Mercurial > repos > iuc > tooldistillator
changeset 1:65a69de1e294 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 30f10306f4283140f7e54cfe1b8bc1f76f4ef834
| author | iuc |
|---|---|
| date | Fri, 24 May 2024 10:47:33 +0000 |
| parents | 6e868bf6c38e |
| children | a7387ce2a8ca |
| files | macro.xml test-data/amrfinderplus/AMRFinderPlus_Nucleotide_identified_sequences.fasta test-data/amrfinderplus/AMRFinderPlus_Point_mutation_report.tsv test-data/amrfinderplus/AMRFinderPlus_report.tsv test-data/summarize/amrfinderplus_output.json tooldistillator.xml |
| diffstat | 6 files changed, 368 insertions(+), 34 deletions(-) [+] |
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--- a/macro.xml Tue Apr 30 08:42:33 2024 +0000 +++ b/macro.xml Fri May 24 10:47:33 2024 +0000 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">0.8.4.1</token> + <token name="@TOOL_VERSION@">0.8.5.0</token> <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">21.05</token> <xml name="version_command">
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amrfinderplus/AMRFinderPlus_Nucleotide_identified_sequences.fasta Fri May 24 10:47:33 2024 +0000 @@ -0,0 +1,209 @@ +>contig_153_polypolish:4412-4645 strand:- merE broad-spectrum mercury transporter MerE +ATGAACAGCCCAGAGCACTTGCCGTCTGAGACGCACAAACCGATCACCGGCTACTTGTGG +GGCGCGCTGGCCGTGCTCACCTGTCCCTGCCATTTGCCGATTCTCGCCATTGTGCTAGCC +GGCACGACGGCCGGCGCGTTCATCGGGGAGCACTGGGGTATTGCAGCCCTCACGCTGACC +GGCTTGTTTGTCCTGTCTGTGACGCGGCTGCTGCGGGCCTTCAAGGGAAGATCA +>contig_153_polypolish:7613-7846 strand:- merT mercuric transport protein MerT +TCTGAACCACAAAACGGGCGCGGCGCGTTCTTCGCCGGTGGGCTGGCCGCCATTCTTGCG +TCGGCCTGCTGCCCGGGGCCGCTGGTTTTGATCGCCTTGGGGTTCAGCGGGGCATGGATC +GGCAACCTGACGGTGCTGGAACCCTATCGCCCGATCTTCATCGGCGCAGCGCTGGTCGCG +CTGCTTTTCGCCCGGCGGCGCATCTACCGCCCGGCGCAAGCCTGCCAAACCGGG +>contig_160_polypolish:86415-86654 strand:- fosA FosA5 family fosfomycin resistance glutathione transferase +GCAGTCAGCCAGCTGGCGCCGAGCGTGGCGTTTTATCAGCAGCTGTTGGGCATGACGCTG +CACGCCCGCTGGGACAGCGGCGCCTATCTCTCCTGCGGCGATTTGTGGCTGTGCCTGTCG +CTGGATCCGCAGCGGCGCATCACCCCGCCGGAGGAGAGCGACTACACCCATTATGCGTTT +AGCATTAGCGAGGCGGATTTCGCTAGCTTCGCCGCCCGCCTTGAGGTTGCCGGCGTCAGC +>contig_30_polypolish:13708-14433 strand:+ blaCTX-M CTX-M family extended-spectrum class A beta-lactamase +AAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACA +GCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGT +AAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAAT +CAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCAC +GTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAAC +GTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCC +CGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCC +ATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAAT +CTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAA +GGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCCGGGTTGTGGGG +GATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAG +ATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCC +GTCGCG +>contig_30_polypolish:17856-18287 strand:+ merR mercury resistance transcriptional regulator MerR +ATGGAAAATAATTTGGAAAACCTGACCATTGGCGTTTTTGCCAAGGCGGCCGGGGTCAAC +GTGGAGACAATCCGCTTCTATCAGCGCAAGGGCCTGTTGCGGGAACCGGACAAGCCTTAC +GGCAGCATCCGCCGCTATGGGGAGGCGGACGTGGTTCGGGTGAAATTCGTGAAATCGGCA +CAGCGGCTGGGGTTCAGTCTGGACGAGATTGCCGAGCTGTTGCGGCTCGACGATGGCACC +CACTGCGAGGAGGCCAGCAGCCCGGCCGAACACAAGCTCAAGGACGTGCGCGAGAAGATG +GCCGACTTGGCGCGCATGGAAACCGTGCTGTCTGAACTCGTGTGCGCCTGCCATGCACGC +AAGGGGAATGTTTCCTGCCCGTTGATCGCGTCACTACAGGGCGAAGCAGGCCCGGCAAGG +TCAGCTATGCCT +>contig_30_polypolish:20698-21348 strand:+ catA1 type A-1 chloramphenicol O-acetyltransferase +GAAAAAATCACTGGATATACCACCGTTGATATATCCCAATGGCATCGTAAAGAACATTTT +GAGGCATTTCAGTCAGTTGCTCAATGTACCTATAACCAGACCGTTCAGCTGGATATTACG +GCCTTTTTAAAGACCGTAAAGAAAAATAAGCACAAGTTTTATCCGGCCTTTATTCACATT +CTTGCCCGCCTGATGAATGCTCATCCGGAATTCCGTATGGCAATGAAAGACGGTGAGCTG +GTGATATGGGATAGTGTTCACCCTTGTTACACCGTTTTCCATGAGCAAACTGAAACGTTT +TCATCGCTCTGGAGTGAATACCACGACGATTTCCGGCAGTTTCTACACATATATTCGCAA +GATGTGGCGTGTTACGGTGAAAACCGGCCTATTTCCCTAAAGGGTTTATTGAGAATATGT +TTTTCGTCTCAGCCAATCCCACGGGTGAGTTTCACCAGTTTTGATTTAAACGTGGCCAAT +ATGGACAACTTCTTCGCCCCCGTTTTCACCATGGGCAAATATTATACGCAAGGCGACAAG +GTGCTGATGCCGCTGGCGATTCAGGTTCATCATGCCGTTTGTGATGGCTTCCATGTCGGC +AGAATGCTTAATGAATTACAACAGTACTGCGATGAGTGGCAGGGCGGGGCG +>contig_30_polypolish:3018-3344 strand:+ merR mercury resistance transcriptional regulator MerR +TTTGCCAAGGCGGCCGGGGTCAACGTGGAGACAATCCGCTTCTATCAGCGCAAGGGCCTG +TTGCGGGAACCGGACAAGCCTTACGGCGGCATCCGCCGCTATGGGGAGGCGGACGTGGTT +CGGGTGAAATTCGTGAAATCGGCACAGCGGCTGGGGTTCAGTCTGGACGAGATTGCCGAG +CTGTTGCGGCTCGACGATGGCACCCACTGCGAGGAGGCCAGCAGCTTGGCCGAACACAAG +CTCAAGGACGTGCGCGAGAAGATGGCCGACTTGGCGCGCATGGAAACCGTGCTGTCTGAA +CTCGTGTGCGCCTGCCATGCACGAAGG +>contig_30_polypolish:5821-6243 strand:+ catA1 type A-1 chloramphenicol O-acetyltransferase +GAAAAAATCACTGGATATACCACCGTTGATATATCCCAATGGCATCGTAAAGAACATTTT +GAGGCATTTCAGTCAGTTGCTCAATGTACCTATAACCAGACCGTTCAGCTGGATATTACG +GCCTTTTTAAAGACCGTAAAGAAAAATAAGCACAAGTTTTATCCGGCCTTTATTCACATT +CTTGCCCGCCTGATGAATGCTCATCCGGAATTCCGTATGGCAATGAAAGACGGTGAGCTG +GTGATATGGGATAGTGTTCACCCTTGTTACACCGTTTTCCATGAGCAAACTGAAACGTTT +TCATCGCTCTGGAGTGAATACCACGACGATTTCCGGCAGTTTCTACACATATATTCGCAA +GATGTGGCGTGTTACGGTGAAAACACGGCCTATTTCCCTAAAGGGTTTATTGAGAATATG +TTT +>contig_35_polypolish:4787-5644 strand:- aac(3)-IIe aminoglycoside N-acetyltransferase AAC(3)-IIe +ATGCATACGCGGAAGGCAATAACGGAGGCAATTCGAAAATTAGGAGTCCAAACCGGTGAC +CTGTTGATGGTGCATGCCTCACTTAAAGCGATTGGTCCGGTCGAAGGAGGAGCGGAGACG +GTCGTTGCCGCGTTACGCTCCGCGGTTGGGCCGACTGGCACTGTGATGGGATACGCGTCG +TGGGACCGATCACCCTACGAGGAGACTCTGAATGGCGCTCGGTTGGATGACAAAGCCCGC +CGTACCTGGCCGCCGTTCGATCCCGCAACGGCCGGGACTTACCGTGGGTTCGGCCTGCTG +AATCAATTTCTGGTTCAAGCCCCCGGCGCGCGGCGCAGCGCGCACCCCGATGCATCGATG +GTCGCGGTTGGTCCGCTAGCTGAAACGCTGACGGAGCCTCACGAACTCGGTCACGCCTTG +GGGGAAGGGTCGCCCGTCGAGCGGTTCGTCCGCCTTGGCGGGAAGGCCCTGCTGTTGGGT +GCGCCGCTAAACTCCGTTACCGCATTGCACTACGCCGAGGCGGTTGCGGATATCCCCAAC +AAACGATGGGTGACGTATGAGATGCCGATGCTTGGAAGAAACGGTGAAGTCGCCTGGAAA +ACGGCATCAGAATACGATTCAAACGGCATTCTCGATTGCTTTGCTATCGAAGGAAAGCCG +GATGCGGTCGAAACTATAGCAAATGCTTACGTGAAGCTCGGTCGCCATCGAGAAGGTGTC +GTGGGCTTTGCTCAGTGCTACCTGTTCGACGCGCAGGACATCGTGACGTTCGGCGTCACC +TATCTTGAGAAGCACTTCGGAGCCACTCCGATCGTGCCAGCACACGAAGCCGCCCAGCGC +TCTTGCGAGCCTTCCGGT +>contig_36_polypolish:9168-9608 strand:+ blaSHV SHV family class A beta-lactamase +ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACAC +GCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTA +GGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCCGGCGCGCCGATGAA +CGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTG +GATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGAC +TACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCC +GCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGC +CCCGCAGGATTGACTGCCTTT +>contig_36_polypolish:9587-10024 strand:+ blaSHV SHV family class A beta-lactamase +CCCCGCAGGATTGACTGCCTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGC +TGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCC +AGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAA +CGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTG +CTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAGCGGGGTGCGCGCGGG +ATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGG +GATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTG +ATCGAGCACTGGCAACGC +>contig_37_polypolish:18-569 strand:+ aac(6')-Ib3 aminoglycoside N-acetyltransferase AAC(6')-Ib3 +GTGACCAACAGCAACGATTCCGTCACACTGCGCCTCATGACTGAGCATGACCTTGCGATG +CTCTATGAGTGGCTAAATCGATCTCATATCGTCGAGTGGTGGGGCGGAGAAGAAGCACGC +CCGACACTTGCTGACGTACAGGAACAGTACTTGCCAAGCGTTTTAGCGCAAGAGTCCGTC +ACTCCATACATTGCAATGCTGAATGGAGAGCCGATTGGGTATGCCCAGTCGTACGTTGCT +CTTGGAAGCGGGGACGGATGGTGGGAAGAAGAAACCGATCCAGGAGTACGCGGAATAGAC +CAGTTACTGGCGAATGCATCACAACTGGGCAAAGGCTTGGGAACCAAGCTGGTTCGAGCT +CTGGTTGAGTTGCTGTTCAATGATCCCGAGGTCACCAAGATCCAAACGGACCCGTCGCCG +AGCAACTTGCGAGCGATCCGATGCTACGAGAAAGCGGGGTTTGAGAGGCAAGGTACCGTA +ACCACCCCAGATGGTCCAGCCGTGTACATGGTTCAAACACGCCAGGCATTCGAGCGAACA +CGCAGTGATGCC +>contig_37_polypolish:3006-3863 strand:+ blaTEM-1 broad-spectrum class A beta-lactamase TEM-1 +ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCT +GTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCA +CGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCC +GAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCC +CGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTG +GTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTA +TGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATC +GGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTT +GATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATG +CCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCT +TCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGC +TCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCT +CGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTAC +ACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCC +TCACTGATTAAGCATTGG +>contig_37_polypolish:642-1424 strand:+ aadA1 ANT(3'')-Ia family aminoglycoside nucleotidyltransferase AadA1 +ATGAGGGAAGCGGTGATCGCCGAAGTATCGACTCAACTATCAGAGGTAGTTGGCGTCATC +GAGCGCCATCTCGAACCGACGTTGCTGGCCGTACATTTGTACGGCTCCGCAGTGGATGGC +GGCCTGAAGCCACACAGTGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAA +ACAACGCGGCGAGCTTTGATCAACGACCTTTGGAAACTTCGGCTTCCCGGAGAGAGCGAG +ATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTAT +CCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATC +TTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACAT +AGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGAT +CTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGC +GATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGGCAAA +ATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAG +CCCGTCATACTTGAAGCTAGGCAGGCTTATCTTGGACAAGAAGATCGCTTGGCCTCGCGC +GCAGATCAGTTGGAAGAATTTGTTCACTACGTGAAAGGCGAGATCACCAAGGTAGTCGGC +AAA +>contig_37_polypolish:8924-9133 strand:- merC organomercurial transporter MerC +CTTGAGCCAGTACGAGGACTGTTCATCAGCCGCCTGCTGCCGCTGTTTGCCGCGCTGGCC +TTCTCGGCGAACGCGCTGGGTTGGTTCAGTCATCGGCAATGGCTGCGCAGTCTGCTCGGC +ATGATCGGCCCGGCCATCGTGTTTGCGGCCACGGTCTGGCTGCTCGGCAACTGGTGGACG +GCGAACCTGATGTACGTCGGCACCGGCCTT +>contig_39_polypolish:3496-3825 strand:- qacE quaternary ammonium compound efflux SMR transporter QacE +ATGAAAGGCTGGCTTTTTCTTGTTATCGCAATAGTTGGCGAAGTAATCGCAACATCCGCA +TTAAAATCTAGCGAGGGCTTTACTAAGCTTGCCCCTTCCGCCGTTGTCATAATCGGTTAT +GGCATCGCATTTTATTTTCTTTCTCTGGTTCTGAAATCCATCCCTGTCGGTGTTGCTTAT +GCAGTCTGGTCGGGACTCGGCGTCGTCATAATTACAGCCATTGCCTGGTTGCTTCATGGG +CAAAAGCTTGATGCGTGGGGCTTTGTAGGTATGGGGCTCATAGTTAGTGGTGTAGTAGTT +TTAAACTTGCTTTCCAAAGCAAGTGCCCAC +>contig_39_polypolish:4010-4327 strand:- dfrA30 trimethoprim-resistant dihydrofolate reductase DfrA30 +GGGGCGCTCCCCAATAGGAAATACGCGGTCGTTACTCGCTCAGCTCGGACGGCCAATAAT +GACAACGTAGTAGTATTCCCGTCGATCGAAGAGGCCATGGGCGGTCTAGCTAAACTCACC +GGTCACGTTATAGTGTCTGGTGGCGGGGAGATTTACAGAGAAACGTTGCCCATGGCCTCT +ACGCTCCATGTATCGACGATCGACATTGAGCCAGAAGGGGATGTTTTCTTCCCGAATATT +CCCAACTTCTTCGAAGTTGTTTTTGAGCAACATTTTAGTTCAAACATTAACTATTGCTAT +CAAATTTGGAAAAAGGGT +>contig_40_polypolish:2574-3359 strand:+ aph(3'')-Ib aminoglycoside O-phosphotransferase APH(3'')-Ib +ATATTTTTTGGTGAATCGCATTCTGACTGGTTGCCTGTCAGAGGCGGAGAATCTGGTGAT +TTTGTTTTTCGACGTGGTGACGGGCATGCCTTCGCGAAAATCGCACCTGCTTCCCGCCGC +GGTGAGCTCGCTGGAGAGCGTGACCGCCTCATTTGGCTCAAAGGTCGAGGTGTGGCTTGC +CCCGAGGTGATCAACTGGCAGGAGGAACAGGAGGGTGCATGCTTGGTGATAACGGCAATT +CCGGGAGTACCGGCGGCTGATCTGTCTGGAGCGGATTTGCTCAAAGCGTGGCCGTCAATG +GGGCAGCAACTTGGCGCTGTTCACAGCCTATCGGTTGATCAATGTCCGTTTGAGCGCAGG +CTGTCGCGAATGTTCGGACGCGCCGTTGATGTGGTGTCCCGCAATGCCGTCAATCCCGAC +TTCTTACCGGACGAGGACAAGAGTACGCCGCAGCTCGATCTTTTGGCTCGTGTCGAACGA +GAGCTACCGGTGCGGCTCGACCAAGAGCGCACCGATATGGTTGTTTGCCATGGTGATCCC +TGCATGCCGAACTTCATGGTGGACCCTAAAACTCTTCAATGCACGGGTCTGATCGACCTT +GGGCGGCTCGGAACAGCAGATCGCTATGCCGATTTGGCACTCATGATTGCTAACGCCGAA +GAGAACTGGGCAGCGCCAGATGAAGCAGAGCGCGCCTTCGCTGTCCTATTCAATGTATTG +GGGATCGAAGCCCCCGACCGCGAACGCCTTGCCTTCTATCTGCGATTGGACCCTCTGACT +TGGGGT +>contig_40_polypolish:3555-4103 strand:+ aph(6)-Id aminoglycoside O-phosphotransferase APH(6)-Id +GGAGCAGTCCGGTTGCTCGGTCGTGAGAACAATCTGATGTTGCTCGAATATGCCGGGGAG +CGAATGCTCTCTCACATCGTTGCCGAGCACGGCGACTACCGAGCGACCGAAATTGCAGCG +GAACTAATGGCGAAGCTGTATGCCGCATCTGAGGAACCCCTGCCTTCTGCCCTTCTCCCG +ATCCGGGATCGCTTTGCAGCTTTGTTTCAGCGGGCGCGCGATGATCAAAACGCAGGTTGT +CAAACTGACTACGTCCACGCGGCGATTATAGCCGATCAAATGATGAGCAATGCCTCGGAA +CTGCGTGGGCTACATGGCGATCTGCATCATGAAAACATCATGTTCTCCAGTCGCGGCTGG +CTGGTGATAGATCCCGTCGGTCTGGTCGGTGAAGTGGGCTTTGGCGCCGCCAATATGTTC +TACGATCCGGCTGACAGAGACGACCTTTGTCTCGATCCTAGACGCATTGCACAGATGGCG +GACGCATTCTCTCGTGCGCTGGACGTCGATCCGCGTCGCCTGCTCGACCGTGCGTACGCT +TATGGGTGC +>contig_40_polypolish:632-1258 strand:+ aph(3')-Ia aminoglycoside