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Adding test files for AMRFinder #384

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26 changes: 26 additions & 0 deletions data/modules/amrfinder/test_both.expected
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Protein id Contig id Start Stop Strand Element symbol Element name Scope Type Subtype Class Subclass Method Target length Reference sequence length % Coverage of reference % Identity to reference Alignment length Closest reference accession Closest reference name HMM accession HMM description Hierarchy node
NA contig01 1 984 + blaTEMp_G162T Escherichia amoxicillin-clavulanic acid/piperacillin-tazobactam/ticarcillin-clavulanic acid resistant blaTEM promoter core AMR POINT BETA-LACTAM AMOXICILLIN-CLAVULANIC_ACID/PIPERACILLIN-TAZOBACTAM/TICARCILLIN-CLAVULANIC_ACID POINTN 984 1176 83.67 99.80 984 NZ_CP095603.1:148777-149952 blaTEM promoter region NA NA NA
blaTEM-156 contig01 101 961 + blaTEM-156 class A beta-lactamase TEM-156 core AMR AMR BETA-LACTAM BETA-LACTAM ALLELEP 286 286 100.00 100.00 286 WP_061158039.1 class A beta-lactamase TEM-156 NF000531.2 TEM family class A beta-lactamase blaTEM-156
blaPDC-114_blast contig02 1 1191 + blaPDC PDC family class C beta-lactamase core AMR AMR BETA-LACTAM CEPHALOSPORIN BLASTP 397 397 100.00 99.75 397 WP_061189306.1 class C beta-lactamase PDC-114 NF000422.6 PDC family class C beta-lactamase blaPDC
blaOXA-436_partial contig03 101 802 + blaOXA OXA-48 family class D beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM PARTIALP 233 265 87.92 100.00 233 WP_058842180.1 OXA-48 family carbapenem-hydrolyzing class D beta-lactamase OXA-436 NF012161.0 class D beta-lactamase blaOXA-48_fam
vanG contig04 101 1147 + vanG D-alanine--D-serine ligase VanG core AMR AMR GLYCOPEPTIDE VANCOMYCIN EXACTP 349 349 100.00 100.00 349 WP_063856695.1 D-alanine--D-serine ligase VanG NF000091.3 D-alanine--D-serine ligase VanG vanG
NA contig04 1261 2391 + blaEC BlaEC family class C beta-lactamase plus AMR AMR BETA-LACTAM BETA-LACTAM BLASTX 377 377 100.00 98.14 377 WP_063610930.1 extended-spectrum class C beta-lactamase EC-15 NA NA blaEC
NA contig08 1 700 + blaTEMp_G162T Escherichia amoxicillin-clavulanic acid/piperacillin-tazobactam/ticarcillin-clavulanic acid resistant blaTEM promoter core AMR POINT BETA-LACTAM AMOXICILLIN-CLAVULANIC_ACID/PIPERACILLIN-TAZOBACTAM/TICARCILLIN-CLAVULANIC_ACID POINTN 700 1176 59.52 99.71 700 NZ_CP095603.1:148777-149952 blaTEM promoter region NA NA NA
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 blaTEM
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 aph(3'')-Ib
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 sul2
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 blaOXA-9_fam
NA contig11 1 984 + blaTEMp_G162T Escherichia amoxicillin-clavulanic acid/piperacillin-tazobactam/ticarcillin-clavulanic acid resistant blaTEM promoter core AMR POINT BETA-LACTAM AMOXICILLIN-CLAVULANIC_ACID/PIPERACILLIN-TAZOBACTAM/TICARCILLIN-CLAVULANIC_ACID POINTN 984 1176 83.67 96.04 984 NZ_CP095603.1:148777-149952 blaTEM promoter region NA 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 blaTEM
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 qacR
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 emrD3
