Merge branch 'master' into dev

okirialbert · Jul 18, 2023 · 80beec7 · 80beec7
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diff --git a/README.md b/README.md
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 This software and the accompanying database are designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences. We have also added "plus" stress, heat, and biocide resistance and virulence factors for [some organisms](https://github.com/evolarjun/amr/wiki/Curated-organisms).
 
 ## See [the wiki for documentation](https://github.com/ncbi/amr/wiki)
-[Please subscribe to our announce list](https://www.ncbi.nlm.nih.gov/mailman/listinfo/amrfinder-announce) for announcements of database and software updates.
+## [Citing AMRFinderPlus](https://github.com/ncbi/amr/wiki#how-to-cite)
+## Please [subscribe to our announce list](https://www.ncbi.nlm.nih.gov/mailman/listinfo/amrfinder-announce) for announcements of database and software updates.
 
 ----
 # Licenses

diff --git a/test_both.expected b/test_both.expected
@@ -7,7 +7,7 @@ NA	contig04	1261	2391	+	blaEC	BlaEC family class C beta-lactamase	plus	AMR	AMR	B
 NA	contig08	101	700	+	blaTEM	TEM family class A beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	PARTIAL_CONTIG_ENDX	200	286	69.93	100.00	200	WP_061158039.1	class A beta-lactamase TEM-156	NA	NA
 aph3pp-Ib_partial_5p_neg	contig09	1	675	-	aph(3'')-Ib	aminoglycoside O-phosphotransferase APH(3'')-Ib	core	AMR	AMR	AMINOGLYCOSIDE	STREPTOMYCIN	PARTIAL_CONTIG_ENDP	225	267	81.27	100.00	217	WP_001082319.1	aminoglycoside O-phosphotransferase APH(3'')-Ib	NF032896.1	APH(3'') family aminoglycoside O-phosphotransferase
 sul2_partial_3p_neg	contig09	715	1377	-	sul2	sulfonamide-resistant dihydropteroate synthase Sul2	core	AMR	AMR	SULFONAMIDE	SULFONAMIDE	PARTIAL_CONTIG_ENDP	221	271	81.55	100.00	221	WP_001043265.1	sulfonamide-resistant dihydropteroate synthase Sul2	NA	NA
-NA	contig10	486	1307	+	blaOXA	OXA-9 family class D beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	INTERNAL_STOP	274	274	100.00	99.64	274	WP_000722315.1	oxacillin-hydrolyzing class D beta-lactamase OXA-9	NA	NA
+NA	contig10	486	1307	+	blaOXA	OXA-9 family oxacillin-hydrolyzing class D beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	INTERNAL_STOP	274	274	100.00	99.64	274	WP_000722315.1	oxacillin-hydrolyzing class D beta-lactamase OXA-9	NA	NA
 blaTEM-internal_stop	contig11	113	547	+	blaTEM	TEM family class A beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	INTERNAL_STOP	144	286	50.35	97.22	144	WP_000027057.1	broad-spectrum class A beta-lactamase TEM-1	NA	NA
 qacR-curated_blast	contig12	71	637	+	qacR	multidrug-binding transcriptional regulator QacR	plus	STRESS	BIOCIDE	QUATERNARY AMMONIUM	QUATERNARY AMMONIUM	BLASTP	188	188	100.00	99.47	188	ADK23698.1	multidrug-binding transcriptional regulator QacR	NA	NA
 emrD3-suppressed-in-vibrio	contig13	1	1137	+	emrD3	multidrug efflux MFS transporter EmrD-3	plus	AMR	AMR	EFFLUX	EFFLUX	EXACTP	379	379	100.00	100.00	379	ABQ18953.1	multidrug efflux MFS transporter EmrD-3	NA	NA

diff --git a/test_dna.expected b/test_dna.expected
@@ -7,7 +7,7 @@ NA	contig04	1261	2391	+	blaEC	BlaEC family class C beta-lactamase	plus	AMR	AMR	B
 NA	contig08	101	700	+	blaTEM	TEM family class A beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	PARTIAL_CONTIG_ENDX	200	286	69.93	100.00	200	WP_061158039.1	class A beta-lactamase TEM-156	NA	NA
 NA	contig09	1	651	-	aph(3'')-Ib	aminoglycoside O-phosphotransferase APH(3'')-Ib	core	AMR	AMR	AMINOGLYCOSIDE	STREPTOMYCIN	PARTIAL_CONTIG_ENDX	217	267	81.27	100.00	217	WP_001082319.1	aminoglycoside O-phosphotransferase APH(3'')-Ib	NA	NA
 NA	contig09	715	1377	-	sul2	sulfonamide-resistant dihydropteroate synthase Sul2	core	AMR	AMR	SULFONAMIDE	SULFONAMIDE	PARTIAL_CONTIG_ENDX	221	271	81.55	100.00	221	WP_001043265.1	sulfonamide-resistant dihydropteroate synthase Sul2	NA	NA
-NA	contig10	486	1307	+	blaOXA	OXA-9 family class D beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	INTERNAL_STOP	274	274	100.00	99.64	274	WP_000722315.1	oxacillin-hydrolyzing class D beta-lactamase OXA-9	NA	NA
+NA	contig10	486	1307	+	blaOXA	OXA-9 family oxacillin-hydrolyzing class D beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	INTERNAL_STOP	274	274	100.00	99.64	274	WP_000722315.1	oxacillin-hydrolyzing class D beta-lactamase OXA-9	NA	NA
 NA	contig11	101	958	+	blaTEM	TEM family class A beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	INTERNAL_STOP	286	286	100.00	93.01	286	WP_061158039.1	class A beta-lactamase TEM-156	NA	NA
 NA	contig12	71	634	+	qacR	multidrug-binding transcriptional regulator QacR	plus	STRESS	BIOCIDE	QUATERNARY AMMONIUM	QUATERNARY AMMONIUM	BLASTX	188	188	100.00	99.47	188	ADK23698.1	multidrug-binding transcriptional regulator QacR	NA	NA
 NA	contig13	1	1137	+	emrD3	multidrug efflux MFS transporter EmrD-3	plus	AMR	AMR	EFFLUX	EFFLUX	EXACTX	379	379	100.00	100.00	379	ABQ18953.1	multidrug efflux MFS transporter EmrD-3	NA	NA