O-phosphotransferase APH(3')-Ia +ATGAGCCATATTCAACGGGAAACGTCTTGCTCGAGGCCGCGATTAAATTCCAACATGGAT +GCTGATTTATATGGGTATAAATGGGCTCGCGATAATGTCGGGCAATCAGGTGCGACAATC +TATCGATTGTATGGGAAGCCCGATGCGCCAGAGTTGTTTCTGAAACATGGCAAAGGTAGC +GTTGCCAATGATGTTACAGATGAGATGGTCAGACTAAACTGGCTGACGGAATTTATGCCT +CTTCCGACCATCAAGCATTTTATCCGTACTCCTGATGATGCATGGTTACTCACCACTGCG +ATCCCCGGGAAAACAGCATTCCGGGTATTAGAAGAATATCCTGATTCAGGTGAAAATATT +GTTGATGCGCTGGCAGTGTTCCTGCGCCGGTTGCATTCGATTCCTGTTTGTAATTGTCCT +TTTAACAACGATCGCGTATTTCGTCTCGCTCAGGCGCAATCACGAATGAATAACGGTTTG +GTTGATGCGAGTGATTTTGATGACGAGCGTAATGGCTGGCCTGTTGAACAAGTCTGGAAA +GAAATGCATAAGCTTTTGCCATTCTCACCGGATTCAGTCGTCACTCATGGTGATTTCTCA +CTTGATAACCTTATTTTTGACGAGGGA +>contig_41_polypolish:100023-100541 strand:- terD tellurium resistance membrane protein TerD +ATGAGCGTTTCACTATCTAAAGGCGGCAACGTTTCCCTGAGCAAAACCGCGCCAAGCATG +AAAAACGTGCTGGTTGGCCTTGGCTGGGATGCACGTTCTACGGACGGTCAGGACTTTGAC +CTCGATGCTTCCGCATTTCTGCTGGCAGCCAATGGCAAGGTTCGTGGCGATGCAGATTTC +ATTTTCTATAACAACCTGAAATCTGCTGATGGTTCCGTTACTCATACCGGTGATAACCGT +ACCGGTGAAGGTGATGGCGACGATGAATCCCTCAAAATCAAACTGGACGCGGTACACGGG +GATGTCGACAAAATTATTTTCGTTGTCACTATCCATGATGCTCAGGCTCGTCGCCAGAGC +TTCGGTCAGGTTTCCGGCGCATTTATCCGTCTGGTGAATGATGACAATCAGACTGAAGTT +GCTCGCTACGATCTGACAGAAGACGCTTCTACTGAAACTGCCATGCTGTTTGGGGAGCTG +TATCGTCACAACGGAGAATGGAAATTCCGTGCGGTTGGC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amrfinderplus/AMRFinderPlus_Point_mutation_report.tsv Fri May 24 10:47:33 2024 +0000 @@ -0,0 +1,35 @@ +Protein identifier Contig id Start Stop Strand Gene symbol Sequence name Scope Element type Element subtype Class Subclass Method Target length Reference sequence length % Coverage of reference sequence % Identity to reference sequence Alignment length Accession of closest sequence Name of closest sequence HMM id HMM description Hierarchy node +NA contig_107_polypolish 5 861 - 23S_A2074A Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 857 2912 29.36 81.82 869 NC_022347.1:1040292-1037381 23S ribosomal RNA NA NA NA +NA contig_107_polypolish 5 861 - 23S_A2074A Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 857 2912 29.36 81.95 870 NC_002163.1:396449-399360 23S ribosomal RNA NA NA NA +NA contig_107_polypolish 5 861 - 23S_A2075A Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 857 2912 29.36 81.82 869 NC_022347.1:1040292-1037381 23S ribosomal RNA NA NA NA +NA contig_107_polypolish 5 861 - 23S_A2075A Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 857 2912 29.36 81.95 870 NC_002163.1:396449-399360 23S ribosomal RNA NA NA NA +NA contig_107_polypolish 5 861 - 23S_C2627C Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 857 2912 29.36 81.82 869 NC_022347.1:1040292-1037381 23S ribosomal RNA NA NA NA +NA contig_107_polypolish 5 861 - 23S_C2627C Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 857 2912 29.36 81.95 870 NC_002163.1:396449-399360 23S ribosomal RNA NA NA NA +NA contig_10_polypolish 345 1334 - 23S_A2074A Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 990 2912 33.93 80.56 1003 NC_002163.1:396449-399360 23S ribosomal RNA NA NA NA +NA contig_10_polypolish 345 1334 - 23S_A2075A Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 990 2912 33.93 80.56 1003 NC_002163.1:396449-399360 23S ribosomal RNA NA NA NA +NA contig_10_polypolish 345 1334 - 23S_C2627C Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 990 2912 33.93 80.56 1003 NC_002163.1:396449-399360 23S ribosomal RNA NA NA NA +NA contig_10_polypolish 416 1334 - 23S_A2074A Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 919 2912 31.49 81.10 931 NC_022347.1:1040292-1037381 23S ribosomal RNA NA NA NA +NA contig_10_polypolish 416 1334 - 23S_A2075A Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 919 2912 31.49 81.10 931 NC_022347.1:1040292-1037381 23S ribosomal RNA NA NA NA +NA contig_10_polypolish 416 1334 - 23S_C2627C Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 919 2912 31.49 81.10 931 NC_022347.1:1040292-1037381 23S ribosomal RNA NA NA NA +NA contig_11_polypolish 1319 2308 - 23S_A2074A Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 990 2912 33.93 80.56 1003 NC_002163.1:396449-399360 23S ribosomal RNA NA NA NA +NA contig_11_polypolish 1319 2308 - 23S_A2075A Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 990 2912 33.93 80.56 1003 NC_002163.1:396449-399360 23S ribosomal RNA NA NA NA +NA contig_11_polypolish 1319 2308 - 23S_C2627C Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 990 2912 33.93 80.56 1003 NC_002163.1:396449-399360 23S ribosomal RNA NA NA NA +NA contig_11_polypolish 1390 2308 - 23S_A2074A Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 919 2912 31.49 81.10 931 NC_022347.1:1040292-1037381 23S ribosomal RNA NA NA NA +NA contig_11_polypolish 1390 2308 - 23S_A2075A Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 919 2912 31.49 81.10 931 NC_022347.1:1040292-1037381 23S ribosomal RNA NA NA NA +NA contig_11_polypolish 1390 2308 - 23S_C2627C Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 919 2912 31.49 81.10 931 NC_022347.1:1040292-1037381 23S ribosomal RNA NA NA NA +NA contig_12_polypolish 61 472 - 23S_A2074A Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 412 2912 14.08 82.01 417 NC_022347.1:1040292-1037381 23S ribosomal RNA NA NA NA +NA contig_12_polypolish 61 472 - 23S_A2074A Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 412 2912 14.08 82.30 418 NC_002163.1:396449-399360 23S ribosomal RNA NA NA NA +NA contig_12_polypolish 61 472 - 23S_A2075A Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 412 2912 14.08 82.01 417 NC_022347.1:1040292-1037381 23S ribosomal RNA NA NA NA +NA contig_12_polypolish 61 472 - 23S_A2075A Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 412 2912 14.08 82.30 418 NC_002163.1:396449-399360 23S ribosomal RNA NA NA NA +NA contig_7_polypolish 39847 40836 - 23S_A2074A Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 990 2912 33.93 80.56 1003 NC_002163.1:396449-399360 23S ribosomal RNA NA NA NA +NA contig_7_polypolish 39847 40836 - 23S_A2075A Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 990 2912 33.93 80.56 1003 NC_002163.1:396449-399360 23S ribosomal RNA NA NA NA +NA contig_7_polypolish 39847 40836 - 23S_C2627C Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 990 2912 33.93 80.56 1003 NC_002163.1:396449-399360 23S ribosomal RNA NA NA NA +NA contig_7_polypolish 39918 40836 - 23S_A2074A Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 919 2912 31.49 81.10 931 NC_022347.1:1040292-1037381 23S ribosomal RNA NA NA NA +NA contig_7_polypolish 39918 40836 - 23S_A2075A Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 919 2912 31.49 81.10 931 NC_022347.1:1040292-1037381 23S ribosomal RNA NA NA NA +NA contig_7_polypolish 39918 40836 - 23S_C2627C Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 919 2912 31.49 81.10 931 NC_022347.1:1040292-1037381 23S ribosomal RNA NA NA NA +NA contig_82_polypolish 31069 31987 + 23S_A2074A Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 919 2912 31.49 81.10 931 NC_022347.1:1040292-1037381 23S ribosomal RNA NA NA NA +NA contig_82_polypolish 31069 31987 + 23S_A2075A Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 919 2912 31.49 81.10 931 NC_022347.1:1040292-1037381 23S ribosomal RNA NA NA NA +NA contig_82_polypolish 31069 31987 + 23S_C2627C Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 919 2912 31.49 81.10 931 NC_022347.1:1040292-1037381 23S ribosomal RNA NA NA NA +NA contig_82_polypolish 31069 32058 + 23S_A2074A Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 990 2912 33.93 80.56 1003 NC_002163.1:396449-399360 23S ribosomal RNA NA NA NA +NA contig_82_polypolish 31069 32058 + 23S_A2075A Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 990 2912 33.93 80.56 1003 NC_002163.1:396449-399360 23S ribosomal RNA NA NA NA +NA contig_82_polypolish 31069 32058 + 23S_C2627C Campylobacter 23S ribosomal RNA [WILDTYPE] core AMR POINT MACROLIDE MACROLIDE POINTN 990 2912 33.93 80.56 1003 NC_002163.1:396449-399360 23S ribosomal RNA NA NA NA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amrfinderplus/AMRFinderPlus_report.tsv Fri May 24 10:47:33 2024 +0000 @@ -0,0 +1,58 @@ +Protein identifier Contig id Start Stop Strand Gene symbol Sequence name Scope Element type Element subtype Class Subclass Method Target length Reference sequence length % Coverage of reference sequence % Identity to reference sequence Alignment length Accession of closest sequence Name of closest sequence HMM id HMM description Hierarchy node +NA contig_153_polypolish 4412 4645 - merE broad-spectrum mercury transporter MerE plus STRESS METAL MERCURY MERCURY BLASTX 78 78 100.00 96.15 78 AAC38236.1 broad-spectrum mercury transporter MerE NA NA merE +NA contig_153_polypolish 7613 7846 - merT mercuric transport protein MerT plus STRESS METAL MERCURY MERCURY PARTIALX 78 116 67.24 92.31 78 CAA70196.1 mercuric transport protein MerT NA NA merT +NA contig_160_polypolish 86415 86654 - fosA FosA5 family fosfomycin resistance glutathione transferase core AMR AMR FOSFOMYCIN FOSFOMYCIN PARTIALX 80 139 57.55 98.75 80 WP_114473955.1 fosfomycin resistance glutathione transferase FosA9 NA NA fosA5_fam +NA contig_30_polypolish 3018 3344 + merR mercury resistance transcriptional regulator MerR plus STRESS METAL MERCURY MERCURY PARTIALX 109 144 75.69 93.58 109 BAA20334.1 mercury resistance transcriptional regulator MerR NA NA merR_Ps +NA contig_30_polypolish 5821 6243 + catA1 type A-1 chloramphenicol O-acetyltransferase core AMR AMR PHENICOL CHLORAMPHENICOL PARTIALX 141 219 64.38 98.58 141 WP_000412211.1 type A-1 chloramphenicol O-acetyltransferase NA NA catA1 +NA contig_30_polypolish 5821 6243 + catA1 type A-1 chloramphenicol O-acetyltransferase core AMR AMR PHENICOL CHLORAMPHENICOL PARTIALX 141 219 64.38 98.58 141 WP_063843217.1 type A-1 chloramphenicol O-acetyltransferase NA NA catA1 +NA contig_30_polypolish 13708 14433 + blaCTX-M CTX-M family extended-spectrum class A beta-lactamase core AMR AMR BETA-LACTAM CEPHALOSPORIN INTERNAL_STOP 242 291 84.54 90.24 246 WP_063860025.1 extended-spectrum class A beta-lactamase CTX-M-179 NA NA blaCTX-M +NA contig_30_polypolish 17856 18287 + merR mercury resistance transcriptional regulator MerR plus STRESS METAL MERCURY MERCURY BLASTX 144 144 100.00 92.36 144 CAA77320.1 mercury resistance transcriptional regulator MerR NA NA merR_Ps +NA contig_30_polypolish 20698 21348 + catA1 type A-1 chloramphenicol O-acetyltransferase core AMR AMR PHENICOL CHLORAMPHENICOL BLASTX 217 219 99.09 92.17 217 WP_000412211.1 type A-1 chloramphenicol O-acetyltransferase NA NA catA1 +NA contig_35_polypolish 4787 5644 - aac(3)-IIe aminoglycoside N-acetyltransferase AAC(3)-IIe core AMR AMR AMINOGLYCOSIDE GENTAMICIN EXACTX 286 286 100.00 100.00 286 WP_000557452.1 aminoglycoside N-acetyltransferase AAC(3)-IIe NA NA aac(3)-IIe +NA contig_36_polypolish 9168 9608 + blaSHV SHV family class A beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM PARTIALX 147 286 51.40 99.32 147 WP_002904004.1 extended-spectrum class A beta-lactamase SHV-12 NA NA blaSHV +NA contig_36_polypolish 9168 9608 + blaSHV SHV family class A beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM PARTIALX 147 286 51.40 99.32 147 WP_004176269.1 broad-spectrum class A beta-lactamase SHV-11 NA NA blaSHV +NA contig_36_polypolish 9168 9608 + blaSHV SHV family class A beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM PARTIALX 147 286 51.40 99.32 147 WP_004183952.1 broad-spectrum class A beta-lactamase SHV-60 NA NA blaSHV +NA contig_36_polypolish 9168 9608 + blaSHV SHV family class A beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM PARTIALX 147 286 51.40 99.32 147 WP_032488413.1 extended-spectrum class A beta-lactamase SHV-2a NA NA blaSHV +NA contig_36_polypolish 9168 9608 + blaSHV SHV family class A beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM PARTIALX 147 286 51.40 99.32 147 WP_032494802.1 extended-spectrum class A beta-lactamase SHV-129 NA NA blaSHV +NA contig_36_polypolish 9168 9608 + blaSHV SHV family class A beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM PARTIALX 147 286 51.40 99.32 147 WP_063864610.1 inhibitor-resistant broad-spectrum class A beta-lactamase SHV-107 NA NA blaSHV +NA contig_36_polypolish 9168 9608 + blaSHV SHV family class A beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM PARTIALX 147 286 51.40 99.32 147 WP_063864613.1 class A beta-lactamase SHV-110 NA NA blaSHV +NA contig_36_polypolish 9168 9608 + blaSHV SHV family class A beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM PARTIALX 147 286 51.40 99.32 147 WP_063864619.1 extended-spectrum class A beta-lactamase SHV-13 NA NA blaSHV +NA contig_36_polypolish 9168 9608 + blaSHV SHV family class A beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM PARTIALX 