22	96.67	card	Y11946.1:1-981	AAC(6')-Ib7 is a plasmid-encoded aminoglycoside acetyltransferase in E. cloacae and C. freundii	aminoglycoside
+SAMN13042171.fasta	contig00035	14582	15457	+	CTX-M-15	1-876/876	===============	0/0	100.00	100.00	card	AY044436:1436-2312	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
+SAMN13042171.fasta	contig00035	20098	20754	+	QnrS1	1-657/657	===============	0/0	100.00	100.00	card	DQ485529.1:1-658	QnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri	fluoroquinolone
+SAMN13042171.fasta	contig00063	2129	2494	-	determinant_of_bleomycin_resistance	1-366/366	===============	0/0	100.00	100.00	card	KC503911.1:9884-10250	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.	glycopeptide
+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
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
@@ -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
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
@@ -0,0 +1,5 @@
+gene_name	detected	alleles
+KPC	False	
+NDM	True	NDM-1
+OXA	True	OXA-9
+rpoB2	False	
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
@@ -1,47 +0,0 @@
-#FILE	SEQUENCE	START	END	STRAND	GENE	COVERAGE	COVERAGE_MAP	GAPS	%COVERAGE	%IDENTITY	DATABASE	ACCESSION	PRODUCT	RESISTANCE
-SAMN13042171.fasta	contig00001	181303	181975	+	kdpE	1-673/678	===============	0/0	99.26	76.08	card	U00096.3:721056-721734	kdpE 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.	aminoglycoside
-SAMN13042171.fasta	contig00001	362878	363231	-	ramA	21-375/375	========/======	1/1	94.40	80.56	card	JQ727668:1-376	RamA (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.	cephamycin/aminocoumarin/aminoglycoside/carbapenem/fluoroquinolone/cephalosporin/triclosan/tetracycline/acridine_dye/phenicol/monobactam/glycylcycline/antibacterial_free_fatty_acids/penem/diaminopyrimidine/penam/macrolide/rifamycin
-SAMN13042171.fasta	contig00001	568102	569295	+	Klebsiella_pneumoniae_acrA	1-1197/1197	========/======	2/3	99.75	95.07	card	AJ318073.1:794-1991	AcrA is a subunit of the AcrAB multidrug efflux system that in K. pneumoniae which is encoded by the acrRAB operon.	aminocoumarin/carbapenem/aminoglycoside/triclosan/tetracycline/acridine_dye/cephalosporin/fluoroquinolone/monobactam/glycylcycline/phenicol/diaminopyrimidine/antibacterial_free_fatty_acids/macrolide/penam/rifamycin
-SAMN13042171.fasta	contig00001	569318	572462	+	acrB	1-3148/3150	========/======	1/3	99.84	83.74	card	U00096.3:481254-484404	Protein 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.	antibacterial_free_fatty_acids/diaminopyrimidine/rifamycin/penam/macrolide/aminoglycoside/carbapenem/aminocoumarin/phenicol/monobactam/glycylcycline/fluoroquinolone/cephalosporin/tetracycline/triclosan/acridine_dye
-SAMN13042171.fasta	contig00001	698224	699350	+	Escherichia_coli_ampH	1-1127/1158	===============	0/0	97.32	77.46	card	AP012030.1:395554-396712	AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli.	cephalosporin/penam
-SAMN13042171.fasta	contig00002	345289	346827	-	Klebsiella_pneumoniae_KpnH	1-1539/1539	===============	0/0	100.00	84.41	card	ASTU01000063.1:61249-62788	KpnH 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.	isoniazid/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
-SAMN13042171.fasta	contig00002	346843	348015	-	Klebsiella_pneumoniae_KpnG	1-1173/1173	===============	0/0	100.00	94.54	card	ACWO01000051.1:22093-23266	KpnG 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	penam/macrolide/nitroimidazole/nucleoside/benzalkonium_chloride/lincosamide/isoniazid/bicyclomycin/antibacterial_free_fatty_acids/diaminopyrimidine/penem/fluoroquinolone/cephalosporin/acridine_dye/oxazolidinone/fosfomycin/phenicol/rhodamine/peptide/rifamycin/tetracycline/glycylcycline/aminoglycoside/carbapenem
-SAMN13042171.fasta	contig00002	348162	348671	-	emrR	1-510/531	===============	0/0	96.05	83.33	card	U00096.3:2810770-2811301	EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.	rifamycin/nitroimidazole/nucleoside/macrolide/penam/bicyclomycin/antibacterial_free_fatty_acids/diaminopyrimidine/lincosamide/isoniazid/benzalkonium_chloride/fosfomycin/glycylcycline/phenicol/cephalosporin/fluoroquinolone/oxazolidinone/acridine_dye/tetracycline/rhodamine/peptide
