remove blank space and fix separator of the rules txt files

Author: lcerdeira

rules/Acinetobacter_baumannii.txt

@@ -41,8 +41,7 @@ ACI0039	s__Acinetobacter baumannii	blaOXA-237	blaOXA-237	WP_000854010.1	-	-	ARO:
 ACI0041	s__Acinetobacter baumannii	blaOXA-143_fam	blaOXA-143_fam	-	-	NF000464.2	ARO:3007701	-	Gene presence detected	acquired	-	carbapenem	nonwildtype	R	not applicable	EUCAST v14.0 (2024)	-	ECO:0001103 natural variation mutant evidence	strong		Phenotype of this gene family inferred from MICs of several members.	
 ACI0042	s__Acinetobacter baumannii	blaOXA-143	blaOXA-143	WP_063861042.1	-	-	ARO:3001654	-	Gene presence detected	acquired	-	carbapenem	nonwildtype	R	not applicable	EUCAST v14.0 (2024)	19770279	ECO:0001103 natural variation mutant evidence	strong		MIC >32 mg/L (imipenem) ; MIC >32 mg/L (meropenem) 	
 ACI0043	s__Acinetobacter baumannii	blaOXA-182	blaOXA-182	WP_063861266.1	-	-	ARO:3001709	-	Gene presence detected	acquired	-	carbapenem	nonwildtype	R	not applicable	EUCAST v14.0 (2024)	20884158	ECO:0001103 natural variation mutant evidence	moderate	lacks evidence of the degree to which MIC is affected	Phenotype of this gene in Acinetobacter baumannii inferred from the other members of the family.	
-ACI0044	s__Acinetobacter baumannii	blaOXA-231	blaOXA-231	WP_063862128.1	-	-	ARO:3001670	-	Gene presence detected	acquired	-	carbapenem	nonwildtype	R	not applicable	EUCAST v14.0 (2024)	"22736746
-24566181"	ECO:0001103 natural variation mutant evidence	strong		MIC >32 mg/L (imipenem) ; MIC >32 mg/L (meropenem) 	
+ACI0044	s__Acinetobacter baumannii	blaOXA-231	blaOXA-231	WP_063862128.1	-	-	ARO:3001670	-	Gene presence detected	acquired	-	carbapenem	nonwildtype	R	not applicable	EUCAST v14.0 (2024)	"22736746, 24566181"	ECO:0001103 natural variation mutant evidence	strong		MIC >32 mg/L (imipenem) ; MIC >32 mg/L (meropenem) 	
 ACI0045	s__Acinetobacter baumannii	blaOXA-253	blaOXA-253	WP_032495764.1	-	-	ARO:3001689	-	Gene presence detected	acquired	-	carbapenem	nonwildtype	R	not applicable	EUCAST v14.0 (2024)	24566181	ECO:0001103 natural variation mutant evidence	strong		MIC >32 mg/L (imipenem) ; MIC >32 mg/L (meropenem) 	
 ACI0046	s__Acinetobacter baumannii	blaNDM	blaNDM	-	-	NF000259.2	ARO:3000057	-	Gene presence detected	acquired	-	carbapenem	nonwildtype	R	not applicable	EUCAST v14.0 (2024)	-	ECO:0001103 natural variation mutant evidence	moderate	lacks evidence of the degree to which MIC is affected	Phenotype of this gene family inferred from MICs of several members.	
 ACI0047	s__Acinetobacter baumannii	blaNDM-1	blaNDM-1	WP_004201164.1	-	-	ARO:3000589	-	Gene presence detected	acquired	-	carbapenem	nonwildtype	R	not applicable	EUCAST v14.0 (2024)	21693460	ECO:0001103 natural variation mutant evidence	strong		MIC >32 mg/L (imipenem) ; MIC >32 mg/L (meropenem) 	
@@ -132,10 +131,8 @@ ACI0130	s__Acinetobacter baumannii	blaOXA-143	blaOXA-143	WP_063861042.1	-	-	ARO:
 ACI0131	s__Acinetobacter baumannii	blaOXA-143	blaOXA-143	WP_063861042.1	-	-	ARO:3001654	-	Gene presence detected	acquired	meropenem	-	nonwildtype	R	MIC > 8 mg/L	EUCAST v14.0 (2024)	19770279	ECO:0001103 natural variation mutant evidence	strong		MIC >32 mg/L (meropenem) 	
 ACI0132	s__Acinetobacter baumannii	blaOXA-182	blaOXA-182	WP_063861266.1	-	-	ARO:3001709	-	Gene presence detected	acquired	imipenem	-	nonwildtype	R	MIC > 4 mg/L	EUCAST v14.0 (2024)	20884158	ECO:0001103 natural variation mutant evidence	moderate	lacks evidence of the degree to which MIC is affected	Phenotype of this gene in Acinetobacter baumannii inferred from the other members of the family.	