147 286 51.40 99.32 147 WP_063864622.1 extended-spectrum class A beta-lactamase SHV-134 NA NA blaSHV +NA contig_36_polypolish 9168 9608 + blaSHV SHV family class A beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM PARTIALX 147 286 51.40 99.32 147 WP_063864638.1 extended-spectrum class A beta-lactamase SHV-152 NA NA blaSHV +NA contig_36_polypolish 9168 9608 + blaSHV SHV family class A beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM PARTIALX 147 286 51.40 99.32 147 WP_063864641.1 class A beta-lactamase SHV-155 NA NA blaSHV +NA contig_36_polypolish 9168 9608 + blaSHV SHV family class A beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM PARTIALX 147 286 51.40 99.32 147 WP_063864645.1 class A beta-lactamase SHV-159 NA NA blaSHV +NA contig_36_polypolish 9168 9608 + blaSHV SHV family class A beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM PARTIALX 147 286 51.40 99.32 147 WP_063864654.1 class A beta-lactamase SHV-172 NA NA blaSHV +NA contig_36_polypolish 9168 9608 + blaSHV SHV family class A beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM PARTIALX 147 286 51.40 99.32 147 WP_063864656.1 class A beta-lactamase SHV-178 NA NA blaSHV +NA contig_36_polypolish 9168 9608 + blaSHV SHV family class A beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM PARTIALX 147 286 51.40 99.32 147 WP_063864666.1 class A beta-lactamase SHV-190 NA NA blaSHV +NA contig_36_polypolish 9168 9608 + blaSHV SHV family class A beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM PARTIALX 147 286 51.40 99.32 147 WP_063864674.1 extended-spectrum class A beta-lactamase SHV-31 NA NA blaSHV +NA contig_36_polypolish 9168 9608 + blaSHV SHV family class A beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM PARTIALX 147 286 51.40 99.32 147 WP_063864681.1 broad-spectrum class A beta-lactamase SHV-40 NA NA blaSHV +NA contig_36_polypolish 9168 9608 + blaSHV SHV family class A beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM PARTIALX 147 286 51.40 99.32 147 WP_063864693.1 inhibitor-resistant broad-spectrum class A beta-lactamase SHV-56 NA NA blaSHV +NA contig_36_polypolish 9168 9608 + blaSHV SHV family class A beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM PARTIALX 147 286 51.40 99.32 147 WP_063864709.1 broad-spectrum class A beta-lactamase SHV-79 NA NA blaSHV +NA contig_36_polypolish 9168 9608 + blaSHV SHV family class A beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM PARTIALX 147 286 51.40 99.32 147 WP_063864718.1 class A beta-lactamase SHV-96 NA NA blaSHV +NA contig_36_polypolish 9168 9608 + blaSHV SHV family class A beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM PARTIALX 147 286 51.40 99.32 147 WP_096807447.1 class A beta-lactamase SHV-200 NA NA blaSHV +NA contig_36_polypolish 9168 9608 + blaSHV SHV family class A beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM PARTIALX 147 286 51.40 99.32 147 WP_122630870.1 class A beta-lactamase SHV-215 NA NA blaSHV +NA contig_36_polypolish 9168 9608 + blaSHV SHV family class A beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM PARTIALX 147 286 51.40 99.32 147 WP_122630880.1 class A beta-lactamase SHV-228 NA NA blaSHV +NA contig_36_polypolish 9587 10024 + blaSHV SHV family class A beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM PARTIALX 146 286 51.05 95.89 146 WP_002904004.1 extended-spectrum class A beta-lactamase SHV-12 NA NA blaSHV +NA contig_36_polypolish 9587 10024 + blaSHV SHV family class A beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM PARTIALX 146 286 51.05 95.89 146 WP_011117369.1 extended-spectrum class A beta-lactamase SHV-5 NA NA blaSHV +NA contig_36_polypolish 9587 10024 + blaSHV SHV family class A beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM PARTIALX 146 286 51.05 95.89 146 WP_020316986.1 extended-spectrum class A beta-lactamase SHV-7 NA NA blaSHV +NA contig_36_polypolish 9587 10024 + blaSHV SHV family class A beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM PARTIALX 146 286 51.05 95.89 146 WP_063864635.1 extended-spectrum class A beta-lactamase SHV-15 NA NA blaSHV +NA contig_36_polypolish 9587 10024 + blaSHV SHV family class A beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM PARTIALX 146 286 51.05 95.89 146 WP_063864640.1 extended-spectrum class A beta-lactamase SHV-154 NA NA blaSHV +NA contig_36_polypolish 9587 10024 + blaSHV SHV family class A beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM PARTIALX 146 286 51.05 95.89 146 WP_063864647.1 extended-spectrum class A beta-lactamase SHV-160 NA NA blaSHV +NA contig_36_polypolish 9587 10024 + blaSHV SHV family class A beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM PARTIALX 146 286 51.05 95.89 146 WP_063864652.1 extended-spectrum class A beta-lactamase SHV-165 NA NA blaSHV +NA contig_36_polypolish 9587 10024 + blaSHV SHV family class A beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM PARTIALX 146 286 51.05 95.89 146 WP_063864692.1 extended-spectrum class A beta-lactamase SHV-55 NA NA blaSHV +NA contig_36_polypolish 9587 10024 + blaSHV SHV family class A beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM PARTIALX 146 286 51.05 95.89 146 WP_063864698.1 extended-spectrum class A beta-lactamase SHV-64 NA NA blaSHV +NA contig_36_polypolish 9587 10024 + blaSHV SHV family class A beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM PARTIALX 146 286 51.05 95.89 146 WP_063864700.1 extended-spectrum class A beta-lactamase SHV-66 NA NA blaSHV +NA contig_36_polypolish 9587 10024 + blaSHV SHV family class A beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM PARTIALX 146 286 51.05 95.89 146 WP_268871888.1 class A beta-lactamase SHV-230 NA NA blaSHV +NA contig_37_polypolish 18 569 + aac(6')-Ib3 aminoglycoside N-acetyltransferase AAC(6')-Ib3 core AMR AMR AMINOGLYCOSIDE AMIKACIN/KANAMYCIN/TOBRAMYCIN ALLELEX 184 184 100.00 100.00 184 WP_032488579.1 aminoglycoside N-acetyltransferase AAC(6')-Ib3 NA NA aac(6')-Ib3 +NA contig_37_polypolish 642 1424 + aadA1 ANT(3'')-Ia family aminoglycoside nucleotidyltransferase AadA1 core AMR AMR AMINOGLYCOSIDE STREPTOMYCIN BLASTX 261 262 100.00 97.71 262 WP_001206315.1 ANT(3'')-Ia family aminoglycoside nucleotidyltransferase AadA1 NA NA aadA1 +NA contig_37_polypolish 3006 3863 + blaTEM-1 broad-spectrum class A beta-lactamase TEM-1 core AMR AMR BETA-LACTAM BETA-LACTAM ALLELEX 286 286 100.00 100.00 286 WP_000027057.1 broad-spectrum class A beta-lactamase TEM-1 NA NA blaTEM-1 +NA contig_37_polypolish 8924 9133 - merC organomercurial transporter MerC plus STRESS METAL MERCURY ORGANOMERCURY PARTIALX 70 140 50.00 90.00 70 AAC33908.1 organomercurial transporter MerC NA NA merC +NA contig_39_polypolish 3496 3825 - qacE quaternary ammonium compound efflux SMR transporter QacE core STRESS BIOCIDE QUATERNARY AMMONIUM QUATERNARY AMMONIUM EXACTX 110 110 100.00 100.00 110 WP_010890145.1 quaternary ammonium compound efflux SMR transporter QacE NA NA qacE +NA contig_39_polypolish 4010 4327 - dfrA30 trimethoprim-resistant dihydrofolate reductase DfrA30 core AMR AMR TRIMETHOPRIM TRIMETHOPRIM PARTIALX 106 157 67.52 98.11 106 WP_063844408.1 trimethoprim-resistant dihydrofolate reductase DfrA30 NA NA dfrA30 +NA contig_40_polypolish 632 1258 + aph(3')-Ia aminoglycoside O-phosphotransferase APH(3')-Ia core AMR AMR AMINOGLYCOSIDE KANAMYCIN PARTIALX 209 271 77.12 99.04 209 WP_000018329.1 aminoglycoside O-phosphotransferase APH(3')-Ia NA NA aph(3')-Ia +NA contig_40_polypolish 632 1258 + aph(3')-Ia aminoglycoside O-phosphotransferase APH(3')-Ia core AMR AMR AMINOGLYCOSIDE KANAMYCIN PARTIALX 209 271 77.12 99.04 209 WP_063842148.1 aminoglycoside O-phosphotransferase APH(3')-Ia NA NA aph(3')-Ia +NA contig_40_polypolish 2574 3359 + aph(3'')-Ib aminoglycoside O-phosphotransferase APH(3'')-Ib core AMR AMR AMINOGLYCOSIDE STREPTOMYCIN BLASTX 262 267 98.13 100.00 262 WP_001082319.1 aminoglycoside O-phosphotransferase APH(3'')-Ib NA NA aph(3'')-Ib +NA contig_40_polypolish 3555 4103 + aph(6)-Id aminoglycoside O-phosphotransferase APH(6)-Id core AMR AMR AMINOGLYCOSIDE STREPTOMYCIN PARTIALX 183 278 65.83 98.91 183 WP_000480968.1 aminoglycoside O-phosphotransferase APH(6)-Id NA NA aph(6)-Id +NA contig_40_polypolish 3555 4103 + aph(6)-Id aminoglycoside O-phosphotransferase APH(6)-Id core AMR AMR AMINOGLYCOSIDE STREPTOMYCIN PARTIALX 183 278 65.83 98.91 183 WP_000480972.1 aminoglycoside O-phosphotransferase APH(6)-Id NA NA aph(6)-Id +NA contig_40_polypolish 3555 4103 + aph(6)-Id aminoglycoside O-phosphotransferase APH(6)-Id core AMR AMR AMINOGLYCOSIDE STREPTOMYCIN PARTIALX 183 278 65.83 98.91 183 WP_063842183.1 aminoglycoside O-phosphotransferase APH(6)-Id NA NA aph(6)-Id +NA contig_41_polypolish 100023 100541 - terD tellurium resistance membrane protein TerD plus STRESS METAL TELLURIUM TELLURIUM BLASTX 173 192 90.10 98.84 173 AAA98292.1 tellurium resistance membrane protein TerD NA NA terD
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summarize/amrfinderplus_output.json Fri May 24 10:47:33 2024 +0000 @@ -0,0 +1,1 @@ +[{"analysis_software_version": "3.11.26", "reference_database_version": "v3.11-2023-04-17.1", "analysis_software_name": "amrfinderplus", "results": [{"name": "amrfinderplus_report", "file_path": "tests/data/dummy/amrfinderplus/AMRFinderPlus_report.tsv", "hid": "12345", "galaxy_id": null, "content": [{"Protein identifier": null, "Contig id": "contig_153_polypolish", "Start": 4412, "Stop": 4645, "Strand": "-", "Gene symbol": "merE", "Sequence name": "broad-spectrum mercury transporter MerE", "Scope": "plus", "Element type": "STRESS", "Element subtype": "METAL", "Class": "MERCURY", "Subclass": "MERCURY", "Method": "BLASTX", "Target length": 78, "Reference sequence length": 78, "% Coverage of reference sequence": 100.0, "% Identity to reference sequence": 96.15, "Alignment length": 78, "Accession of closest sequence": "AAC38236.1", "Name of closest sequence": "broad-spectrum mercury transporter MerE", "HMM id": null, "HMM description": null, "Hierarchy node": "merE"}, {"Protein identifier": null, "Contig id": "contig_153_polypolish", "Start": 7613, "Stop": 7846, "Strand": "-", "Gene symbol": "merT", "Sequence name": "mercuric transport protein MerT", "Scope": "plus", "Element type": "STRESS", "Element subtype": "METAL", "Class": "MERCURY", "Subclass": "MERCURY", "Method": "PARTIALX", "Target length": 78, "Reference sequence length": 116, "% Coverage of reference sequence": 67.24, "% Identity to reference sequence": 92.31, "Alignment length": 78, "Accession of closest sequence": "CAA70196.1", "Name of closest sequence": "mercuric transport protein MerT", "HMM id": null, "HMM description": null, "Hierarchy node": "merT"}, {"Protein identifier": null, "Contig id": "contig_160_polypolish", "Start": 86415, "Stop": 86654, "Strand": "-", "Gene symbol": "fosA", "Sequence name": "FosA5 family fosfomycin resistance glutathione transferase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "FOSFOMYCIN", "Subclass": "FOSFOMYCIN", "Method": "PARTIALX", "Target length": 80, "Reference sequence length": 139, "% Coverage of reference sequence": 57.55, "% Identity to reference sequence": 98.75, "Alignment length": 80, "Accession of closest sequence": "WP_114473955.1", "Name of closest sequence": "fosfomycin resistance glutathione transferase FosA9", "HMM id": null, "HMM description": null, "Hierarchy node": "fosA5_fam"}, {"Protein identifier": null, "Contig id": "contig_30_polypolish", "Start": 3018, "Stop": 3344, "Strand": "+", "Gene symbol": "merR", "Sequence name": "mercury resistance transcriptional regulator MerR", "Scope": "plus", "Element type": "STRESS", "Element subtype": "METAL", "Class": "MERCURY", "Subclass": "MERCURY", "Method": "PARTIALX", "Target length": 109, "Reference sequence length": 144, "% Coverage of reference sequence": 75.69, "% Identity to reference sequence": 93.58, "Alignment length": 109, "Accession of closest sequence": "BAA20334.1", "Name of closest sequence": "mercury resistance transcriptional regulator MerR", "HMM id": null, "HMM description": null, "Hierarchy node": "merR_Ps"}, {"Protein identifier": null, "Contig id": "contig_30_polypolish", "Start": 5821, "Stop": 6243, "Strand": "+", "Gene symbol": "catA1", "Sequence name": "type A-1 chloramphenicol O-acetyltransferase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "PHENICOL", "Subclass": "CHLORAMPHENICOL", "Method": "PARTIALX", "Target length": 141, "Reference sequence length": 219, "% Coverage of reference sequence": 64.38, "% Identity to reference sequence": 98.58, "Alignment length": 141, "Accession of closest sequence": "WP_000412211.1", "Name of closest sequence": "type A-1 chloramphenicol O-acetyltransferase", "HMM id": null, "HMM description": null, "Hierarchy node": "catA1"}, {"Protein