-SAMN13042171.fasta	contig00002	389327	392479	-	oqxB	1-3153/3153	===============	0/0	100.00	95.53	card	EU370913.1:47851-51004	RND efflux pump conferring resistance to fluoroquinolone	tetracycline/triclosan/acridine_dye/fluoroquinolone/penam/nitrofuran/macrolide/phenicol/monobactam/glycylcycline/aminocoumarin/aminoglycoside/carbapenem/diaminopyrimidine/antibacterial_free_fatty_acids
-SAMN13042171.fasta	contig00002	392503	393678	-	oqxA	1-1176/1176	===============	0/0	100.00	93.71	card	EU370913.1:46652-47828	RND efflux pump conferring resistance to fluoroquinolone	phenicol/monobactam/glycylcycline/penam/fluoroquinolone/nitrofuran/macrolide/tetracycline/triclosan/acridine_dye/antibacterial_free_fatty_acids/aminoglycoside/carbapenem/diaminopyrimidine/aminocoumarin
-SAMN13042171.fasta	contig00003	27739	29154	-	mdtK	1-1416/1425	========/======	2/2	99.30	76.71	card	CP014358.1:2161326-2162751	A multidrug and toxic compound extrusions (MATE) transporter conferring resistance to norfloxacin doxorubicin and acriflavine.	glycylcycline/fluoroquinolone/tetracycline/acridine_dye
-SAMN13042171.fasta	contig00003	144300	145294	+	mdtA	178-1172/1248	.=======/======	2/2	79.65	78.51	card	U00096:2154016-2155264	MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.	antibacterial_free_fatty_acids/aminoglycoside/diaminopyrimidine/carbapenem/aminocoumarin/phenicol/glycylcycline/monobactam/penam/fluoroquinolone/macrolide/acridine_dye/triclosan/tetracycline
-SAMN13042171.fasta	contig00003	145364	148486	+	mdtB	1-3123/3123	========/======	2/4	99.94	80.90	card	U00096:2155263-2158386	MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.	aminocoumarin/aminoglycoside/diaminopyrimidine/carbapenem/antibacterial_free_fatty_acids/acridine_dye/tetracycline/triclosan/penam/fluoroquinolone/macrolide/phenicol/glycylcycline/monobactam
-SAMN13042171.fasta	contig00003	148487	151564	+	mdtC	1-3078/3078	===============	0/0	100.00	82.00	card	U00096:2158386-2161464	MdtC 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.	diaminopyrimidine/carbapenem/aminoglycoside/antibacterial_free_fatty_acids/aminocoumarin/glycylcycline/monobactam/phenicol/acridine_dye/triclosan/tetracycline/macrolide/fluoroquinolone/penam
-SAMN13042171.fasta	contig00003	152979	153244	+	baeS	2-267/1404	===............	0/0	18.95	80.45	card	AP009048:2165013-2166417	BaeS 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.	aminocoumarin/carbapenem/diaminopyrimidine/aminoglycoside/antibacterial_free_fatty_acids/tetracycline/triclosan/acridine_dye/macrolide/fluoroquinolone/penam/monobactam/glycylcycline/phenicol
-SAMN13042171.fasta	contig00003	154462	155174	+	baeR	1-713/723	===============	0/0	98.62	82.61	card	AP009048.1:2166413-2167136	BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.	phenicol/monobactam/glycylcycline/tetracycline/triclosan/acridine_dye/penam/fluoroquinolone/macrolide/aminoglycoside/carbapenem/diaminopyrimidine/antibacterial_free_fatty_acids/aminocoumarin
-SAMN13042171.fasta	contig00003	277916	279555	-	yojI	1-1640/1644	========/======	6/6	99.57	75.65	card	U00096.3:2306972-2308616	YojI 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.	peptide/nitroimidazole/rifamycin/pleuromutilin/penam/fluoroquinolone/cephalosporin/macrolide/tetracycline/acridine_dye
-SAMN13042171.fasta	contig00004	25617	26032	+	FosA5	1-416/420	===============	0/0	99.05	93.51	card	KP143090.1:1200-1620	fosA5 is a fosfomycin resistance gene isolated from clinical strain of Escherichia coli E265. It is susceptible to amikacin tetracycline and imipenem and resistant to sulphonamide cephalosporins gentamicin ciprofloxacin chloramphenicol and streptomycin	fosfomycin
-SAMN13042171.fasta	contig00006	173	577	-	H-NS	1-405/414	===============	0/0	97.83	87.16	card	BA000007.3:1737691-1738105	H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.	bicyclomycin/antibacterial_free_fatty_acids/diaminopyrimidine/benzalkonium_chloride/isoniazid/lincosamide/nitroimidazole/rifamycin/nucleoside/penam/macrolide/aminoglycoside/carbapenem/rhodamine/cephamycin/aminocoumarin/peptide/fosfomycin/phenicol/glycylcycline/monobactam/fluoroquinolone/cephalosporin/acridine_dye/oxazolidinone/triclosan/tetracycline