NA contig14 1 1089 + pmrB_C84R Escherichia colistin resistant PmrB core AMR POINT COLISTIN COLISTIN POINTX 363 363 100.00 99.72 363 WP_001300761.1 two-component system sensor histidine kinase PmrB NA NA pmrB
pmrB_C84R contig14 1093 2181 + pmrB_C84R Escherichia colistin resistant PmrB core AMR POINT COLISTIN COLISTIN POINTP 363 363 100.00 99.72 363 WP_001300761.1 two-component system sensor histidine kinase PmrB NA NA pmrB
NA contig15 1 2905 + 23S_A2058T Escherichia azithromycin/erythromycin/telithromycin resistant 23S core AMR POINT MACROLIDE AZITHROMYCIN/ERYTHROMYCIN/TELITHROMYCIN POINTN 2905 2905 100.00 99.97 2905 NC_004431.1:237160-240064 23S ribosomal RNA NA NA NA
NA contig16 1 720 + nfsA_K141Ter Escherichia nitrofurantoin resistant NfsA core AMR POINT NITROFURAN NITROFURANTOIN POINTX 240 240 100.00 99.17 240 WP_089631889.1 nitroreductase NfsA NA NA nfsA
NA contig16 1 720 + nfsA_R15C Escherichia nitrofurantoin resistant NfsA core AMR POINT NITROFURAN NITROFURANTOIN POINTX 240 240 100.00 99.17 240 WP_089631889.1 nitroreductase NfsA NA NA nfsA
NA contig17 1 247 + ampC_T-14TGT Escherichia cephalosporin resistant ampC promoter core AMR POINT BETA-LACTAM CEPHALOSPORIN POINTN 247 245 100.00 99.19 247 NZ_CP041538.1:1149245-1149489 ampC/blaEC promoter region NA NA NA
stxA2a_prot contig18 279 1238 + stxA2 Shiga toxin Stx2 subunit A plus VIRULENCE VIRULENCE STX2 stxA2 EXACTP 319 319 100.00 100.00 319 TJA36680.1 Shiga toxin Stx2 subunit A NF041702.1 Shiga toxin Stx2 subunit A stxA2_acd
NA contig18 279 1516 + stx2a_operon stx2a operon plus VIRULENCE STX_TYPE STX2 STX2A COMPLETE 1238 NA NA 100.00 408 AAS07600.1,AAM90978.1 Shiga toxin stx2a NA NA stxA2a::stxB2a
stxB2a_prot contig18 1250 1519 + stxB2 Shiga toxin Stx2a subunit B plus VIRULENCE VIRULENCE STX2 stxB2a EXACTP 89 89 100.00 100.00 89 AAM90978.1 Shiga toxin Stx2a subunit B NF033660.0 Shiga toxin Stx2 subunit B stxB2a
nimIJ_hmm contigX 1 501 + nimIJ NimIJ family 5-nitroimidazole reductase core AMR AMR NITROIMIDAZOLE NITROIMIDAZOLE HMM 166 165 98.18 76.54 162 WP_005812825.1 NimIJ family 5-nitroimidazole reductase NF000262.1 NimIJ family 5-nitroimidazole reductase nimIJ
25 changes: 25 additions & 0 deletions data/modules/amrfinder/test_dna.expected
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Protein id Contig id Start Stop Strand Element symbol Element name Scope Type Subtype Class Subclass Method Target length Reference sequence length % Coverage of reference % Identity to reference Alignment length Closest reference accession Closest reference name HMM accession HMM description Hierarchy node
NA contig01 1 984 + blaTEMp_G162T Escherichia amoxicillin-clavulanic acid/piperacillin-tazobactam/ticarcillin-clavulanic acid resistant blaTEM promoter core AMR POINT BETA-LACTAM AMOXICILLIN-CLAVULANIC_ACID/PIPERACILLIN-TAZOBACTAM/TICARCILLIN-CLAVULANIC_ACID POINTN 984 1176 83.67 99.80 984 NZ_CP095603.1:148777-149952 blaTEM promoter region NA NA NA
NA contig01 101 958 + blaTEM-156 class A beta-lactamase TEM-156 core AMR AMR BETA-LACTAM BETA-LACTAM ALLELEX 286 286 100.00 100.00 286 WP_061158039.1 class A beta-lactamase TEM-156 NA NA blaTEM-156
NA contig02 1 1191 + blaPDC PDC family class C beta-lactamase core AMR AMR BETA-LACTAM CEPHALOSPORIN BLASTX 397 397 100.00 99.75 397 WP_061189306.1 class C beta-lactamase PDC-114 NA NA blaPDC