identifier": null, "Contig id": "contig_30_polypolish", "Start": 5821, "Stop": 6243, "Strand": "+", "Gene symbol": "catA1", "Sequence name": "type A-1 chloramphenicol O-acetyltransferase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "PHENICOL", "Subclass": "CHLORAMPHENICOL", "Method": "PARTIALX", "Target length": 141, "Reference sequence length": 219, "% Coverage of reference sequence": 64.38, "% Identity to reference sequence": 98.58, "Alignment length": 141, "Accession of closest sequence": "WP_063843217.1", "Name of closest sequence": "type A-1 chloramphenicol O-acetyltransferase", "HMM id": null, "HMM description": null, "Hierarchy node": "catA1"}, {"Protein identifier": null, "Contig id": "contig_30_polypolish", "Start": 13708, "Stop": 14433, "Strand": "+", "Gene symbol": "blaCTX-M", "Sequence name": "CTX-M family extended-spectrum class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "CEPHALOSPORIN", "Method": "INTERNAL_STOP", "Target length": 242, "Reference sequence length": 291, "% Coverage of reference sequence": 84.54, "% Identity to reference sequence": 90.24, "Alignment length": 246, "Accession of closest sequence": "WP_063860025.1", "Name of closest sequence": "extended-spectrum class A beta-lactamase CTX-M-179", "HMM id": null, "HMM description": null, "Hierarchy node": "blaCTX-M"}, {"Protein identifier": null, "Contig id": "contig_30_polypolish", "Start": 17856, "Stop": 18287, "Strand": "+", "Gene symbol": "merR", "Sequence name": "mercury resistance transcriptional regulator MerR", "Scope": "plus", "Element type": "STRESS", "Element subtype": "METAL", "Class": "MERCURY", "Subclass": "MERCURY", "Method": "BLASTX", "Target length": 144, "Reference sequence length": 144, "% Coverage of reference sequence": 100.0, "% Identity to reference sequence": 92.36, "Alignment length": 144, "Accession of closest sequence": "CAA77320.1", "Name of closest sequence": "mercury resistance transcriptional regulator MerR", "HMM id": null, "HMM description": null, "Hierarchy node": "merR_Ps"}, {"Protein identifier": null, "Contig id": "contig_30_polypolish", "Start": 20698, "Stop": 21348, "Strand": "+", "Gene symbol": "catA1", "Sequence name": "type A-1 chloramphenicol O-acetyltransferase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "PHENICOL", "Subclass": "CHLORAMPHENICOL", "Method": "BLASTX", "Target length": 217, "Reference sequence length": 219, "% Coverage of reference sequence": 99.09, "% Identity to reference sequence": 92.17, "Alignment length": 217, "Accession of closest sequence": "WP_000412211.1", "Name of closest sequence": "type A-1 chloramphenicol O-acetyltransferase", "HMM id": null, "HMM description": null, "Hierarchy node": "catA1"}, {"Protein identifier": null, "Contig id": "contig_35_polypolish", "Start": 4787, "Stop": 5644, "Strand": "-", "Gene symbol": "aac(3)-IIe", "Sequence name": "aminoglycoside N-acetyltransferase AAC(3)-IIe", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "AMINOGLYCOSIDE", "Subclass": "GENTAMICIN", "Method": "EXACTX", "Target length": 286, "Reference sequence length": 286, "% Coverage of reference sequence": 100.0, "% Identity to reference sequence": 100.0, "Alignment length": 286, "Accession of closest sequence": "WP_000557452.1", "Name of closest sequence": "aminoglycoside N-acetyltransferase AAC(3)-IIe", "HMM id": null, "HMM description": null, "Hierarchy node": "aac(3)-IIe"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9168, "Stop": 9608, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 147, "Reference sequence length": 286, "% Coverage of reference sequence": 51.4, "% Identity to reference sequence": 99.32, "Alignment length": 147, "Accession of closest sequence": "WP_002904004.1", "Name of closest sequence": "extended-spectrum class A beta-lactamase SHV-12", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9168, "Stop": 9608, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 147, "Reference sequence length": 286, "% Coverage of reference sequence": 51.4, "% Identity to reference sequence": 99.32, "Alignment length": 147, "Accession of closest sequence": "WP_004176269.1", "Name of closest sequence": "broad-spectrum class A beta-lactamase SHV-11", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9168, "Stop": 9608, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 147, "Reference sequence length": 286, "% Coverage of reference sequence": 51.4, "% Identity to reference sequence": 99.32, "Alignment length": 147, "Accession of closest sequence": "WP_004183952.1", "Name of closest sequence": "broad-spectrum class A beta-lactamase SHV-60", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9168, "Stop": 9608, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 147, "Reference sequence length": 286, "% Coverage of reference sequence": 51.4, "% Identity to reference sequence": 99.32, "Alignment length": 147, "Accession of closest sequence": "WP_032488413.1", "Name of closest sequence": "extended-spectrum class A beta-lactamase SHV-2a", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9168, "Stop": 9608, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 147, "Reference sequence length": 286, "% Coverage of reference sequence": 51.4, "% Identity to reference sequence": 99.32, "Alignment length": 147, "Accession of closest sequence": "WP_032494802.1", "Name of closest sequence": "extended-spectrum class A beta-lactamase SHV-129", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9168, "Stop": 9608, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 147, "Reference sequence length": 286, "% Coverage of reference sequence": 51.4, "% Identity to reference sequence": 99.32, "Alignment length": 147, "Accession of closest sequence": "WP_063864610.1", "Name of closest sequence": "inhibitor-resistant broad-spectrum class A beta-lactamase SHV-107", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9168, "Stop": 9608, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 147, "Reference sequence length": 286, "% Coverage of reference sequence": 51.4, "% Identity to reference sequence": 99.32, "Alignment length": 147, "Accession of closest sequence": "WP_063864613.1", "Name of closest sequence": "class A beta-lactamase SHV-110", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9168, "Stop": 9608, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 147, "Reference sequence length": 286, "% Coverage of reference sequence": 51.4, "% Identity to reference sequence": 99.32, "Alignment length": 147, "Accession of closest sequence": "WP_063864619.1", "Name of closest sequence": "extended-spectrum class A beta-lactamase SHV-13", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9168, "Stop": 9608, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 147, "Reference sequence length": 286, "% Coverage of reference sequence": 51.4, "% Identity to reference sequence": 99.32, "Alignment length": 147, "Accession of closest sequence": "WP_063864622.1", "Name of closest sequence": "extended-spectrum class A beta-lactamase SHV-134", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9168, "Stop": 9608, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 147, "Reference sequence length": 286, "% Coverage of reference sequence": 51.4, "% Identity to reference sequence": 99.32, "Alignment length": 147, "Accession of closest sequence": "WP_063864638.1", "Name of closest sequence": "extended-spectrum class A beta-lactamase SHV-152", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9168, "Stop": 9608, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 147, "Reference sequence length": 286, "% Coverage of reference sequence": 51.4, "% Identity to reference sequence": 99.32, "Alignment length": 147, "Accession of closest sequence": "WP_063864641.1", "Name of closest sequence": "class A beta-lactamase SHV-155", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9168, "Stop": 9608, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 147, "Reference sequence length": 286, "% Coverage of reference sequence": 51.4, "% Identity to reference sequence": 99.32, "Alignment length": 147, "Accession of closest sequence": "WP_063864645.1", "Name of closest sequence": "class A beta-lactamase SHV-159", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9168, "Stop": 9608, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 147, "Reference sequence length": 286, "% Coverage of reference sequence": 51.4, "% Identity to reference sequence": 99.32, "Alignment length": 147, "Accession of closest sequence": "WP_063864654.1", "Name of closest sequence": "class A beta-lactamase SHV-172", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9168, "Stop": 9608, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 147, "Reference sequence length": 286, "% Coverage of reference sequence": 51.4, "% Identity to reference sequence": 99.32, "Alignment length": 147, "Accession of closest sequence": "WP_063864656.1", "Name of closest sequence": "class A beta-lactamase SHV-178", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9168, "Stop": 9608, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 147, "Reference sequence length": 286, "% Coverage of reference sequence": 51.4, "% Identity to reference sequence": 99.32, "Alignment length": 147, "Accession of closest sequence": "WP_063864666.1", "Name of closest sequence": "class A beta-lactamase SHV-190", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9168, "Stop": 9608, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 147, "Reference sequence length": 286, "% Coverage of reference sequence": 51.4, "% Identity to reference sequence": 99.32, "Alignment length": 147, "Accession of closest sequence": "WP_063864674.1", "Name of closest sequence": "extended-spectrum class A beta-lactamase SHV-31", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9168, "Stop": 9608, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 147, "Reference sequence length": 286, "% Coverage of reference sequence": 51.4, "% Identity to reference sequence": 99.32, "Alignment length": 147, "Accession of closest sequence": "WP_063864681.1", "Name of closest sequence": "broad-spectrum class A beta-lactamase SHV-40", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9168, "Stop": 9608, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 147, "Reference sequence length": 286, "% Coverage of reference sequence": 51.4, "% Identity to reference sequence": 99.32, "Alignment length": 147, "Accession of closest sequence": "WP_063864693.1", "Name of closest sequence": "inhibitor-resistant broad-spectrum class A beta-lactamase SHV-56", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9168, "Stop": 9608, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 147, "Reference sequence length": 286, "% Coverage of reference sequence": 51.4, "% Identity to reference sequence": 99.32, "Alignment length": 147, "Accession of closest sequence": "WP_063864709.1", "Name of closest sequence": "broad-spectrum class A beta-lactamase SHV-79", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9168, "Stop": 9608, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 147, "Reference sequence length": 286, "% Coverage of reference sequence": 51.4, "% Identity to reference sequence": 99.32, "Alignment length": 147, "Accession of closest sequence": "WP_063864718.1", "Name of closest sequence": "class A beta-lactamase SHV-96", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9168, "Stop": 9608, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 147, "Reference sequence length": 286, "% Coverage of reference sequence": 51.4, "% Identity to reference sequence": 99.32, "Alignment length": 147, "Accession of closest sequence": "WP_096807447.1", "Name of closest sequence": "class A beta-lactamase SHV-200", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9168, "Stop": 9608, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 147, "Reference sequence length": 286, "% Coverage of reference sequence": 51.4, "% Identity to reference sequence": 99.32, "Alignment length": 147, "Accession of closest sequence": "WP_122630870.1", "Name of closest sequence": "class A beta-lactamase SHV-215", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9168, "Stop": 9608, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 147, "Reference sequence length": 286, "% Coverage of reference sequence": 51.4, "% Identity to reference sequence": 99.32, "Alignment length": 147, "Accession of closest sequence": "WP_122630880.1", "Name of closest sequence": "class A beta-lactamase SHV-228", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9587, "Stop": 10024, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 146, "Reference sequence length": 286, "% Coverage