-SAMN13042171.fasta	contig00007	21771	22687	-	pmrF	16-932/969	===============	0/0	94.63	76.77	card	U00096:2367071-2368040	PmrF 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.	peptide
-SAMN13042171.fasta	contig00008	29896	31020	-	Klebsiella_pneumoniae_OmpK37	1-1125/1125	===============	0/0	100.00	92.71	card	AJ011502.1:301-1426	Klebsiella pneumoniae outer membrane porin protein. Is preferentially detected in porin-deficient strains. Functional characterization of this new porin revealed a narrower pore than those of porins OmpK35 and OmpK36 which did not allow penetration by certain ##-lactams. Also when a resistant strain expresses porin OmpK37 is less susceptible to cefotaxime and cefoxitin than when it is expressing either OmpK36 or OmpK35.	cephalosporin/penam/cephamycin/monobactam/carbapenem/penem
-SAMN13042171.fasta	contig00008	175297	175659	+	Klebsiella_pneumoniae_KpnE	1-363/363	===============	0/0	100.00	88.43	card	AP006725.1:2483890-2484253	KpnE 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	diaminopyrimidine/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
-SAMN13042171.fasta	contig00008	175646	175975	+	Klebsiella_pneumoniae_KpnF	1-330/330	===============	0/0	100.00	92.42	card	AP006725.1:2484239-2484569	KpnF 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.	fosfomycin/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
-SAMN13042171.fasta	contig00008	217869	218728	-	OKP-B-18	1-860/861	===============	0/0	99.88	99.53	card	AM850920:41-902	OKP-B-18 is a beta-lactamase found in Klebsiella pneumoniae	cephalosporin/penam
-SAMN13042171.fasta	contig00009	93196	94580	+	tolC	1-1403/1488	========/======	2/18	93.08	78.40	card	FJ768952:1-1489	TolC 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.	rifamycin/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
-SAMN13042171.fasta	contig00009	108077	108898	-	bacA	1-822/822	===============	0/0	100.00	80.53	card	U00096.3:3203310-3204132	The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.	peptide
-SAMN13042171.fasta	contig00012	114632	116380	-	msbA	1-1749/1749	===============	0/0	100.00	80.96	card	U00096.3:966621-968370	MsbA 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). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability.	peptide/rifamycin/pleuromutilin/nitroimidazole/tetracycline/acridine_dye/cephalosporin/macrolide/penam/fluoroquinolone
-SAMN13042171.fasta	contig00012	155728	155882	-	macB	1586-1740/1935	............==.	0/0	8.01	76.13	card	AY768532:1-1936	MacB is an ATP-binding cassette (ABC) transporter that exports macrolides with 14- or 15- membered lactones. It forms an antibiotic efflux complex with MacA and TolC. macB corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.	macrolide/cephalosporin/fluoroquinolone/penam/acridine_dye/tetracycline/pleuromutilin/rifamycin/nitroimidazole/peptide
-SAMN13042171.fasta	contig00015	140084	143160	+	acrF	1-3080/3105	========/======	7/9	99.00	76.74	card	U00096:3415033-3418138	AcrF is a inner membrane transporter similar to AcrB.	aminoglycoside/carbapenem/diaminopyrimidine/antibacterial_free_fatty_acids/aminocoumarin/cephamycin/phenicol/monobactam/glycylcycline/tetracycline/triclosan/acridine_dye/fluoroquinolone/penam/cephalosporin/macrolide
-SAMN13042171.fasta	contig00016	114383	115015	-	CRP	1-633/633	===============	0/0	100.00	87.36	card	AP009048.1:4153664-4154297	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	tetracycline/triclosan/acridine_dye/fluoroquinolone/penam/macrolide/phenicol/monobactam/glycylcycline/aminocoumarin/aminoglycoside/carbapenem/diaminopyrimidine/antibacterial_free_fatty_acids
-SAMN13042171.fasta	contig00018	59247	60613	-	cpxA	1-1367/1374	===============	0/0	99.49	81.71	card	BA000007.3:4903689-4905063	CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.	acridine_dye/tetracycline/triclosan/macrolide/fluoroquinolone/penam/glycylcycline/monobactam/phenicol/aminocoumarin/diaminopyrimidine/carbapenem/aminoglycoside/antibacterial_free_fatty_acids
