| Next changeset 1:a37bb163d05d (2023-05-27) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14 |
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added:
amrfinderplus.xml macro.xml test-data/PROKKA_05252023.faa test-data/PROKKA_05252023.gff test-data/amrfinderplus_database.loc test-data/annotation_ncbi.gff3 test-data/enterococcus_faecalis.faa test-data/enterococcus_faecalis.fna test-data/enterococcus_faecalis_bakta.gff3 test-data/input_ncbi.faa test-data/test-db/AMR.LIB test-data/test-db/AMR.LIB.h3f test-data/test-db/AMR.LIB.h3i test-data/test-db/AMR.LIB.h3m test-data/test-db/AMR.LIB.h3p test-data/test-db/AMRProt test-data/test-db/AMRProt-mutation.tab test-data/test-db/AMRProt-suppress test-data/test-db/AMRProt-susceptible.tab test-data/test-db/AMRProt.pdb test-data/test-db/AMRProt.phr test-data/test-db/AMRProt.pin test-data/test-db/AMRProt.pjs test-data/test-db/AMRProt.psq test-data/test-db/AMRProt.ptf test-data/test-db/AMRProt.pto test-data/test-db/AMR_CDS test-data/test-db/AMR_DNA-Enterococcus_faecium test-data/test-db/AMR_DNA-Enterococcus_faecium.ndb test-data/test-db/AMR_DNA-Enterococcus_faecium.nhr test-data/test-db/AMR_DNA-Enterococcus_faecium.nin test-data/test-db/AMR_DNA-Enterococcus_faecium.njs test-data/test-db/AMR_DNA-Enterococcus_faecium.not test-data/test-db/AMR_DNA-Enterococcus_faecium.nsq test-data/test-db/AMR_DNA-Enterococcus_faecium.ntf test-data/test-db/AMR_DNA-Enterococcus_faecium.nto test-data/test-db/AMR_DNA-Enterococcus_faecium.tab test-data/test-db/database_format_version.txt test-data/test-db/fam.tab test-data/test-db/taxgroup.tab test-data/test-db/version.txt test-data/test_1/amrfinderplus_flank_output.fasta test-data/test_1/amrfinderplus_mutation_all_report.tsv test-data/test_1/amrfinderplus_nucleotide_output.fasta test-data/test_1/amrfinderplus_results.tsv test-data/test_2/amrfinderplus_flanking_output.fasta test-data/test_2/amrfinderplus_mutation_all.tsv test-data/test_2/amrfinderplus_nucleotide_output.fasta test-data/test_2/amrfinderplus_results.tsv test-data/test_3/amrfinderplus_nucleotide_output.fasta test-data/test_3/amrfinderplus_results.tsv test-data/test_4/amrfinderplus_protein_output.fasta test-data/test_4/amrfinderplus_results.tsv test-data/test_5/amrfinderplus_flanking_output.fasta test-data/test_5/amrfinderplus_mutation_all.tsv test-data/test_5/amrfinderplus_nucleotide_output.fasta test-data/test_5/amrfinderplus_results.tsv test-data/test_6/amrfinderplus_protein_output.fasta test-data/test_6/amrfinderplus_results.tsv test-data/test_7/amrfinderplus_protein_output.fasta test-data/test_7/amrfinderplus_results.tsv test-data/test_8/amrfinderplus_mutation_all.tsv test-data/test_8/amrfinderplus_nucleotide_output.fasta test-data/test_8/amrfinderplus_protein_output.fasta test-data/test_8/amrfinderplus_results.tsv tool-data/amrfinderplus_database.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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| diff -r 000000000000 -r a968af0a91f9 amrfinderplus.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/amrfinderplus.xml Fri May 26 09:19:12 2023 +0000 |