of reference sequence": 51.05, "% Identity to reference sequence": 95.89, "Alignment length": 146, "Accession of closest sequence": "WP_002904004.1", "Name of closest sequence": "extended-spectrum class A beta-lactamase SHV-12", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9587, "Stop": 10024, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 146, "Reference sequence length": 286, "% Coverage of reference sequence": 51.05, "% Identity to reference sequence": 95.89, "Alignment length": 146, "Accession of closest sequence": "WP_011117369.1", "Name of closest sequence": "extended-spectrum class A beta-lactamase SHV-5", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9587, "Stop": 10024, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 146, "Reference sequence length": 286, "% Coverage of reference sequence": 51.05, "% Identity to reference sequence": 95.89, "Alignment length": 146, "Accession of closest sequence": "WP_020316986.1", "Name of closest sequence": "extended-spectrum class A beta-lactamase SHV-7", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9587, "Stop": 10024, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 146, "Reference sequence length": 286, "% Coverage of reference sequence": 51.05, "% Identity to reference sequence": 95.89, "Alignment length": 146, "Accession of closest sequence": "WP_063864635.1", "Name of closest sequence": "extended-spectrum class A beta-lactamase SHV-15", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9587, "Stop": 10024, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 146, "Reference sequence length": 286, "% Coverage of reference sequence": 51.05, "% Identity to reference sequence": 95.89, "Alignment length": 146, "Accession of closest sequence": "WP_063864640.1", "Name of closest sequence": "extended-spectrum class A beta-lactamase SHV-154", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9587, "Stop": 10024, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 146, "Reference sequence length": 286, "% Coverage of reference sequence": 51.05, "% Identity to reference sequence": 95.89, "Alignment length": 146, "Accession of closest sequence": "WP_063864647.1", "Name of closest sequence": "extended-spectrum class A beta-lactamase SHV-160", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9587, "Stop": 10024, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 146, "Reference sequence length": 286, "% Coverage of reference sequence": 51.05, "% Identity to reference sequence": 95.89, "Alignment length": 146, "Accession of closest sequence": "WP_063864652.1", "Name of closest sequence": "extended-spectrum class A beta-lactamase SHV-165", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9587, "Stop": 10024, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 146, "Reference sequence length": 286, "% Coverage of reference sequence": 51.05, "% Identity to reference sequence": 95.89, "Alignment length": 146, "Accession of closest sequence": "WP_063864692.1", "Name of closest sequence": "extended-spectrum class A beta-lactamase SHV-55", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9587, "Stop": 10024, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 146, "Reference sequence length": 286, "% Coverage of reference sequence": 51.05, "% Identity to reference sequence": 95.89, "Alignment length": 146, "Accession of closest sequence": "WP_063864698.1", "Name of closest sequence": "extended-spectrum class A beta-lactamase SHV-64", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9587, "Stop": 10024, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 146, "Reference sequence length": 286, "% Coverage of reference sequence": 51.05, "% Identity to reference sequence": 95.89, "Alignment length": 146, "Accession of closest sequence": "WP_063864700.1", "Name of closest sequence": "extended-spectrum class A beta-lactamase SHV-66", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9587, "Stop": 10024, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 146, "Reference sequence length": 286, "% Coverage of reference sequence": 51.05, "% Identity to reference sequence": 95.89, "Alignment length": 146, "Accession of closest sequence": "WP_268871888.1", "Name of closest sequence": "class A beta-lactamase SHV-230", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_37_polypolish", "Start": 18, "Stop": 569, "Strand": "+", "Gene symbol": "aac(6')-Ib3", "Sequence name": "aminoglycoside N-acetyltransferase AAC(6')-Ib3", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "AMINOGLYCOSIDE", "Subclass": "AMIKACIN/KANAMYCIN/TOBRAMYCIN", "Method": "ALLELEX", "Target length": 184, "Reference sequence length": 184, "% Coverage of reference sequence": 100.0, "% Identity to reference sequence": 100.0, "Alignment length": 184, "Accession of closest sequence": "WP_032488579.1", "Name of closest sequence": "aminoglycoside N-acetyltransferase AAC(6')-Ib3", "HMM id": null, "HMM description": null, "Hierarchy node": "aac(6')-Ib3"}, {"Protein identifier": null, "Contig id": "contig_37_polypolish", "Start": 642, "Stop": 1424, "Strand": "+", "Gene symbol": "aadA1", "Sequence name": "ANT(3'')-Ia family aminoglycoside nucleotidyltransferase AadA1", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "AMINOGLYCOSIDE", "Subclass": "STREPTOMYCIN", "Method": "BLASTX", "Target length": 261, "Reference sequence length": 262, "% Coverage of reference sequence": 100.0, "% Identity to reference sequence": 97.71, "Alignment length": 262, "Accession of closest sequence": "WP_001206315.1", "Name of closest sequence": "ANT(3'')-Ia family aminoglycoside nucleotidyltransferase AadA1", "HMM id": null, "HMM description": null, "Hierarchy node": "aadA1"}, {"Protein identifier": null, "Contig id": "contig_37_polypolish", "Start": 3006, "Stop": 3863, "Strand": "+", "Gene symbol": "blaTEM-1", "Sequence name": "broad-spectrum class A beta-lactamase TEM-1", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "ALLELEX", "Target length": 286, "Reference sequence length": 286, "% Coverage of reference sequence": 100.0, "% Identity to reference sequence": 100.0, "Alignment length": 286, "Accession of closest sequence": "WP_000027057.1", "Name of closest sequence": "broad-spectrum class A beta-lactamase TEM-1", "HMM id": null, "HMM description": null, "Hierarchy node": "blaTEM-1"}, {"Protein identifier": null, "Contig id": "contig_37_polypolish", "Start": 8924, "Stop": 9133, "Strand": "-", "Gene symbol": "merC", "Sequence name": "organomercurial transporter MerC", "Scope": "plus", "Element type": "STRESS", "Element subtype": "METAL", "Class": "MERCURY", "Subclass": "ORGANOMERCURY", "Method": "PARTIALX", "Target length": 70, "Reference sequence length": 140, "% Coverage of reference sequence": 50.0, "% Identity to reference sequence": 90.0, "Alignment length": 70, "Accession of closest sequence": "AAC33908.1", "Name of closest sequence": "organomercurial transporter MerC", "HMM id": null, "HMM description": null, "Hierarchy node": "merC"}, {"Protein identifier": null, "Contig id": "contig_39_polypolish", "Start": 3496, "Stop": 3825, "Strand": "-", "Gene symbol": "qacE", "Sequence name": "quaternary ammonium compound efflux SMR transporter QacE", "Scope": "core", "Element type": "STRESS", "Element subtype": "BIOCIDE", "Class": "QUATERNARY AMMONIUM", "Subclass": "QUATERNARY AMMONIUM", "Method": "EXACTX", "Target length": 110, "Reference sequence length": 110, "% Coverage of reference sequence": 100.0, "% Identity to reference sequence": 100.0, "Alignment length": 110, "Accession of closest sequence": "WP_010890145.1", "Name of closest sequence": "quaternary ammonium compound efflux SMR transporter QacE", "HMM id": null, "HMM description": null, "Hierarchy node": "qacE"}, {"Protein identifier": null, "Contig id": "contig_39_polypolish", "Start": 4010, "Stop": 4327, "Strand": "-", "Gene symbol": "dfrA30", "Sequence name": "trimethoprim-resistant dihydrofolate reductase DfrA30", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "TRIMETHOPRIM", "Subclass": "TRIMETHOPRIM", "Method": "PARTIALX", "Target length": 106, "Reference sequence length": 157, "% Coverage of reference sequence": 67.52, "% Identity to reference sequence": 98.11, "Alignment length": 106, "Accession of closest sequence": "WP_063844408.1", "Name of closest sequence": "trimethoprim-resistant dihydrofolate reductase DfrA30", "HMM id": null, "HMM description": null, "Hierarchy node": "dfrA30"}, {"Protein identifier": null, "Contig id": "contig_40_polypolish", "Start": 632, "Stop": 1258, "Strand": "+", "Gene symbol": "aph(3')-Ia", "Sequence name": "aminoglycoside O-phosphotransferase APH(3')-Ia", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "AMINOGLYCOSIDE", "Subclass": "KANAMYCIN", "Method": "PARTIALX", "Target length": 209, "Reference sequence length": 271, "% Coverage of reference sequence": 77.12, "% Identity to reference sequence": 99.04, "Alignment length": 209, "Accession of closest sequence": "WP_000018329.1", "Name of closest sequence": "aminoglycoside O-phosphotransferase APH(3')-Ia", "HMM id": null, "HMM description": null, "Hierarchy node": "aph(3')-Ia"}, {"Protein identifier": null, "Contig id": "contig_40_polypolish", "Start": 632, "Stop": 1258, "Strand": "+", "Gene symbol": "aph(3')-Ia", "Sequence name": "aminoglycoside O-phosphotransferase APH(3')-Ia", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "AMINOGLYCOSIDE", "Subclass": "KANAMYCIN", "Method": "PARTIALX", "Target length": 209, "Reference sequence length": 271, "% Coverage of reference sequence": 77.12, "% Identity to reference sequence": 99.04, "Alignment length": 209, "Accession of closest sequence": "WP_063842148.1", "Name of closest sequence": "aminoglycoside O-phosphotransferase APH(3')-Ia", "HMM id": null, "HMM description": null, "Hierarchy node": "aph(3')-Ia"}, {"Protein identifier": null, "Contig id": "contig_40_polypolish", "Start": 2574, "Stop": 3359, "Strand": "+", "Gene symbol": "aph(3'')-Ib", "Sequence name": "aminoglycoside O-phosphotransferase APH(3'')-Ib", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "AMINOGLYCOSIDE", "Subclass": "STREPTOMYCIN", "Method": "BLASTX", "Target length": 262, "Reference sequence length": 267, "% Coverage of reference sequence": 98.13, "% Identity to reference sequence": 100.0, "Alignment length": 262, "Accession of closest sequence": "WP_001082319.1", "Name of closest sequence": "aminoglycoside O-phosphotransferase APH(3'')-Ib", "HMM id": null, "HMM description": null, "Hierarchy node": "aph(3'')-Ib"}, {"Protein identifier": null, "Contig id": "contig_40_polypolish", "Start": 3555, "Stop": 4103, "Strand": "+", "Gene symbol": "aph(6)-Id", "Sequence name": "aminoglycoside O-phosphotransferase APH(6)-Id", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "AMINOGLYCOSIDE", "Subclass": "STREPTOMYCIN", "Method": "PARTIALX", "Target length": 183, "Reference sequence length": 278, "% Coverage of reference sequence": 65.83, "% Identity to reference sequence": 98.91, "Alignment length": 183, "Accession of closest sequence": "WP_000480968.1", "Name of closest sequence": "aminoglycoside O-phosphotransferase APH(6)-Id", "HMM id": null, "HMM description": null, "Hierarchy node": "aph(6)-Id"}, {"Protein identifier": null, "Contig id": "contig_40_polypolish", "Start": 3555, "Stop": 4103, "Strand": "+", "Gene symbol": "aph(6)-Id", "Sequence name": "aminoglycoside O-phosphotransferase APH(6)-Id", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "AMINOGLYCOSIDE", "Subclass": "STREPTOMYCIN", "Method": "PARTIALX", "Target length": 183, "Reference sequence length": 278, "% Coverage of reference sequence": 65.83, "% Identity to reference sequence": 98.91, "Alignment length": 183, "Accession of closest sequence": "WP_000480972.1", "Name of closest sequence": "aminoglycoside O-phosphotransferase APH(6)-Id", "HMM id": null, "HMM description": null, "Hierarchy node": "aph(6)-Id"}, {"Protein identifier": null, "Contig id": "contig_40_polypolish", "Start": 3555, "Stop": 4103, "Strand": "+", "Gene symbol": "aph(6)-Id", "Sequence name": "aminoglycoside O-phosphotransferase APH(6)-Id", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "AMINOGLYCOSIDE", "Subclass": "STREPTOMYCIN", "Method": "PARTIALX", "Target length": 183, "Reference sequence length": 278, "% Coverage of reference sequence": 65.83, "% Identity to reference sequence": 98.91, "Alignment length": 183, "Accession of closest sequence": "WP_063842183.1", "Name of closest sequence": "aminoglycoside O-phosphotransferase APH(6)-Id", "HMM id": null, "HMM description": null, "Hierarchy node": "aph(6)-Id"}, {"Protein identifier": null, "Contig id": "contig_41_polypolish", "Start": 100023, "Stop": 100541, "Strand": "-", "Gene