 ACI0133	s__Acinetobacter baumannii	blaOXA-182	blaOXA-182	WP_063861266.1	-	-	ARO:3001709	-	Gene presence detected	acquired	meropenem	-	nonwildtype	R	MIC > 8 mg/L	EUCAST v14.0 (2024)	20884158	ECO:0001103 natural variation mutant evidence	moderate	lacks evidence of the degree to which MIC is affected	Phenotype of this gene in Acinetobacter baumannii inferred from the other members of the family.	
-ACI0134	s__Acinetobacter baumannii	blaOXA-231	blaOXA-231	WP_063862128.1	-	-	ARO:3001670	-	Gene presence detected	acquired	imipenem	-	nonwildtype	R	MIC > 4 mg/L	EUCAST v14.0 (2024)	"22736746
-24566181"	ECO:0001103 natural variation mutant evidence	strong		MIC >32 mg/L (imipenem)	
-ACI0135	s__Acinetobacter baumannii	blaOXA-231	blaOXA-231	WP_063862128.1	-	-	ARO:3001670	-	Gene presence detected	acquired	meropenem	-	nonwildtype	R	MIC > 8 mg/L	EUCAST v14.0 (2024)	"22736746
-24566181"	ECO:0001103 natural variation mutant evidence	strong		MIC >32 mg/L (meropenem) 	
+ACI0134	s__Acinetobacter baumannii	blaOXA-231	blaOXA-231	WP_063862128.1	-	-	ARO:3001670	-	Gene presence detected	acquired	imipenem	-	nonwildtype	R	MIC > 4 mg/L	EUCAST v14.0 (2024)	"22736746, 24566181"	ECO:0001103 natural variation mutant evidence	strong		MIC >32 mg/L (imipenem)	
+ACI0135	s__Acinetobacter baumannii	blaOXA-231	blaOXA-231	WP_063862128.1	-	-	ARO:3001670	-	Gene presence detected	acquired	meropenem	-	nonwildtype	R	MIC > 8 mg/L	EUCAST v14.0 (2024)	"22736746, 24566181"	ECO:0001103 natural variation mutant evidence	strong		MIC >32 mg/L (meropenem) 	
 ACI0136	s__Acinetobacter baumannii	blaOXA-253	blaOXA-253	WP_032495764.1	-	-	ARO:3001689	-	Gene presence detected	acquired	imipenem	-	nonwildtype	R	MIC > 4 mg/L	EUCAST v14.0 (2024)	24566181	ECO:0001103 natural variation mutant evidence	strong		MIC >32 mg/L (imipenem)	
 ACI0137	s__Acinetobacter baumannii	blaOXA-253	blaOXA-253	WP_032495764.1	-	-	ARO:3001689	-	Gene presence detected	acquired	meropenem	-	nonwildtype	R	MIC > 8 mg/L	EUCAST v14.0 (2024)	24566181	ECO:0001103 natural variation mutant evidence	strong		MIC >32 mg/L (meropenem) 	
 ACI0138	s__Acinetobacter baumannii	blaNDM	blaNDM	-	-	NF000259.2	ARO:3000057	-	Gene presence detected	acquired	imipenem	-	nonwildtype	R	MIC > 4 mg/L	EUCAST v14.0 (2024)	-	ECO:0001103 natural variation mutant evidence	moderate	lacks evidence of the degree to which MIC is affected	Phenotype of this gene family inferred from MICs of several members.	