| [ |
| b'@@ -0,0 +1,453 @@\n+<tool id="amrfinderplus" name="AMRFinderPlus" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n+ <description>\n+ NCBI Antimicrobial Resistance Gene Finder \n+ </description>\n+ <macros>\n+ <import>macro.xml</import>\n+ </macros>\n+ <expand macro=\'edam\'/>\n+ <expand macro="requirements"/>\n+ <expand macro="version_command"/>\n+\n+ <command detect_errors="aggressive"><![CDATA[\n+ amrfinder\n+ #*======================================\n+ CPU option\n+ ======================================*#\n+ --threads \\${GALAXY_SLOTS:-1}\n+ #*======================================\n+ DATABASE\n+ ======================================*#\n+ --database \'$input_option.amrfinder_db_select.fields.path\'\n+ #*======================================\n+ INPUT TYPE\n+ ======================================*#\n+ #if $input_option.input_mode.input_select == \'nucleotide\'\n+ --nucleotide $input_option.input_mode.nucleotide_input\n+ #if $input_option.input_mode.nucleotide_flank5_size > 0\n+ --nucleotide_flank5_size $input_option.input_mode.nucleotide_flank5_size\n+ --nucleotide_flank5_output \'amrfinderplus_flanking_sequence_output.fasta\'\n+ #end if\n+ --nucleotide_output \'amrfinderplus_nucleotide_output.fasta\'\n+ #elif $input_option.input_mode.input_select == \'protein\'\n+ --protein $input_option.input_mode.protein_input\n+ #if $input_option.input_mode.gff_annotation\n+ --gff $input_option.input_mode.gff_annotation\n+ #end if\n+ #if $input_option.input_mode.annotation_format\n+ --annotation_format $input_option.input_mode.annotation_format\n+ #end if\n+ --protein_output \'amrfinderplus_protein_output.fasta\'\n+ #else\n+ --nucleotide $input_option.input_mode.nucleotide_input\n+ #if $input_option.input_mode.nucleotide_flank5_size and $input_option.input_mode.nucleotide_flank5_size > 0\n+ --nucleotide_flank5_size $input_option.input_mode.nucleotide_flank5_size\n+ --nucleotide_flank5_output \'amrfinderplus_flanking_sequence_output.fasta\'\n+ #end if\n+ --protein $input_option.input_mode.protein_input\n+ --gff $input_option.input_mode.gff_annotation\n+ --annotation_format $input_option.input_mode.annotation_format\n+ --nucleotide_output \'amrfinderplus_nucleotide_output.fasta\'\n+ --protein_output \'amrfinderplus_protein_output.fasta\'\n+ #end if\n+ #*======================================\n+ ORGANISM PART\n+ ======================================*#\n+ #if $organism_options.organism_conditionnal.organism_select\n+ --organism \'$organism_options.organism_conditionnal.organism\'\n+ #if $organism_options.organism_conditionnal.mutation_all\n+ $organism_options.organism_conditionnal.mutation_all \'mutation_all_report.tsv\'\n+ #end if\n+ #if $options.plus\n+ $organism_options.organism_conditionnal.report_common \n+ #end if\n+ #end if\n+ #*======================================\n+ OPTIONS\n+ ======================================*#\n+ --ident_min \'$options.ident_min\'\n+ --coverage_min \'$options.coverage_min\'\n+ #if \'$options.translation_table\'\n+ --translation_table \'$options.translation_table\'\n+ #end if\n+ #if \'$options.name\'\n+ --name \'$options.name\'\n+ #end if\n+ $options.plus\n+ $options.report_all_equal\n+ $options.print_node\n+ --output \'amrfinderplus_report.tsv\'\n+\n+ ]]></command>\n+ <inputs>\n+ <!