symbol": "terD", "Sequence name": "tellurium resistance membrane protein TerD", "Scope": "plus", "Element type": "STRESS", "Element subtype": "METAL", "Class": "TELLURIUM", "Subclass": "TELLURIUM", "Method": "BLASTX", "Target length": 173, "Reference sequence length": 192, "% Coverage of reference sequence": 90.1, "% Identity to reference sequence": 98.84, "Alignment length": 173, "Accession of closest sequence": "AAA98292.1", "Name of closest sequence": "tellurium resistance membrane protein TerD", "HMM id": null, "HMM description": null, "Hierarchy node": "terD"}]}, {"name": "point_mutation_report", "file_path": "tests/data/dummy/amrfinderplus/AMRFinderPlus_Point_mutation_report.tsv", "hid": "12345", "galaxy_id": null, "content": [{"Protein identifier": null, "Contig id": "contig_107_polypolish", "Start": 5, "Stop": 861, "Strand": "-", "Gene symbol": "23S_A2074A", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 857, "Reference sequence length": 2912, "% Coverage of reference sequence": 29.36, "% Identity to reference sequence": 81.82, "Alignment length": 869, "Accession of closest sequence": "NC_022347.1:1040292-1037381", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_107_polypolish", "Start": 5, "Stop": 861, "Strand": "-", "Gene symbol": "23S_A2074A", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 857, "Reference sequence length": 2912, "% Coverage of reference sequence": 29.36, "% Identity to reference sequence": 81.95, "Alignment length": 870, "Accession of closest sequence": "NC_002163.1:396449-399360", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_107_polypolish", "Start": 5, "Stop": 861, "Strand": "-", "Gene symbol": "23S_A2075A", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 857, "Reference sequence length": 2912, "% Coverage of reference sequence": 29.36, "% Identity to reference sequence": 81.82, "Alignment length": 869, "Accession of closest sequence": "NC_022347.1:1040292-1037381", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_107_polypolish", "Start": 5, "Stop": 861, "Strand": "-", "Gene symbol": "23S_A2075A", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 857, "Reference sequence length": 2912, "% Coverage of reference sequence": 29.36, "% Identity to reference sequence": 81.95, "Alignment length": 870, "Accession of closest sequence": "NC_002163.1:396449-399360", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_107_polypolish", "Start": 5, "Stop": 861, "Strand": "-", "Gene symbol": "23S_C2627C", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 857, "Reference sequence length": 2912, "% Coverage of reference sequence": 29.36, "% Identity to reference sequence": 81.82, "Alignment length": 869, "Accession of closest sequence": "NC_022347.1:1040292-1037381", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_107_polypolish", "Start": 5, "Stop": 861, "Strand": "-", "Gene symbol": "23S_C2627C", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 857, "Reference sequence length": 2912, "% Coverage of reference sequence": 29.36, "% Identity to reference sequence": 81.95, "Alignment length": 870, "Accession of closest sequence": "NC_002163.1:396449-399360", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_10_polypolish", "Start": 345, "Stop": 1334, "Strand": "-", "Gene symbol": "23S_A2074A", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 990, "Reference sequence length": 2912, "% Coverage of reference sequence": 33.93, "% Identity to reference sequence": 80.56, "Alignment length": 1003, "Accession of closest sequence": "NC_002163.1:396449-399360", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_10_polypolish", "Start": 345, "Stop": 1334, "Strand": "-", "Gene symbol": "23S_A2075A", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 990, "Reference sequence length": 2912, "% Coverage of reference sequence": 33.93, "% Identity to reference sequence": 80.56, "Alignment length": 1003, "Accession of closest sequence": "NC_002163.1:396449-399360", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_10_polypolish", "Start": 345, "Stop": 1334, "Strand": "-", "Gene symbol": "23S_C2627C", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 990, "Reference sequence length": 2912, "% Coverage of reference sequence": 33.93, "% Identity to reference sequence": 80.56, "Alignment length": 1003, "Accession of closest sequence": "NC_002163.1:396449-399360", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_10_polypolish", "Start": 416, "Stop": 1334, "Strand": "-", "Gene symbol": "23S_A2074A", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 919, "Reference sequence length": 2912, "% Coverage of reference sequence": 31.49, "% Identity to reference sequence": 81.1, "Alignment length": 931, "Accession of closest sequence": "NC_022347.1:1040292-1037381", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_10_polypolish", "Start": 416, "Stop": 1334, "Strand": "-", "Gene symbol": "23S_A2075A", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 919, "Reference sequence length": 2912, "% Coverage of reference sequence": 31.49, "% Identity to reference sequence": 81.1, "Alignment length": 931, "Accession of closest sequence": "NC_022347.1:1040292-1037381", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_10_polypolish", "Start": 416, "Stop": 1334, "Strand": "-", "Gene symbol": "23S_C2627C", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 919, "Reference sequence length": 2912, "% Coverage of reference sequence": 31.49, "% Identity to reference sequence": 81.1, "Alignment length": 931, "Accession of closest sequence": "NC_022347.1:1040292-1037381", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_11_polypolish", "Start": 1319, "Stop": 2308, "Strand": "-", "Gene symbol": "23S_A2074A", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 990, "Reference sequence length": 2912, "% Coverage of reference sequence": 33.93, "% Identity to reference sequence": 80.56, "Alignment length": 1003, "Accession of closest sequence": "NC_002163.1:396449-399360", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_11_polypolish", "Start": 1319, "Stop": 2308, "Strand": "-", "Gene symbol": "23S_A2075A", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 990, "Reference sequence length": 2912, "% Coverage of reference sequence": 33.93, "% Identity to reference sequence": 80.56, "Alignment length": 1003, "Accession of closest sequence": "NC_002163.1:396449-399360", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_11_polypolish", "Start": 1319, "Stop": 2308, "Strand": "-", "Gene symbol": "23S_C2627C", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 990, "Reference sequence length": 2912, "% Coverage of reference sequence": 33.93, "% Identity to reference sequence": 80.56, "Alignment length": 1003, "Accession of closest sequence": "NC_002163.1:396449-399360", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_11_polypolish", "Start": 1390, "Stop": 2308, "Strand": "-", "Gene symbol": "23S_A2074A", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 919, "Reference sequence length": 2912, "% Coverage of reference sequence": 31.49, "% Identity to reference sequence": 81.1, "Alignment length": 931, "Accession of closest sequence": "NC_022347.1:1040292-1037381", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_11_polypolish", "Start": 1390, "Stop": 2308, "Strand": "-", "Gene symbol": "23S_A2075A", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 919, "Reference sequence length": 2912, "% Coverage of reference sequence": 31.49, "% Identity to reference sequence": 81.1, "Alignment length": 931, "Accession of closest sequence": "NC_022347.1:1040292-1037381", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_11_polypolish", "Start": 1390, "Stop": 2308, "Strand": "-", "Gene symbol": "23S_C2627C", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 919, "Reference sequence length": 2912, "% Coverage of reference sequence": 31.49, "% Identity to reference sequence": 81.1, "Alignment length": 931, "Accession of closest sequence": "NC_022347.1:1040292-1037381", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_12_polypolish", "Start": 61, "Stop": 472, "Strand": "-", "Gene symbol": "23S_A2074A", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 412, "Reference sequence length": 2912, "% Coverage of reference sequence": 14.08, "% Identity to reference sequence": 82.01, "Alignment length": 417, "Accession of closest sequence": "NC_022347.1:1040292-1037381", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_12_polypolish", "Start": 61, "Stop": 472, "Strand": "-", "Gene symbol": "23S_A2074A", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 412, "Reference sequence length": 2912, "% Coverage of reference sequence": 14.08, "% Identity to reference sequence": 82.3, "Alignment length": 418, "Accession of closest sequence": "NC_002163.1:396449-399360", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_12_polypolish", "Start": 61, "Stop": 472, "Strand": "-", "Gene symbol": "23S_A2075A", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 412, "Reference sequence length": 2912, "% Coverage of reference sequence": 14.08, "% Identity to reference sequence": 82.01, "Alignment length": 417, "Accession of closest sequence": "NC_022347.1:1040292-1037381", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_12_polypolish", "Start": 61, "Stop": 472, "Strand": "-", "Gene symbol": "23S_A2075A", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 412, "Reference sequence length": 2912, "% Coverage of reference sequence": 14.08, "% Identity to reference sequence": 82.3, "Alignment length": 418, "Accession of closest sequence": "NC_002163.1:396449-399360", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_7_polypolish", "Start": 39847, "Stop": 40836, "Strand": "-", "Gene symbol": "23S_A2074A", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 990, "Reference sequence length": 2912, "% Coverage of reference sequence": 33.93, "% Identity to reference sequence": 80.56, "Alignment length": 1003, "Accession of closest sequence": "NC_002163.1:396449-399360", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_7_polypolish", "Start": 39847, "Stop": 40836, "Strand": "-", "Gene symbol": "23S_A2075A", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 990, "Reference sequence length": 2912, "% Coverage of reference sequence": 33.93, "% Identity to reference sequence": 80.56, "Alignment length": 1003, "Accession of closest sequence": "NC_002163.1:396449-399360", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_7_polypolish", "Start": 39847, "Stop": 40836, "Strand": "-", "Gene symbol": "23S_C2627C", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 990, "Reference sequence length": 2912, "% Coverage of reference sequence": 33.93, "% Identity to reference sequence": 80.56, "Alignment length": 1003, "Accession of closest sequence": "NC_002163.1:396449-399360", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_7_polypolish", "Start": 39918, "Stop": 40836, "Strand": "-", "Gene symbol": "23S_A2074A", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 919, "Reference sequence length": 2912, "% Coverage of reference sequence": 31.49, "% Identity to reference sequence": 81.1, "Alignment length": 931, "Accession of closest sequence": "NC_022347.1:1040292-1037381", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_7_polypolish", "Start": 39918, "Stop": 40836, "Strand": "-", "Gene symbol": "23S_A2075A", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 919, "Reference sequence length": 2912, "% Coverage of reference sequence": 31.49, "% Identity to reference sequence": 81.1, "Alignment length": 931, "Accession of closest sequence": "NC_022347.1:1040292-1037381", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_7_polypolish", "Start": 39918, "Stop": 40836, "Strand": "-", "Gene symbol": "23S_C2627C", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 919, "Reference sequence length": 2912, "% Coverage of reference sequence": 31.49, "% Identity to reference sequence": 81.1, "Alignment length": 931, "Accession of closest sequence": "NC_022347.1:1040292-1037381", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_82_polypolish", "Start": 31069, "Stop": 31987, "Strand": "+", "Gene symbol": "23S_A2074A", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 919, "Reference sequence length": 2912, "% Coverage of reference sequence": 31.49, "% Identity to reference sequence": 81.1, "Alignment length": 931, "Accession of closest sequence": "NC_022347.1:1040292-1037381", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_82_polypolish", "Start": 31069, "Stop": 31987, "Strand": "+", "Gene symbol": "23S_A2075A", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 