-SAMN13042171.fasta	contig00019	55611	58724	+	acrD	1-3114/3114	========/======	2/2	99.97	80.58	card	AP009048.1:2586251-2589365	AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR.	aminocoumarin/aminoglycoside/carbapenem/diaminopyrimidine/antibacterial_free_fatty_acids/tetracycline/triclosan/acridine_dye/fluoroquinolone/penam/macrolide/phenicol/monobactam/glycylcycline
-SAMN13042171.fasta	contig00024	52994	54169	+	mdtH	1-1176/1209	===============	0/0	97.27	77.04	card	U00096:1124118-1125327	Multidrug resistance protein MdtH	nitroimidazole/rifamycin/nucleoside/penam/macrolide/antibacterial_free_fatty_acids/bicyclomycin/diaminopyrimidine/benzalkonium_chloride/isoniazid/lincosamide/fosfomycin/phenicol/glycylcycline/fluoroquinolone/cephalosporin/tetracycline/acridine_dye/oxazolidinone/rhodamine/peptide
-SAMN13042171.fasta	contig00024	60718	61881	+	mdtG	18-1181/1227	========/======	3/8	94.54	76.03	card	CP000800.1:1191728-1192955	The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.	macrolide/penam/rifamycin/nitroimidazole/nucleoside/isoniazid/lincosamide/benzalkonium_chloride/bicyclomycin/antibacterial_free_fatty_acids/diaminopyrimidine/cephalosporin/fluoroquinolone/acridine_dye/oxazolidinone/tetracycline/fosfomycin/glycylcycline/phenicol/rhodamine/peptide
-SAMN13042171.fasta	contig00025	3007	3375	-	marA	1-369/384	===============	0/0	96.09	81.57	card	AP009048.1:1621288-1621672	In 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.	antibacterial_free_fatty_acids/penem/diaminopyrimidine/macrolide/penam/rifamycin/cephamycin/aminocoumarin/carbapenem/aminoglycoside/cephalosporin/fluoroquinolone/tetracycline/triclosan/acridine_dye/monobactam/glycylcycline/phenicol
-SAMN13042171.fasta	contig00028	4483	5688	+	Escherichia_coli_mdfA	1-1206/1233	========/======	2/2	97.73	78.21	card	JQ394987:1-1234	Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter.	antibacterial_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
-SAMN13042171.fasta	contig00030	26098	26477	-	Nocardia_rifampin_resistant_beta-subunit_of_RNA_polymerase_(rpoB2)	2980-3359/3489	......../...===	2/2	10.86	76.11	card	AP006618.1:4835200-4838689	Due 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.	rifamycin
-SAMN13042171.fasta	contig00030	26758	26924	-	Nocardia_rifampin_resistant_beta-subunit_of_RNA_polymerase_(rpoB2)	2605-2771/3489	...........=...	0/0	4.79	75.45	card	AP006618.1:4835200-4838689	Due 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.	rifamycin
-SAMN13042171.fasta	contig00035	7853	8713	-	TEM-150	1-861/861	===============	0/0	100.00	99.88	card	AM183304:209-1070	TEM-150 is a beta-lactamase found in Enterobacter spp. E. coli and Klebsiella pneumoniae.	penem/monobactam/cephalosporin/penam
-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
-SAMN13042171.fasta	contig00035	10297	11098	-	ANT(3'')-IIa	168-972/972	..======/======	1/3	82.51	99.25	card	X02340.1:223-1195	ANT(3'')-IIa is a aminoglycoside nucleotidyltransferase identified in Acinetobacter spp. via horizontal gene transfer mechanisms.	aminoglycoside
-SAMN13042171.fasta	contig00035	10991	11741	-	AAC(6')-Ib7	234-980/980	...=====/======	2/4	76.22	96.67	card	Y11946.1:1-981	AAC(6')-Ib7 is a plasmid-encoded aminoglycoside acetyltransferase in E. cloacae and C. freundii	aminoglycoside
-SAMN13042171.fasta	contig00035	14582	15457	+	CTX-M-15	1-876/876	===============	0/0	100.00	100.00	card	AY044436:1436-2312	CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family	cephalosporin
-SAMN13042171.fasta	contig00035	20098	20754	+	QnrS1	1-657/657	===============	0/0	100.00	100.00	card	DQ485529.1:1-658	QnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri	fluoroquinolone
-SAMN13042171.fasta	contig00063	2129	2494	-	determinant_of_bleomycin_resistance	1-366/366	===============	0/0	100.00	100.00	card	KC503911.1:9884-10250	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.	glycopeptide
-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
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
@@ -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
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
@@ -1,5 +0,0 @@
-gene_name	detected
-KPC	False
-NDM	True
-OXA	True
-rpoB2	False