NA contig03 101 802 + blaOXA OXA-48 family class D beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM PARTIALX 234 265 88.30 100.00 234 WP_058842180.1 OXA-48 family carbapenem-hydrolyzing class D beta-lactamase OXA-436 NA NA blaOXA-48_fam
NA contig04 101 1147 + vanG D-alanine--D-serine ligase VanG core AMR AMR GLYCOPEPTIDE VANCOMYCIN EXACTX 349 349 100.00 100.00 349 WP_063856695.1 D-alanine--D-serine ligase VanG NA NA vanG
NA contig04 1261 2391 + blaEC BlaEC family class C beta-lactamase plus AMR AMR BETA-LACTAM BETA-LACTAM BLASTX 377 377 100.00 98.14 377 WP_063610930.1 extended-spectrum class C beta-lactamase EC-15 NA NA blaEC
NA contig08 1 700 + blaTEMp_G162T Escherichia amoxicillin-clavulanic acid/piperacillin-tazobactam/ticarcillin-clavulanic acid resistant blaTEM promoter core AMR POINT BETA-LACTAM AMOXICILLIN-CLAVULANIC_ACID/PIPERACILLIN-TAZOBACTAM/TICARCILLIN-CLAVULANIC_ACID POINTN 700 1176 59.52 99.71 700 NZ_CP095603.1:148777-149952 blaTEM promoter region NA NA NA
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 blaTEM
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 aph(3'')-Ib
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 sul2
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 blaOXA-9_fam
NA contig11 1 984 + blaTEMp_G162T Escherichia amoxicillin-clavulanic acid/piperacillin-tazobactam/ticarcillin-clavulanic acid resistant blaTEM promoter core AMR POINT BETA-LACTAM AMOXICILLIN-CLAVULANIC_ACID/PIPERACILLIN-TAZOBACTAM/TICARCILLIN-CLAVULANIC_ACID POINTN 984 1176 83.67 96.04 984 NZ_CP095603.1:148777-149952 blaTEM promoter region NA 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 blaTEM
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 qacR
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 emrD3
NA contig14 1 1089 + pmrB_C84R Escherichia colistin resistant PmrB core AMR POINT COLISTIN COLISTIN POINTX 363 363 100.00 99.72 363 WP_001300761.1 two-component system sensor histidine kinase PmrB NA NA pmrB
NA contig14 1093 2181 + pmrB_C84R Escherichia colistin resistant PmrB core AMR POINT COLISTIN COLISTIN POINTX 363 363 100.00 99.72 363 WP_001300761.1 two-component system sensor histidine kinase PmrB NA NA pmrB
NA contig15 1 2905 + 23S_A2058T Escherichia azithromycin/erythromycin/telithromycin resistant 23S core AMR POINT MACROLIDE AZITHROMYCIN/ERYTHROMYCIN/TELITHROMYCIN POINTN 2905 2905 100.00 99.97 2905 NC_004431.1:237160-240064 23S ribosomal RNA NA NA NA
NA contig16 1 720 + nfsA_K141Ter Escherichia nitrofurantoin resistant NfsA core AMR POINT NITROFURAN NITROFURANTOIN POINTX 240 240 100.00 99.17 240 WP_089631889.1 nitroreductase NfsA NA NA nfsA
NA contig16 1 720 + nfsA_R15C Escherichia nitrofurantoin resistant NfsA core AMR POINT NITROFURAN NITROFURANTOIN POINTX 240 240 100.00 99.17 240 WP_089631889.1 nitroreductase NfsA NA NA nfsA
NA contig17 1 247 + ampC_T-14TGT Escherichia cephalosporin resistant ampC promoter core AMR POINT BETA-LACTAM CEPHALOSPORIN POINTN 247 245 100.00 99.19 247 NZ_CP041538.1:1149245-1149489 ampC/blaEC promoter region NA NA NA
NA contig18 279 1235 + stxA2 Shiga toxin Stx2 subunit A plus VIRULENCE VIRULENCE STX2 stxA2 EXACTX 319 319 100.00 100.00 319 TJA36680.1 Shiga toxin Stx2 subunit A NA NA stxA2_acd
NA contig18 279 1516 + stx2a_operon stx2a operon plus VIRULENCE STX_TYPE STX2 STX2A COMPLETE 1238 NA NA 100.00 408 AAS07600.1,AAM90978.1 Shiga toxin stx2a NA NA stxA2a::stxB2a