919, "Reference sequence length": 2912, "% Coverage of reference sequence": 31.49, "% Identity to reference sequence": 81.1, "Alignment length": 931, "Accession of closest sequence": "NC_022347.1:1040292-1037381", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_82_polypolish", "Start": 31069, "Stop": 31987, "Strand": "+", "Gene symbol": "23S_C2627C", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 919, "Reference sequence length": 2912, "% Coverage of reference sequence": 31.49, "% Identity to reference sequence": 81.1, "Alignment length": 931, "Accession of closest sequence": "NC_022347.1:1040292-1037381", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_82_polypolish", "Start": 31069, "Stop": 32058, "Strand": "+", "Gene symbol": "23S_A2074A", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 990, "Reference sequence length": 2912, "% Coverage of reference sequence": 33.93, "% Identity to reference sequence": 80.56, "Alignment length": 1003, "Accession of closest sequence": "NC_002163.1:396449-399360", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_82_polypolish", "Start": 31069, "Stop": 32058, "Strand": "+", "Gene symbol": "23S_A2075A", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 990, "Reference sequence length": 2912, "% Coverage of reference sequence": 33.93, "% Identity to reference sequence": 80.56, "Alignment length": 1003, "Accession of closest sequence": "NC_002163.1:396449-399360", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_82_polypolish", "Start": 31069, "Stop": 32058, "Strand": "+", "Gene symbol": "23S_C2627C", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 990, "Reference sequence length": 2912, "% Coverage of reference sequence": 33.93, "% Identity to reference sequence": 80.56, "Alignment length": 1003, "Accession of closest sequence": "NC_002163.1:396449-399360", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}]}, {"name": "nucleotide_sequence", "file_path": "tests/data/dummy/amrfinderplus/AMRFinderPlus_Nucleotide_identified_sequences.fasta", "hid": "12345", "galaxy_id": null, "content": [{"Name": "contig_153_polypolish:4412-4645", "Contig id": "contig_153_polypolish", "Start": "4412", "Stop": "4645", "Strand": "-", "Gene symbol": "merE", "Sequence name": "broad-spectrum mercury transporter MerE", "Length": 234, "Sequence": "ATGAACAGCCCAGAGCACTTGCCGTCTGAGACGCACAAACCGATCACCGGCTACTTGTGGGGCGCGCTGGCCGTGCTCACCTGTCCCTGCCATTTGCCGATTCTCGCCATTGTGCTAGCCGGCACGACGGCCGGCGCGTTCATCGGGGAGCACTGGGGTATTGCAGCCCTCACGCTGACCGGCTTGTTTGTCCTGTCTGTGACGCGGCTGCTGCGGGCCTTCAAGGGAAGATCA"}, {"Name": "contig_153_polypolish:7613-7846", "Contig id": "contig_153_polypolish", "Start": "7613", "Stop": "7846", "Strand": "-", "Gene symbol": "merT", "Sequence name": "mercuric transport protein MerT", "Length": 234, "Sequence": "TCTGAACCACAAAACGGGCGCGGCGCGTTCTTCGCCGGTGGGCTGGCCGCCATTCTTGCGTCGGCCTGCTGCCCGGGGCCGCTGGTTTTGATCGCCTTGGGGTTCAGCGGGGCATGGATCGGCAACCTGACGGTGCTGGAACCCTATCGCCCGATCTTCATCGGCGCAGCGCTGGTCGCGCTGCTTTTCGCCCGGCGGCGCATCTACCGCCCGGCGCAAGCCTGCCAAACCGGG"}, {"Name": "contig_160_polypolish:86415-86654", "Contig id": "contig_160_polypolish", "Start": "86415", "Stop": "86654", "Strand": "-", "Gene symbol": "fosA", "Sequence name": "FosA5 family fosfomycin resistance glutathione transferase", "Length": 240, "Sequence": "GCAGTCAGCCAGCTGGCGCCGAGCGTGGCGTTTTATCAGCAGCTGTTGGGCATGACGCTGCACGCCCGCTGGGACAGCGGCGCCTATCTCTCCTGCGGCGATTTGTGGCTGTGCCTGTCGCTGGATCCGCAGCGGCGCATCACCCCGCCGGAGGAGAGCGACTACACCCATTATGCGTTTAGCATTAGCGAGGCGGATTTCGCTAGCTTCGCCGCCCGCCTTGAGGTTGCCGGCGTCAGC"}, {"Name": "contig_30_polypolish:13708-14433", "Contig id": "contig_30_polypolish", "Start": "13708", "Stop": "14433", "Strand": "+", "Gene symbol": "blaCTX-M", "Sequence name": "CTX-M family extended-spectrum class A beta-lactamase", "Length": 726, "Sequence": "AAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCCGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCG"}, {"Name": "contig_30_polypolish:17856-18287", "Contig id": "contig_30_polypolish", "Start": "17856", "Stop": "18287", "Strand": "+", "Gene symbol": "merR", "Sequence name": "mercury resistance transcriptional regulator MerR", "Length": 432, "Sequence": "ATGGAAAATAATTTGGAAAACCTGACCATTGGCGTTTTTGCCAAGGCGGCCGGGGTCAACGTGGAGACAATCCGCTTCTATCAGCGCAAGGGCCTGTTGCGGGAACCGGACAAGCCTTACGGCAGCATCCGCCGCTATGGGGAGGCGGACGTGGTTCGGGTGAAATTCGTGAAATCGGCACAGCGGCTGGGGTTCAGTCTGGACGAGATTGCCGAGCTGTTGCGGCTCGACGATGGCACCCACTGCGAGGAGGCCAGCAGCCCGGCCGAACACAAGCTCAAGGACGTGCGCGAGAAGATGGCCGACTTGGCGCGCATGGAAACCGTGCTGTCTGAACTCGTGTGCGCCTGCCATGCACGCAAGGGGAATGTTTCCTGCCCGTTGATCGCGTCACTACAGGGCGAAGCAGGCCCGGCAAGGTCAGCTATGCCT"}, {"Name": "contig_30_polypolish:20698-21348", "Contig id": "contig_30_polypolish", "Start": "20698", "Stop": "21348", "Strand": "+", "Gene symbol": "catA1", "Sequence name": "type A-1 chloramphenicol O-acetyltransferase", "Length": 651, "Sequence": "GAAAAAATCACTGGATATACCACCGTTGATATATCCCAATGGCATCGTAAAGAACATTTTGAGGCATTTCAGTCAGTTGCTCAATGTACCTATAACCAGACCGTTCAGCTGGATATTACGGCCTTTTTAAAGACCGTAAAGAAAAATAAGCACAAGTTTTATCCGGCCTTTATTCACATTCTTGCCCGCCTGATGAATGCTCATCCGGAATTCCGTATGGCAATGAAAGACGGTGAGCTGGTGATATGGGATAGTGTTCACCCTTGTTACACCGTTTTCCATGAGCAAACTGAAACGTTTTCATCGCTCTGGAGTGAATACCACGACGATTTCCGGCAGTTTCTACACATATATTCGCAAGATGTGGCGTGTTACGGTGAAAACCGGCCTATTTCCCTAAAGGGTTTATTGAGAATATGTTTTTCGTCTCAGCCAATCCCACGGGTGAGTTTCACCAGTTTTGATTTAAACGTGGCCAATATGGACAACTTCTTCGCCCCCGTTTTCACCATGGGCAAATATTATACGCAAGGCGACAAGGTGCTGATGCCGCTGGCGATTCAGGTTCATCATGCCGTTTGTGATGGCTTCCATGTCGGCAGAATGCTTAATGAATTACAACAGTACTGCGATGAGTGGCAGGGCGGGGCG"}, {"Name": "contig_30_polypolish:3018-3344", "Contig id": "contig_30_polypolish", "Start": "3018", "Stop": "3344", "Strand": "+", "Gene symbol": "merR", "Sequence name": "mercury resistance transcriptional regulator MerR", "Length": 327, "Sequence": "TTTGCCAAGGCGGCCGGGGTCAACGTGGAGACAATCCGCTTCTATCAGCGCAAGGGCCTGTTGCGGGAACCGGACAAGCCTTACGGCGGCATCCGCCGCTATGGGGAGGCGGACGTGGTTCGGGTGAAATTCGTGAAATCGGCACAGCGGCTGGGGTTCAGTCTGGACGAGATTGCCGAGCTGTTGCGGCTCGACGATGGCACCCACTGCGAGGAGGCCAGCAGCTTGGCCGAACACAAGCTCAAGGACGTGCGCGAGAAGATGGCCGACTTGGCGCGCATGGAAACCGTGCTGTCTGAACTCGTGTGCGCCTGCCATGCACGAAGG"}, {"Name": "contig_30_polypolish:5821-6243", "Contig id": "contig_30_polypolish", "Start": "5821", "Stop": "6243", "Strand": "+", "Gene symbol": "catA1", "Sequence name": "type A-1 chloramphenicol O-acetyltransferase", "Length": 423, "Sequence": "GAAAAAATCACTGGATATACCACCGTTGATATATCCCAATGGCATCGTAAAGAACATTTTGAGGCATTTCAGTCAGTTGCTCAATGTACCTATAACCAGACCGTTCAGCTGGATATTACGGCCTTTTTAAAGACCGTAAAGAAAAATAAGCACAAGTTTTATCCGGCCTTTATTCACATTCTTGCCCGCCTGATGAATGCTCATCCGGAATTCCGTATGGCAATGAAAGACGGTGAGCTGGTGATATGGGATAGTGTTCACCCTTGTTACACCGTTTTCCATGAGCAAACTGAAACGTTTTCATCGCTCTGGAGTGAATACCACGACGATTTCCGGCAGTTTCTACACATATATTCGCAAGATGTGGCGTGTTACGGTGAAAACACGGCCTATTTCCCTAAAGGGTTTATTGAGAATATGTTT"}, {"Name": "contig_35_polypolish:4787-5644", "Contig id": "contig_35_polypolish", "Start": "4787", "Stop": "5644", "Strand": "-", "Gene symbol": "aac(3)-IIe", "Sequence name": "aminoglycoside N-acetyltransferase AAC(3)-IIe", "Length": 858, "Sequence": "ATGCATACGCGGAAGGCAATAACGGAGGCAATTCGAAAATTAGGAGTCCAAACCGGTGACCTGTTGATGGTGCATGCCTCACTTAAAGCGATTGGTCCGGTCGAAGGAGGAGCGGAGACGGTCGTTGCCGCGTTACGCTCCGCGGTTGGGCCGACTGGCACTGTGATGGGATACGCGTCGTGGGACCGATCACCCTACGAGGAGACTCTGAATGGCGCTCGGTTGGATGACAAAGCCCGCCGTACCTGGCCGCCGTTCGATCCCGCAACGGCCGGGACTTACCGTGGGTTCGGCCTGCTGAATCAATTTCTGGTTCAAGCCCCCGGCGCGCGGCGCAGCGCGCACCCCGATGCATCGATGGTCGCGGTTGGTCCGCTAGCTGAAACGCTGACGGAGCCTCACGAACTCGGTCACGCCTTGGGGGAAGGGTCGCCCGTCGAGCGGTTCGTCCGCCTTGGCGGGAAGGCCCTGCTGTTGGGTGCGCCGCTAAACTCCGTTACCGCATTGCACTACGCCGAGGCGGTTGCGGATATCCCCAACAAACGATGGGTGACGTATGAGATGCCGATGCTTGGAAGAAACGGTGAAGTCGCCTGGAAAACGGCATCAGAATACGATTCAAACGGCATTCTCGATTGCTTTGCTATCGAAGGAAAGCCGGATGCGGTCGAAACTATAGCAAATGCTTACGTGAAGCTCGGTCGCCATCGAGAAGGTGTCGTGGGCTTTGCTCAGTGCTACCTGTTCGACGCGCAGGACATCGTGACGTTCGGCGTCACCTATCTTGAGAAGCACTTCGGAGCCACTCCGATCGTGCCAGCACACGAAGCCGCCCAGCGCTCTTGCGAGCCTTCCGGT"}, {"Name": "contig_36_polypolish:9168-9608", "Contig id": "contig_36_polypolish", "Start": "9168", "Stop": "9608", "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Length": 441, "Sequence": "ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCCGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTT"}, {"Name": "contig_36_polypolish:9587-10024", "Contig id": "contig_36_polypolish", "Start": "9587", "Stop": "10024", "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Length": 438, "Sequence": "CCCCGCAGGATTGACTGCCTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGC"}, {"Name": "contig_37_polypolish:18-569", "Contig id": "contig_37_polypolish", "Start": "18", "Stop": "569", "Strand": "+", "Gene symbol": "aac(6')-Ib3", "Sequence name": "aminoglycoside N-acetyltransferase AAC(6')-Ib3", "Length": 552, "Sequence": "GTGACCAACAGCAACGATTCCGTCACACTGCGCCTCATGACTGAGCATGACCTTGCGATGCTCTATGAGTGGCTAAATCGATCTCATATCGTCGAGTGGTGGGGCGGAGAAGAAGCACGCCCGACACTTGCTGACGTACAGGAACAGTACTTGCCAAGCGTTTTAGCGCAAGAGTCCGTCACTCCATACATTGCAATGCTGAATGGAGAGCCGATTGGGTATGCCCAGTCGTACGTTGCTCTTGGAAGCGGGGACGGATGGTGGGAAGAAGAAACCGATCCAGGAGTACGCGGAATAGACCAGTTACTGGCGAATGCATCACAACTGGGCAAAGGCTTGGGAACCAAGCTGGTTCGAGCTCTGGTTGAGTTGCTGTTCAATGATCCCGAGGTCACCAAGATCCAAACGGACCCGTCGCCGAGCAACTTGCGAGCGATCCGATGCTACGAGAAAGCGGGGTTTGAGAGGCAAGGTACCGTAACCACCCCAGATGGTCCAGCCGTGTACATGGTTCAAACACGCCAGGCATTCGAGCGAACACGCAGTGATGCC"}, {"Name": "contig_37_polypolish:3006-3863", "Contig id": "contig_37_polypolish", "Start": "3006", "Stop": "3863", "Strand": "+", "Gene symbol": "blaTEM-1", "Sequence name": "broad-spectrum class A beta-lactamase TEM-1", "Length": 858, "Sequence": "ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGG"}, {"Name": "contig_37_polypolish:642-1424", "Contig id": "contig_37_polypolish", "Start": "642", "Stop": "1424", "Strand": "+", "Gene symbol": "aadA1", "Sequence name": "ANT(3'')-Ia family aminoglycoside nucleotidyltransferase AadA1", "Length": 783, "Sequence": "ATGAGGGAAGCGGTGATCGCCGAAGTATCGACTCAACTATCAGAGGTAGTTGGCGTCATCGAGCGCCATCTCGAACCGACGTTGCTGGCCGTACATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCACACAGTGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTGGAAACTTCGGCTTCCCGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGGCAGGCTTATCTTGGACAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTTCACTACGTGAAAGGCGAGATCACCAAGGTAGTCGGCAAA"}, {"Name": "contig_37_polypolish:8924-9133", "Contig id": "contig_37_polypolish", "Start": "8924", "Stop": "9133", "Strand": "-", "Gene symbol": "merC", "Sequence name": "organomercurial transporter MerC", "Length": 210, "Sequence": "CTTGAGCCAGTACGAGGACTGTTCATCAGCCGCCTGCTGCCGCTGTTTGCCGCGCTGGCCTTCTCGGCGAACGCGCTGGGTTGGTTCAGTCATCGGCAATGGCTGCGCAGTCTGCTCGGCATGATCGGCCCGGCCATCGTGTTTGCGGCCACGGTCTGGCTGCTCGGCAACTGGTGGACGGCGAACCTGATGTACGTCGGCACCGGCCTT"}, {"Name": "contig_39_polypolish:3496-3825", "Contig id": "contig_39_polypolish", "Start": "3496", "Stop": "3825", "Strand": "-", "Gene symbol": "qacE", "Sequence name": "quaternary ammonium compound efflux SMR transporter QacE", "Length": 330, "Sequence": "ATGAAAGGCTGGCTTTTTCTTGTTATCGCAATAGTTGGCGAAGTAATCGCAACATCCGCATTAAAATCTAGCGAGGGCTTTACTAAGCTTGCCCCTTCCGCCGTTGTCATAATCGGTTATGGCATCGCATTTTATTTTCTTTCTCTGGTTCTGAAATCCATCCCTGTCGGTGTTGCTTATGCAGTCTGGTCGGGACTCGGCGTCGTCATAATTACAGCCATTGCCTGGTTGCTTCATGGGCAAAAGCTTGATGCGTGGGGCTTTGTAGGTATGGGGCTCATAGTTAGTGGTGTAGTAGTTTTAAACTTGCTTTCCAAAGCAAGTGCCCAC"}, {"Name": "contig_39_polypolish:4010-4327", "Contig id": "contig_39_polypolish", "Start": "4010", "Stop": "4327", "Strand": "-", "Gene symbol": "dfrA30", "Sequence name": "trimethoprim-resistant dihydrofolate reductase DfrA30", "Length": 318, "Sequence": "GGGGCGCTCCCCAATAGGAAATACGCGGTCGTTACTCGCTCAGCTCGGACGGCCAATAATGACAACGTAGTAGTATTCCCGTCGATCGAAGAGGCCATGGGCGGTCTAGCTAAACTCACCGGTCACGTTATAGTGTCTGGTGGCGGGGAGATTTACAGAGAAACGTTGCCCATGGCCTCTACGCTCCATGTATCGACGATCGACATTGAGCCAGAAGGGGATGTTTTCTTCCCGAATATTCCCAACTTCTTCGAAGTTGTTTTTGAGCAACATTTTAGTTCAAACATTAACTATTGCTATCAAATTTGGAAAAAGGGT"}, {"Name": "contig_40_polypolish:2574-3359", "Contig id": "contig_40_polypolish", "Start": "2574", "Stop": "3359", "Strand": "+", "Gene symbol": "aph(3'')-Ib", "Sequence name": "aminoglycoside O-phosphotransferase APH(3'')-Ib", "Length": 786, "Sequence": "ATATTTTTTGGTGAATCGCATTCTGACTGGTTGCCTGTCAGAGGCGGAGAATCTGGTGATTTTGTTTTTCGACGTGGTGACGGGCATGCCTTCGCGAAAATCGCACCTGCTTCCCGCCGCGGTGAGCTCGCTGGAGAGCGTGACCGCCTCATTTGGCTCAAAGGTCGAGGTGTGGCTTGCCCCGAGGTGATCAACTGGCAGGAGGAACAGGAGGGTGCATGCTTGGTGATAACGGCAATTCCGGGAGTACCGGCGGCTGATCTGTCTGGAGCGGATTTGCTCAAAGCGTGGCCGTCAATGGGGCAGCAACTTGGCGCTGTTCACAGCCTATCGGTTGATCAATGTCCGTTTGAGCGCAGGCTGTCGCGAATGTTCGGACGCGCCGTTGATGTGGTGTCCCGCAATGCCGTCAATCCCGACTTCTTACCGGACGAGGACAAGAGTACGCCGCAGCTCGATCTTTTGGCTCGTGTCGAACGAGAGCTACCGGTGCGGCTCGACCAAGAGCGCACCGATATGGTTGTTTGCCATGGTGATCCCTGCATGCCGAACTTCATGGTGGACCCTAAAACTCTTCAATGCACGGGTCTGATCGACCTTGGGCGGCTCGGAACAGCAGATCGCTATGCCGATTTGGCACTCATGATTGCTAACGCCGAAGAGAACTGGGCAGCGCCAGATGAAGCAGAGCGCGCCTTCGCTGTCCTATTCAATGTATTGGGGATCGAAGCCCCCGACCGCGAACGCCTTGCCTTCTATCTGCGATTGGACCCTCTGACTTGGGGT"}, {"Name": "contig_40_polypolish:3555-4103", "Contig