rules/Enterobacter.txt

@@ -1,21 +1,21 @@
-ruleID	organism	gene	nodeID	refseq accession	GenBank accession	HMM accession	ARO accession	mutation	variation type	context	drug	drug class	phenotype	clinical category	breakpoint	breakpoint standard	PMID	evidence code	evidence grade	evidence limitations	rule curation note										
-ECC001	s__Enterobacter hormaechei	blaACT	blaACT	-	-	-	-	-	Gene presence detected	core	amoxicillin	-	wildtype	R	MIC >=8 mg/L	"EUCAST v15.0 (2025). Expected resistant phenotypes v 1.2 (13 January, 2023)."	35934231	"ECO:0001103 natural variation mutant evidence, ECO:0001091 knockout phenotypic evidence"	strong												
-ECC002	s__Enterobacter hormaechei	blaACT	blaACT	-	-	-	-	-	Gene presence detected	core	amoxicillin-clavulanic acid	-	wildtype	R	MIC >=8 mg/L	"EUCAST v15.0 (2025). Expected resistant phenotypes v 1.2 (13 January, 2023)."	35934231	"ECO:0001103 natural variation mutant evidence, ECO:0001091 knockout phenotypic evidence"	moderate	lacks evidence of the degree to which MIC is affected											
-ECC003	s__Enterobacter hormaechei	blaACT	blaACT	-	-	-	-	-	Gene presence detected	core	ampicillin	-	wildtype	R	MIC >=8 mg/L	"EUCAST v15.0 (2025). Expected resistant phenotypes v 1.2 (13 January, 2023)."	35934231	"ECO:0001103 natural variation mutant evidence, ECO:0001091 knockout phenotypic evidence"	strong												
-ECC004	s__Enterobacter hormaechei	blaACT	blaACT	-	-	-	-	-	Gene presence detected	core	-	first-generation cephalosporin	wildtype	R	not applicable	"EUCAST v15.0 (2025). Expected resistant phenotypes v 1.2 (13 January, 2023)."	35934231	"ECO:0001103 natural variation mutant evidence, ECO:0000012 functional complementation evidence"	strong												
-ECC005	s__Enterobacter hormaechei	blaACT	blaACT	-	-	-	-	-	Gene presence detected	core	-	second-generation cephalosporin	wildtype	R	not applicable	"Expected resistant phenotypes v 1.2 (13 January, 2023)."	35934231	"ECO:0001103 natural variation mutant evidence, ECO:0001091 knockout phenotypic evidence"	strong												
-ECC006	s__Enterobacter hormaechei	blaACT	blaACT	-	-	-	-	-	Gene presence detected	core	cefuroxime	-	wildtype	R	not applicable	"Expected resistant phenotypes v 1.2 (13 January, 2023)."	35934231	ECO:0001103 natural variation mutant evidence	strong												
-ECC007	s__Enterobacter hormaechei	blaACT	blaACT	-	-	-	-	-	Gene presence detected	core	cefoxitin	-	wildtype	R	not applicable	"Expected resistant phenotypes v 1.2 (13 January, 2023)."	35934231	ECO:0001103 natural variation mutant evidence	strong												
-ECC008	s__Enterobacter hormaechei	oqxA	oqxA	-	-	-	-	-	Gene presence detected	core	-	fluoroquinolone antibiotic	wildtype	S	not applicable	EUCAST v15.0 (2025)	25801572	ECO:0001103 natural variation mutant evidence	strong												
-ECC009	s__Enterobacter hormaechei	oqxB	oqxB	-	-	-	-	-	Gene presence detected	core	-	fluoroquinolone antibiotic	wildtype	S	not applicable	EUCAST v15.0 (2025)	25801572	ECO:0001103 natural variation mutant evidence	strong												
-ECC010	s__Enterobacter hormaechei	fosA	fosA	-	-	-	-	-	Gene presence detected	core	fosfomycin	-	wildtype		not available	EUCAST v15.0 (2025)	28851843	ECO:0001103 natural variation mutant evidence	weak	low clinical relevance	"There are no clinical breakpoints established for fosfomycin in Enterobacterales other than E. coli, as there is a lack of clinical evidence. The ECOFF has not yet been defined due the lack of  enough MIC data determined with the reference method  The breakpoint for E. coli (UTI only) is 8 mg/L. Enterobacter hormaechei carrying this gene have MICs in the range 8-128 mg/L."										