-- DB and file INPUT -->\n+ <section name="input_option" title="Input/Output'..b'---------------------------------+------------------+-----------------------------+------------------------------------------------------------+\n+ | Pseudomonas_aeruginosa | X | | |\n+ +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+\n+ | Salmonella | X | X | |\n+ +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+\n+ | Serratia_marcescens | X | | |\n+ +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+\n+ | Staphylococcus_aureus | X | | |\n+ +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+\n+ | Staphylococcus_pseudintermedius | X | X | |\n+ +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+\n+ | Streptococcus_agalactiae | X | | |\n+ +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+\n+ | Streptococcus_pneumoniae | X | | Use for S. pneumoniae and S. mitis |\n+ +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+\n+ | Streptococcus_pyogenes | X | | |\n+ +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+\n+ | Vibrio_cholerae | X | | |\n+ +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+\n+ \n+\n+ **Supplementary options**\n+ - *nucleotide 5\' flanking size* to extract nucleotide matches and a range of nucleotide in 5\'\n+ - *Minimum identity* to choose threshold in amino acids alignemnt. -1 for a high curation threshold.\n+ - *Minimum coverage* Coverage to protein alignment.\n+ - *Translation table* by default AMRFinderPlus work on bacteria but can be modified to some other Phyla.\n+ - *Plus* option provide more information related to virulence, stress response ...\n+\n+ **Output files**\n+\n+ AMRFinderPlus can generate some differents files :\n+ - The AMRFinderPlus report with identified protein, gene and AMR related informations.\n+ - A report with all detected variants from the reference sequence.\n+ - The protein and/ort nucleotide matched sequences.\n+ - Only when nucleotide a nucleotide fasta file could be provided with 5\' flanking regions.\n+ \n+\n+ ]]></help>\n+ <expand macro="citations"/>\n+</tool>\n' |
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| diff -r 000000000000 -r a968af0a91f9 macro.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macro.xml Fri May 26 09:19:12 2023 +0000 |
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| @@ -0,0 +1,43 @@ +<macros> + <token name="@TOOL_VERSION@">3.11.14</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">21.05</token> + <xml name="version_command"> + <version_command><![CDATA[amrfinder --version]]></version_command> + </xml> + <xml name="edam"> + <edam_operations> + <edam_operation>operation_3482</edam_operation> + </edam_operations> + </xml> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">ncbi-amrfinderplus</requirement> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1038/s41598-021-91456-0</citation> + </citations> + </xml> + + <xml