NA contig18 1250 1516 + stxB2 Shiga toxin Stx2a subunit B plus VIRULENCE VIRULENCE STX2 stxB2a EXACTX 89 89 100.00 100.00 89 AAM90978.1 Shiga toxin Stx2a subunit B NA NA stxB2a
15 changes: 15 additions & 0 deletions data/modules/amrfinder/test_prot.expected
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Protein id Contig id Start Stop Strand Element symbol Element name Scope Type Subtype Class Subclass Method Target length Reference sequence length % Coverage of reference % Identity to reference Alignment length Closest reference accession Closest reference name HMM accession HMM description Hierarchy node
blaTEM-156 contig01 101 961 + blaTEM-156 class A beta-lactamase TEM-156 core AMR AMR BETA-LACTAM BETA-LACTAM ALLELEP 286 286 100.00 100.00 286 WP_061158039.1 class A beta-lactamase TEM-156 NF000531.2 TEM family class A beta-lactamase blaTEM-156
blaPDC-114_blast contig02 1 1191 + blaPDC PDC family class C beta-lactamase core AMR AMR BETA-LACTAM CEPHALOSPORIN BLASTP 397 397 100.00 99.75 397 WP_061189306.1 class C beta-lactamase PDC-114 NF000422.6 PDC family class C beta-lactamase blaPDC
blaOXA-436_partial contig03 101 802 + blaOXA OXA-48 family class D beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM PARTIALP 233 265 87.92 100.00 233 WP_058842180.1 OXA-48 family carbapenem-hydrolyzing class D beta-lactamase OXA-436 NF012161.0 class D beta-lactamase blaOXA-48_fam
vanG contig04 101 1147 + vanG D-alanine--D-serine ligase VanG core AMR AMR GLYCOPEPTIDE VANCOMYCIN EXACTP 349 349 100.00 100.00 349 WP_063856695.1 D-alanine--D-serine ligase VanG NF000091.3 D-alanine--D-serine ligase VanG vanG
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 aph(3'')-Ib
sul2_partial_3p_neg contig09 715 1377 - sul2 sulfonamide-resistant dihydropteroate synthase Sul2 core AMR AMR SULFONAMIDE SULFONAMIDE PARTIALP 221 271 81.55 100.00 221 WP_001043265.1 sulfonamide-resistant dihydropteroate synthase Sul2 NA NA sul2
blaTEM-internal_stop contig11 113 547 + blaTEM TEM family class A beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM PARTIALP 144 286 50.35 97.22 144 WP_000027057.1 broad-spectrum class A beta-lactamase TEM-1 NA NA blaTEM
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 qacR
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 emrD3
pmrB_C84R contig14 1093 2181 + pmrB_C84R Escherichia colistin resistant PmrB core AMR POINT COLISTIN COLISTIN POINTP 363 363 100.00 99.72 363 WP_001300761.1 two-component system sensor histidine kinase PmrB NA NA pmrB
nfsA_R15C_K141STOP contig16 1 423 + nfsA_R15C Escherichia nitrofurantoin resistant NfsA core AMR POINT NITROFURAN NITROFURANTOIN POINTP 140 240 58.33 99.29 140 WP_089631889.1 nitroreductase NfsA NA NA nfsA
stxA2a_prot contig18 279 1238 + stxA2 Shiga toxin Stx2 subunit A plus VIRULENCE VIRULENCE STX2 stxA2 EXACTP 319 319 100.00 100.00 319 TJA36680.1 Shiga toxin Stx2 subunit A NF041702.1 Shiga toxin Stx2 subunit A stxA2_acd
stxB2a_prot contig18 1250 1519 + stxB2 Shiga toxin Stx2a subunit B plus VIRULENCE VIRULENCE STX2 stxB2a EXACTP 89 89 100.00 100.00 89 AAM90978.1 Shiga toxin Stx2a subunit B NF033660.0 Shiga toxin Stx2 subunit B stxB2a
nimIJ_hmm contigX 1 501 + nimIJ NimIJ family 5-nitroimidazole reductase core AMR AMR NITROIMIDAZOLE NITROIMIDAZOLE HMM 166 165 98.18 76.54 162 WP_005812825.1 NimIJ family 5-nitroimidazole reductase NF000262.1 NimIJ family 5-nitroimidazole reductase nimIJ