-ECC011	s__Enterobacter roggenkampii	blaMIR	blaMIR	-	-	-	-	-	Gene presence detected	core	amoxicillin	-	wildtype	R	MIC >=8 mg/L	"EUCAST v15.0 (2025). Expected resistant phenotypes v 1.2 (13 January, 2023)."	35934231	"ECO:0001103 natural variation mutant evidence, ECO:0001091 knockout phenotypic evidence"	strong												
-ECC012	s__Enterobacter roggenkampii	blaMIR	blaMIR	-	-	-	-	-	Gene presence detected	core	amoxicillin-clavulanic acid	-	wildtype	R	MIC >=8 mg/L	"EUCAST v15.0 (2025). Expected resistant phenotypes v 1.2 (13 January, 2023)."	35934231	ECO:0001103 natural variation mutant evidence	moderate	lacks evidence of the degree to which MIC is affected											
-ECC013	s__Enterobacter roggenkampii	blaMIR	blaMIR	-	-	-	-	-	Gene presence detected	core	ampicillin	-	wildtype	R	MIC >=8 mg/L	"EUCAST v15.0 (2025). Expected resistant phenotypes v 1.2 (13 January, 2023)."	35934231	"ECO:0001103 natural variation mutant evidence, ECO:0001091 knockout phenotypic evidence"	strong												
-ECC014	s__Enterobacter roggenkampii	blaMIR	blaMIR	-	-	-	-	-	Gene presence detected	core	-	first-generation cephalosporin	wildtype	R	not applicable	"EUCAST v15.0 (2025). Expected resistant phenotypes v 1.2 (13 January, 2023)."	35934231	ECO:0001103 natural variation mutant evidence	strong												
-ECC015	s__Enterobacter roggenkampii	blaMIR	blaMIR	-	-	-	-	-	Gene presence detected	core	cefuroxime	-	wildtype	R	not applicable	"Expected resistant phenotypes v 1.2 (13 January, 2023)."	35934231	"ECO:0001103 natural variation mutant evidence, ECO:0000012 functional complementation evidence"	strong												
-ECC016	s__Enterobacter roggenkampii	blaMIR	blaMIR	-	-	-	-	-	Gene presence detected	core	cefoxitin	-	wildtype	R	not applicable	"Expected resistant phenotypes v 1.2 (13 January, 2023)."	35934231	ECO:0001103 natural variation mutant evidence	strong												
-ECC017	s__Enterobacter roggenkampii	blaMIR	blaMIR	-	-	-	-	-	Gene presence detected	core	-	second-generation cephalosporin	wildtype	R	not applicable	"Expected resistant phenotypes v 1.2 (13 January, 2023)."	35934231	ECO:0001103 natural variation mutant evidence	strong												
-ECC018	s__Enterobacter roggenkampii	oqxA	oqxA	-	-	-	-	-	Gene presence detected	core	-	fluoroquinolone antibiotic	wildtype	S	not applicable	EUCAST v15.0 (2025)	25801572	ECO:0001103 natural variation mutant evidence	strong												
-ECC019	s__Enterobacter roggenkampii	oqxB	oqxB	-	-	-	-	-	Gene presence detected	core	-	fluoroquinolone antibiotic	wildtype	S	not applicable	EUCAST v15.0 (2025)	25801572	"ECO:0001103 natural variation mutant evidence, ECO:0000012 functional complementation evidence"	strong												
-ECC020	s__Enterobacter roggenkampii	fosA	fosA	-	-	-	-	-	Gene presence detected	core	fosfomycin	-	wildtype		not available	EUCAST v15.0 (2025)	28851843	"ECO:0001103 natural variation mutant evidence, ECO:0000024 protein-binding evidence"	weak	low clinical relevance	"There are no clinical breakpoints established for fosfomycin in Enterobacterales other than E. coli, as there is a lack of clinical evidence. The ECOFF has not yet been defined due the lack of  enough MIC data determined with the reference method  The breakpoint for E. coli (UTI only) is 8 mg/L. Enterobacter hormaechei carrying this gene have MICs in the range 8-128 mg/L."										