name="nucl_input" token_option=""> + <param name="nucleotide_input" type="data" optional="@OPTION@" format="fasta" label="Input nucleotide sequence file" help="Select the nucleotide sequence file to be analyzed"/> + </xml> + <xml name="prot_input" token_option=""> + <param name="protein_input" type="data" optional="@OPTION@" format="fasta" label="Input protein sequence file" help="Select the protein sequence file to be analyzed"/> + </xml> + <xml name="annotation_type" token_option=""> + <param name="gff_annotation" type="data" format="gff3" optional="@OPTION@" multiple="false" label="GFF file for protein locations" help="Protein id should be in the attribute Name=id (9th field) of the rows with type CDS or gene (3rd field)"/> + <param argument="--annotation_format" type="select" optional="@OPTION@" label="Annotation file format" help="Select the annotation format type (eg. bakta or prokka tool, genbank format (default: genbank)"> + <option value="bakta">Bakta</option> + <option value="genbank">Genbank</option> + <option value="microscope">Microscope</option> + <option value="patric">Patric</option> + <option value="prokka">Prokka</option> + <option value="pseudomonasdb">Pseudomonasdb</option> + <option value="rast">Rast</option> + <option value="standard">Standard</option> + </param> + </xml> +</macros> |
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| diff -r 000000000000 -r a968af0a91f9 test-data/PROKKA_05252023.faa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/PROKKA_05252023.faa Fri May 26 09:19:12 2023 +0000 |
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| b'@@ -0,0 +1,18849 @@\n+>FODBOAIN_00001 UDP-N-acetylglucosamine 1-carboxyvinyltransferase\n+MKKIVINGNRPLKGEVTISGAKNSVVALIPAAILADSPVTLDGVPDIQDVHSLIEILEIM\n+GAKITFENNTLIIDPTEVVSVPMPKGKINSLRASYYFMGSLLGRFGEGVVGLPGGCYLGP\n+RPIDLHIKGFEALGAHVTNEHGAMYLRTDEAGLQGTRIFMDMVSIGATINVMLAAVKAKG\n+KTIIENAAREPEIIDIATLLNNMGAKVRGAGTDVIRIEGVEELHGCRHSIIPDRIEAGTY\n+LAMAAAMGEGIKVRNVIYEHLESFIAKLQEMGVKMTIEEDMIEVHPSHDLKMTTVKTYPY\n+PGFATDLQQPLTPLLLKAQGTGEIIDTIYAQRNKHIPELVRMGADASVEGNMIILNGPNQ\n+LHGAEVVASDLRAGACLVTAGLMAEGTTTIYNVEYILRGYDHIIEKLTALGADIQMLETE\n+EQEGPFEVDQ\n+>FODBOAIN_00002 Transcription termination factor Rho\n+MSDYLTMAELENSTLKDIYAYAKEFKIPYYSQMNKKELSLAVIRAQAEKQGFFFMEGILD\n+IVSQDGYGFLRPINYGPSAEDIYISSSQIRRFGLRNGDKVAGKARPPKESERYYGLMHVE\n+SVNGKDPEEAKERPHFPALTPLYPEKQLTLETTAGRLSTRMIDVFAPIGFGQRGLIVAPP\n+KAGKTSVLKEIANGITENHPDVELILLLIDERPEEVTDLERSVKGDVVSSTFDQQPQNHT\n+RVAELVLDRAMRLVEDKRDVVILMDSITRLARAYNLVVPPSGRTLSGGIDPAAFFKPKRF\n+FGAARNIEEGGSLTILATALVDTGSRMDDVIYEEFKGTGNMELHLSRELAERRIFPAIDI\n+KKSSTRKEELLMTPEQLEETWKLRNNMSGDSLEYTDQFIKMLKRTQNNQQLFEVFHDVSF\n+GKQIKRNPKR\n+>FODBOAIN_00003 50S ribosomal protein L31 type B\n+MKQDIHPNYQPVVFMDSTTGFKFLSGSTKGSSETVEWEDGNTYPLLRVEVTSDSHPFYTG\n+RQKFTQADGRVDRFNKKYGLKDENANPDA\n+>FODBOAIN_00004 hypothetical protein\n+MSRKKVGVFCLFLFFTFFIIVPKVEATEEMKTKFTVTPVLPENQVSGTSSYYDLILAPKQ\n+SSTIVLDIKNKTDEKLSIVLTLANASTNDNGLIVYNDFDKPLDSSLKVPLTDLVTLENEE\n+VSVPPHQTVSAKMKVKGLDQPIKGVVLGGVYAHLKDEKTEEENQTMGLTSRYGFNVAIAM\n+RSAENAPLTEVNQLKLAKVTPTIALGAKSLKAVIQNPYAAIFPEVRLEGQVIKKGSSKKI\n+AQRTLKNVRFAPNSSMNFHLDLGKQPLDAGTYIFTGRAILQQDEQQSWPFQQEFTINTRE\n+AKKLNQEATVKWVLPTWWLPTFYTLLVITIGAIYSVIWRNNYQKTSEKESENNG\n+>FODBOAIN_00005 