id": "contig_40_polypolish", "Start": "3555", "Stop": "4103", "Strand": "+", "Gene symbol": "aph(6)-Id", "Sequence name": "aminoglycoside O-phosphotransferase APH(6)-Id", "Length": 549, "Sequence": "GGAGCAGTCCGGTTGCTCGGTCGTGAGAACAATCTGATGTTGCTCGAATATGCCGGGGAGCGAATGCTCTCTCACATCGTTGCCGAGCACGGCGACTACCGAGCGACCGAAATTGCAGCGGAACTAATGGCGAAGCTGTATGCCGCATCTGAGGAACCCCTGCCTTCTGCCCTTCTCCCGATCCGGGATCGCTTTGCAGCTTTGTTTCAGCGGGCGCGCGATGATCAAAACGCAGGTTGTCAAACTGACTACGTCCACGCGGCGATTATAGCCGATCAAATGATGAGCAATGCCTCGGAACTGCGTGGGCTACATGGCGATCTGCATCATGAAAACATCATGTTCTCCAGTCGCGGCTGGCTGGTGATAGATCCCGTCGGTCTGGTCGGTGAAGTGGGCTTTGGCGCCGCCAATATGTTCTACGATCCGGCTGACAGAGACGACCTTTGTCTCGATCCTAGACGCATTGCACAGATGGCGGACGCATTCTCTCGTGCGCTGGACGTCGATCCGCGTCGCCTGCTCGACCGTGCGTACGCTTATGGGTGC"}, {"Name": "contig_40_polypolish:632-1258", "Contig id": "contig_40_polypolish", "Start": "632", "Stop": "1258", "Strand": "+", "Gene symbol": "aph(3')-Ia", "Sequence name": "aminoglycoside O-phosphotransferase APH(3')-Ia", "Length": 627, "Sequence": "ATGAGCCATATTCAACGGGAAACGTCTTGCTCGAGGCCGCGATTAAATTCCAACATGGATGCTGATTTATATGGGTATAAATGGGCTCGCGATAATGTCGGGCAATCAGGTGCGACAATCTATCGATTGTATGGGAAGCCCGATGCGCCAGAGTTGTTTCTGAAACATGGCAAAGGTAGCGTTGCCAATGATGTTACAGATGAGATGGTCAGACTAAACTGGCTGACGGAATTTATGCCTCTTCCGACCATCAAGCATTTTATCCGTACTCCTGATGATGCATGGTTACTCACCACTGCGATCCCCGGGAAAACAGCATTCCGGGTATTAGAAGAATATCCTGATTCAGGTGAAAATATTGTTGATGCGCTGGCAGTGTTCCTGCGCCGGTTGCATTCGATTCCTGTTTGTAATTGTCCTTTTAACAACGATCGCGTATTTCGTCTCGCTCAGGCGCAATCACGAATGAATAACGGTTTGGTTGATGCGAGTGATTTTGATGACGAGCGTAATGGCTGGCCTGTTGAACAAGTCTGGAAAGAAATGCATAAGCTTTTGCCATTCTCACCGGATTCAGTCGTCACTCATGGTGATTTCTCACTTGATAACCTTATTTTTGACGAGGGA"}, {"Name": "contig_41_polypolish:100023-100541", "Contig id": "contig_41_polypolish", "Start": "100023", "Stop": "100541", "Strand": "-", "Gene symbol": "terD", "Sequence name": "tellurium resistance membrane protein TerD", "Length": 519, "Sequence": "ATGAGCGTTTCACTATCTAAAGGCGGCAACGTTTCCCTGAGCAAAACCGCGCCAAGCATGAAAAACGTGCTGGTTGGCCTTGGCTGGGATGCACGTTCTACGGACGGTCAGGACTTTGACCTCGATGCTTCCGCATTTCTGCTGGCAGCCAATGGCAAGGTTCGTGGCGATGCAGATTTCATTTTCTATAACAACCTGAAATCTGCTGATGGTTCCGTTACTCATACCGGTGATAACCGTACCGGTGAAGGTGATGGCGACGATGAATCCCTCAAAATCAAACTGGACGCGGTACACGGGGATGTCGACAAAATTATTTTCGTTGTCACTATCCATGATGCTCAGGCTCGTCGCCAGAGCTTCGGTCAGGTTTCCGGCGCATTTATCCGTCTGGTGAATGATGACAATCAGACTGAAGTTGCTCGCTACGATCTGACAGAAGACGCTTCTACTGAAACTGCCATGCTGTTTGGGGAGCTGTATCGTCACAACGGAGAATGGAAATTCCGTGCGGTTGGC"}]}], "tool_has_database": true}] \ No newline at end of file
--- a/tooldistillator.xml Tue Apr 30 08:42:33 2024 +0000 +++ b/tooldistillator.xml Fri May 24 10:47:33 2024 +0000 @@ -20,7 +20,16 @@ '$tool.select_tool.input' --analysis_software_version '$tool.select_tool.analysis_software_version' --reference_database_version '$tool.select_tool.reference_database_version' - #if $tool.select_tool.tool_list == 'bakta' + #if $tool.select_tool.tool_list == 'amrfinderplus': + #if $tool.select_tool.point_mutation_report_path + --point_mutation_report_path '$tool.select_tool.point_mutation_report_path' + --point_mutation_report_hid '$tool.select_tool.point_mutation_report_path.hid' + #end if + #if $tool.select_tool.nucleotide_sequence_path + --nucleotide_sequence_path '$tool.select_tool.nucleotide_sequence_path' + --nucleotide_sequence_hid '$tool.select_tool.nucleotide_sequence_path.hid' + #end if + #elif $tool.select_tool.tool_list == 'bakta' #if $tool.select_tool.annotation_tabular_path --annotation_tabular_path '$tool.select_tool.annotation_tabular_path' --annotation_tabular_hid '$tool.select_tool.annotation_tabular_path.hid' @@ -191,21 +200,22 @@ <repeat name="tools" title="Tool" min="0"> <conditional name="select_tool"> <param name="tool_list" type="select" label="Available tools"> - <option value="abricate">abricate</option> - <option value="bakta">bakta</option> - <option value="bandage">bandage</option> - <option value="bracken">bracken</option> - <option value="fastp">fastp</option> - <option value="integronfinder2">integronfinder2</option> - <option value="isescan">isescan</option> - <option value="kraken2">kraken2</option> + <option value="abricate">Abricate</option> + <option value="amrfinderplus">AMRFinderPlus</option> + <option value="bakta">Bakta</option> + <option value="bandage">Bandage</option> + <option value="bracken">Bracken</option> + <option value="fastp">Fastp</option> + <option value="integronfinder2">Integronfinder2</option> + <option value="isescan">ISEScan</option> + <option value="kraken2">Kraken2</option> <option value="multiqc">MultiQC</option> - <option value="plasmidfinder">plasmidfinder</option> - <option value="quast">quast</option> - <option value="recentrifuge">recentrifuge</option> - <option value="refseqmasher">refseqmasher</option> - <option value="shovill">shovill</option> - <option value="staramr">staramr</option> + <option value="plasmidfinder">PlasmidFinder</option> + <option value="quast">Quast</option> + <option value="recentrifuge">Recentrifuge</option> + <option value="refseqmasher">RefSeqMasher</option> + <option value="shovill">Shovill</option> + <option value="staramr">Staramr</option> <option value="tabular_file">tabular_generic_file</option> </param> <when value="abricate"> @@ -213,6 +223,13 @@ <expand macro="analysis_software_version"/> <expand macro="reference_database_version"/> </when> + <when value="amrfinderplus"> + <param name="input" type="data" format="tabular" multiple="false" label="AMRFinderPlus report file" help="Tabular file from AMRFinderPlus output"/> + <param argument="--point_mutation_report_path" type="data" format="tabular" multiple="false" optional="true" label="AMRFinderPlus point mutation report file" help="AMRFinderPlus Tabular point mutation report file"/> + <param argument="--nucleotide_sequence_path" type="data" format="fasta" multiple="false" optional="true" label="AMRFinderPlus nucleotide identified sequence fasta file" help="AMRFinderPlus nucleotide identified sequence fasta file"/> + <expand macro="analysis_software_version"/> + <expand macro="reference_database_version"/> + </when> <when value="bakta"> <param name="input" type="data" format="json" multiple="false" label="Bakta report file" help="Json file from bakta output"/> <param argument="--annotation_tabular_path" type="data" format="tabular" multiple="false" optional="true" label="Bakta annotation file" help="Tabular annotation file"/> @@ -419,6 +436,16 @@ </repeat> <repeat name="tools"> <conditional name="select_tool"> + <param name="tool_list" value="amrfinderplus"/> + <param name="input" value="amrfinderplus/AMRFinderPlus_report.tsv" ftype="tabular"/> + <param name="point_mutation_report_path" value="amrfinderplus/AMRFinderPlus_Point_mutation_report.tsv" ftype="tabular"/> + <param name="nucleotide_sequence_path" value="amrfinderplus/AMRFinderPlus_Nucleotide_identified_sequences.fasta" ftype="fasta"/> + <param name="analysis_software_version" value="3.11.26"/> + <param name="reference_database_version" value="v3.11-2023-04-17.1"/> + </conditional> + </repeat> + <repeat name="tools"> + <conditional name="select_tool"> <param name="tool_list" value="bakta"/> <param name="input" value="bakta/bakta.json" ftype="json"/> <param name="annotation_tabular_path" value="bakta/bakta_annotation.tsv" ftype="tabular"/> @@ -568,22 +595,23 @@ </conditional> </repeat> </section> - <output_collection name="output_json" type="list" count="15"> + <output_collection name="output_json" type="list" count="16"> <expand macro="element_assert" name="abricate_0_output" text="Enterococcus faecalis V583"/> - <expand macro="element_assert" name="bakta_1_output" text="hypothetical protein"/> - <expand macro="element_assert" name="bandage_2_output" text="3042326"/> - <expand macro="element_assert" name="bracken_3_output" text="Staphylococcus_aureus"/> - <expand macro="element_assert" name="fastp_4_output" text="705053822"/> - <expand macro="element_assert" name="integronfinder2_5_output" text="2353.0"/> - <expand macro="element_assert" name="isescan_6_output" text="IS200/IS605"/> - <expand macro="element_assert" name="kraken2_7_output" text="Enterococcus_faecalis"/> - <expand macro="element_assert" name="plasmidfinder_8_output" text="repUS40_1_repB"/> - <expand macro="element_assert" name="quast_9_output" text="2944723"/> - <expand macro="element_assert" name="recentrifuge_10_output" text="6.4917947578"/> - <expand macro="element_assert" name="refseqmasher_11_output" text="GCF_000519925.1"/> - <expand macro="element_assert" name="shovill_12_output" text="436224"/> - <expand macro="element_assert" name="staramr_13_output" text="10_Enterococcus_faecalis_S17_L001"/> - <expand macro="element_assert" name="tabular_file_14_output" text="NP_814691"/> + <expand macro="element_assert" name="amrfinderplus_1_output" text="mercury resistance transcriptional regulator MerR"/> + <expand macro="element_assert" name="bakta_2_output" text="hypothetical protein"/> + <expand macro="element_assert" name="bandage_3_output" text="3042326"/> + <expand macro="element_assert" name="bracken_4_output" text="Staphylococcus_aureus"/> + <expand macro="element_assert" name="fastp_5_output" text="705053822"/> + <expand macro="element_assert" name="integronfinder2_6_output" text="2353.0"/> + <expand macro="element_assert" name="isescan_7_output" text="IS200/IS605"/> + <expand macro="element_assert" name="kraken2_8_output" text="Enterococcus_faecalis"/> + <expand macro="element_assert" name="plasmidfinder_9_output" text="repUS40_1_repB"/> + <expand macro="element_assert" name="quast_10_output" text="2944723"/> + <expand macro="element_assert" name="recentrifuge_11_output" text="6.4917947578"/> + <expand macro="element_assert" name="refseqmasher_12_output" text="GCF_000519925.1"/> + <expand macro="element_assert" name="shovill_13_output" text="436224"/> + <expand macro="element_assert" name="staramr_14_output" text="10_Enterococcus_faecalis_S17_L001"/> + <expand macro="element_assert" name="tabular_file_15_output" text="NP_814691"/> </output_collection> </test> @@ -596,12 +624,15 @@ This tool here is extracting information from output files of specific tools and exposing it as JSON files ** Tool input** -ToolDistillator can use several input type from at least 14 different tools : +ToolDistillator can use several input type from at least 15 different tools : +----------------+----------------+-------------------+------------------------------------------------------------+ | Tools | Version | Default input file| Optional files | ++----------------+----------------+-------------------+------------------------------------------------------------+ | Abricate | 1.0.1 | output.tsv | | +----------------+----------------+-------------------+------------------------------------------------------------+ +| AMRFinderPlus | 3.11.26 | report.tsv | point_mutation_report.tsv, nucleotide_sequence.fasta | ++----------------+----------------+-------------------+------------------------------------------------------------+ | Bakta | 1.7.0 | output.json | protein.faa, nucleotide.fna, annotation.gff3, summary.txt | +----------------+----------------+-------------------+------------------------------------------------------------+ | Bandage | 0.8.1 | info.txt | | @@ -616,13 +647,13 @@ +----------------+----------------+-------------------+------------------------------------------------------------+ | Kraken2 | 2.1.2 | taxonomy.tsv | reads_assignation.txt | +----------------+----------------+-------------------+------------------------------------------------------------+ -| Plasmidfinder | 2.1.6 | output.json | genome_hits.fasta, plasmid_hits.fasta | +| PlasmidFinder | 2.1.6 | output.json | genome_hits.fasta, plasmid_hits.fasta | +----------------+----------------+-------------------+------------------------------------------------------------+ | Quast | 5.2.0 | output.tsv | | +----------------+----------------+-------------------+------------------------------------------------------------+ | Recentrifuge | 1.10.0 | data.tsv | report.html, stat.tsv | +----------------+----------------+-------------------+------------------------------------------------------------+ -| Refseqmasher | 0.1.2 | output.tsv | | +| RefSeqMasher | 0.1.2 | output.tsv | | +----------------+----------------+-------------------+------------------------------------------------------------+ | Shovill | 1.1.0 | contigs.fasta | alignment.bam, contigs.gfa | +----------------+----------------+-------------------+------------------------------------------------------------+