+ruleID	organism	gene	nodeID	refseq accession	GenBank accession	HMM accession	ARO accession	mutation	variation type	context	drug	drug class	phenotype	clinical category	breakpoint	breakpoint standard	PMID	evidence code	evidence grade	evidence limitations	rule curation note
+ECC001	s__Enterobacter hormaechei	blaACT	blaACT	-	-	-	-	-	Gene presence detected	core	amoxicillin	-	wildtype	R	MIC >=8 mg/L	"EUCAST v15.0 (2025). Expected resistant phenotypes v 1.2 (13 January, 2023)."	35934231	"ECO:0001103 natural variation mutant evidence, ECO:0001091 knockout phenotypic evidence"	strong		
+ECC002	s__Enterobacter hormaechei	blaACT	blaACT	-	-	-	-	-	Gene presence detected	core	amoxicillin-clavulanic acid	-	wildtype	R	MIC >=8 mg/L	"EUCAST v15.0 (2025). Expected resistant phenotypes v 1.2 (13 January, 2023)."	35934231	"ECO:0001103 natural variation mutant evidence, ECO:0001091 knockout phenotypic evidence"	moderate	lacks evidence of the degree to which MIC is affected	
+ECC003	s__Enterobacter hormaechei	blaACT	blaACT	-	-	-	-	-	Gene presence detected	core	ampicillin	-	wildtype	R	MIC >=8 mg/L	"EUCAST v15.0 (2025). Expected resistant phenotypes v 1.2 (13 January, 2023)."	35934231	"ECO:0001103 natural variation mutant evidence, ECO:0001091 knockout phenotypic evidence"	strong		
+ECC004	s__Enterobacter hormaechei	blaACT	blaACT	-	-	-	-	-	Gene presence detected	core	-	first-generation cephalosporin	wildtype	R	not applicable	"EUCAST v15.0 (2025). Expected resistant phenotypes v 1.2 (13 January, 2023)."	35934231	"ECO:0001103 natural variation mutant evidence, ECO:0000012 functional complementation evidence"	strong		
+ECC005	s__Enterobacter hormaechei	blaACT	blaACT	-	-	-	-	-	Gene presence detected	core	-	second-generation cephalosporin	wildtype	R	not applicable	"Expected resistant phenotypes v 1.2 (13 January, 2023)."	35934231	"ECO:0001103 natural variation mutant evidence, ECO:0001091 knockout phenotypic evidence"	strong		
+ECC006	s__Enterobacter hormaechei	blaACT	blaACT	-	-	-	-	-	Gene presence detected	core	cefuroxime	-	wildtype	R	not applicable	"Expected resistant phenotypes v 1.2 (13 January, 2023)."	35934231	ECO:0001103 natural variation mutant evidence	strong		
+ECC007	s__Enterobacter hormaechei	blaACT	blaACT	-	-	-	-	-	Gene presence detected	core	cefoxitin	-	wildtype	R	not applicable	"Expected resistant phenotypes v 1.2 (13 January, 2023)."	35934231	ECO:0001103 natural variation mutant evidence	strong		
+ECC008	s__Enterobacter hormaechei	oqxA	oqxA	-	-	-	-	-	Gene presence detected	core	-	fluoroquinolone antibiotic	wildtype	S	not applicable	EUCAST v15.0 (2025)	25801572	ECO:0001103 natural variation mutant evidence	strong		
+ECC009	s__Enterobacter hormaechei	oqxB	oqxB	-	-	-	-	-	Gene presence detected	core	-	fluoroquinolone antibiotic	wildtype	S	not applicable	EUCAST v15.0 (2025)	25801572	ECO:0001103 natural variation mutant evidence	strong		
+ECC010	s__Enterobacter hormaechei	fosA	fosA	-	-	-	-	-	Gene presence detected	core	fosfomycin	-	wildtype		not available	EUCAST v15.0 (2025)	28851843	ECO:0001103 natural variation mutant evidence	weak	low clinical relevance	"There are no clinical breakpoints established for fosfomycin in Enterobacterales other than E. coli, as there is a lack of clinical evidence. The ECOFF has not yet been defined due the lack of  enough MIC data determined with the reference method  The breakpoint for E. coli (UTI only) is 8 mg/L. Enterobacter hormaechei carrying this gene have MICs in the range 8-128 mg/L."
+ECC011	s__Enterobacter roggenkampii	blaMIR	blaMIR	-	-	-	-	-	Gene presence detected	core	amoxicillin	-	wildtype	R	MIC >=8 mg/L	"EUCAST v15.0 (2025). Expected resistant phenotypes v 1.2 (13 January, 2023)."	35934231	"ECO:0001103 natural variation mutant evidence, ECO:0001091 knockout phenotypic evidence"	strong		
+ECC012	s__Enterobacter roggenkampii	blaMIR	blaMIR	-	-	-	-	-	Gene presence detected	core	amoxicillin-clavulanic acid	-	wildtype	R	MIC >=8 mg/L	"EUCAST v15.0 (2025). Expected resistant phenotypes v 1.2 (13 January, 2023)."	35934231	ECO:0001103 natural variation mutant evidence	moderate	lacks evidence of the degree to which MIC is affected	
+ECC013	s__Enterobacter roggenkampii	blaMIR	blaMIR	-	-	-	-	-	Gene presence detected	core	ampicillin	-	wildtype	R	MIC >=8 mg/L	"EUCAST v15.0 (2025). Expected resistant phenotypes v 1.2 (13 January, 2023)."	35934231	"ECO:0001103 natural variation mutant evidence, ECO:0001091 knockout phenotypic evidence"	strong		
+ECC014	s__Enterobacter roggenkampii	blaMIR	blaMIR	-	-	-	-	-	Gene presence detected	core	-	first-generation cephalosporin	wildtype	R	not applicable	"EUCAST v15.0 (2025). Expected resistant phenotypes v 1.2 (13 January, 2023)."	35934231	ECO:0001103 natural variation mutant evidence	strong		
+ECC015	s__Enterobacter roggenkampii	blaMIR	blaMIR	-	-	-	-	-	Gene presence detected	core	cefuroxime	-	wildtype	R	not applicable	"Expected resistant phenotypes v 1.2 (13 January, 2023)."	35934231	"ECO:0001103 natural variation mutant evidence, ECO:0000012 functional complementation evidence"	strong		
+ECC016	s__Enterobacter roggenkampii	blaMIR	blaMIR	-	-	-	-	-	Gene presence detected	core	cefoxitin	-	wildtype	R	not applicable	"Expected resistant phenotypes v 1.2 (13 January, 2023)."	35934231	ECO:0001103 natural variation mutant evidence	strong		
+ECC017	s__Enterobacter roggenkampii	blaMIR	blaMIR	-	-	-	-	-	Gene presence detected	core	-	second-generation cephalosporin	wildtype	R	not applicable	"Expected resistant phenotypes v 1.2 (13 January, 2023)."	35934231	ECO:0001103 natural variation mutant evidence	strong		
+ECC018	s__Enterobacter roggenkampii	oqxA	oqxA	-	-	-	-	-	Gene presence detected	core	-	fluoroquinolone antibiotic	wildtype	S	not applicable	EUCAST v15.0 (2025)	25801572	ECO:0001103 natural variation mutant evidence	strong		
+ECC019	s__Enterobacter roggenkampii	oqxB	oqxB	-	-	-	-	-	Gene presence detected	core	-	fluoroquinolone antibiotic	wildtype	S	not applicable	EUCAST v15.0 (2025)	25801572	"ECO:0001103 natural variation mutant evidence, ECO:0000012 functional complementation evidence"	strong		
+ECC020	s__Enterobacter roggenkampii	fosA	fosA	-	-	-	-	-	Gene presence detected	core	fosfomycin	-	wildtype		not available	EUCAST v15.0 (2025)	28851843	"ECO:0001103 natural variation mutant evidence, ECO:0000024 protein-binding evidence"	weak	low clinical relevance	"There are no clinical breakpoints established for fosfomycin in Enterobacterales other than E. coli, as there is a lack of clinical evidence. The ECOFF has not yet been defined due the lack of  enough MIC data determined with the reference method  The breakpoint for E. coli (UTI only) is 8 mg/L. Enterobacter hormaechei carrying this gene have MICs in the range 8-128 mg/L."