hypothetical protein\n+MASWFWLSGGLAVICFMFFLFSLLTSMSFIQHAKEPRSILKETLLSWLMLLLSGGWITIG\n+LLLYFSLKNQ\n+>FODBOAIN_00006 Putative fructokinase\n+MTEKLLGSIEAGGTKFVCGVGTDDLTIVERVSFPTTTPEETMKKVIEFFQQYPLKAIGIG\n+SFGPIDIHVDSPTYGYITSTPKLAWRNFDLLGTMKQHFDVPMAWTTDVNAAAYGEYVAGN\n+GQHTSSCVYYTIGTGVGAGAIQNGEFIEGFSHPEMGHALVRRHPEDTYAGNCPYHGDCLE\n+GIAAGPAVEGRSGKKGHLLEEDHKTWELEAYYLAQAAYNTTLLLAPEVIILGGGVMKQRH\n+LMPKVREKFAELVNGYVETPPLEKYLVTPLLEDNPGTIGCFALAKKALMAQK\n+>FODBOAIN_00007 hypothetical protein\n+MADLKGRFDDAKDKVEGTAKEAQGKVTDDKGKELEGKAQSTFADVKDKARDAGDDLKEGA\n+EKLTDKVKEGFEDLKDKFSKDK\n+>FODBOAIN_00008 FMN reductase (NADPH)\n+MNQTIEQLLSHRSVRHFKKQALTDKQKQQLITAAQAGSSSNFLQAYTIIEIKDPELRREL\n+GRLANCEDYVVNTGVFYVFVADLYRHATILSKEGQSLEPLKTPESLLVAAVDTTIAAQNM\n+AIAAESMDLGICYIGGIRNDLDTVAKRLSLPELTVPLFGLTIGVPETLNGVKPRMPFENI\n+LSENHYQSDKLTDMHTYDELLKDYYASRSSNAQTADWSQKSLSYFSYNRRPEVKIFLQKQ\n+GFDV\n+>FODBOAIN_00009 S-ribosylhomocysteine lyase\n+MARVESFELDHNTVKAPYVRLAGTEQNGDALVEKYDLRFLQPNKDALPTGALHTLEHLLA\n+VNMRDELKGIIDISPMGCRTGFYMIMWDQHSPQEIRDALVNVLNKVINTEVVPAVSAKEC\n+GNYKDHSLFAAKEYAKIVLDQGISLDPFERIL\n+>FODBOAIN_00010 Aspartate-semialdehyde dehydrogenase\n+MGKEYHVAVVGATGAVGTRMIELLAETSLPIASVRLLASKRSAGQEIQFKGQPLIVEELV\n+PESFEGIDLALFSAGGSISEKFAPEAVKRGAVVVDNTSHFRMAKDVPLVVPEVNPEALKN\n+HQGIIANPNCSTIQMMVALEPIRQAFGLERIIVSTYQAVSGAGIRAINELKEQAEDFLEG\n+KPVSEWSAEILPAGSDEKHYPIAFNALPQIDVFSEAGYTYEEWKMMNETKKIMGDNKLKV\n+VATCVRIPVISGHSESVYIEVKQADASVSAIQELMAQAPGVILQDEPSEQLYPQALNSVN\n+QKETFVGRIRQDVDVKNGFHLWIVSDNLLKGAAWNSVQIAETLHEMNLLRVPEND\n+>FODBOAIN_00011 4-hydroxy-tetrahydrodipicolinate synthase\n+MDLTNATIITAMVTPFQESGEIDFDKLPQLVDYLLANHTEGVILAGTTGESPTLTHEEEL\n+QLFQRIIELIDGRIPIICGVGTNDTRDSVAFVKELATIAGIDAVLAVVPYYNKPNQEGMY\n+QHFKTIAEASELPIILYNVPGRTAACLEVETTLRLAQLEKIVAIKECAGLDAITELIERA\n+PKDFLVYTGEDGLAFATKALGGQGVISVASHVFGSSMYEMYQALEQGNLPEAAKIQRQLL\n+PKMNALFSVPSPAPVKAALNHLGIPVGNLRLPLVACTPEEEQRIIRTLEI\n+>FODBOAIN_00012 Ribonuclease J 2\n+MSTIKIVPLGGVRENGKNMYVAEVEDEIFVLDCGLQYPENELLGIDVVIPDFTYLEENSE\n+RIAGVFLTHGHADAIGALPYLLSKIQVPVFGTELTIELAKLSVNSHAETKKFKDFHVIDP\n+HTEIDFGQATVSFFKTTHTIPDSIGVSIKTKEGNIVYTGDFKFDQSAIEMYQTDYGRLAE\n+IGKEGVLALLSDSSNAENPAQVASEAQIADEVFDTIRYWEGRIIVACVASNLQRVQQVLN\n+AADRSGRKVVLTGQDFERIIRTAMKLEKLQLPSEDLLVKPKEMKKYAPEQLLILETGRMG\n+EPIKSLQKMANNTHGVVRIEEGDLVYITTTPTTAMETTVAKTEDIVYRAGATVKQISDNL\n+RVSGHANPNDLQLMLNLMKPKYFIPVQGEYRQLAAHADLAHEIGMPYKDIFITGRGDILE\n+YTKGRMSVAGSTTAENIMIDGIGVGDIGNIVLRDRRILSEDGIFVAVVTINRREKRIVSP\n+AKITSRGFVYVKTSKDLMKESSNIVTEIVEKHLES'..b'PYNYYFHVYERKNLLS\n+>FODBOAIN_02934 hypothetical protein\n+MTKLKRLATKEDEIVDVKIPISNEELKDRAKQYDLLTPKRFATRYNKMLFLPTSFKWNGS\n+EYPIQYNYCINPFCCNFGKEQHKFKDVKGKPSRYKMTGSSKDKGHKGMYCNDNPIGRGVS\n+QNCTVTPLSNWSVVEEIKRLIEINSIQDVEPDYQFHKEGCSEEESTPFNEPKQFYKRGKS\n+RGKSQRYQCKACKKFTNVLPKREETTTYHQQKNTILPMFAKMVVGRVSVSRTCDILGIGV\n+GTYYHKLEWLYRRCLEFLERYETQPLQTKKFNEMWLNTDKMHYYLNNVRKKGQGSKKYTG\n+FEDLNMQTYIVVSAEVLSRYVFRSDVAYDWNISMDELNEDTRKFKEDHLNTFSRKNDRLD\n+WSYYPQEPSANDSENRNAYLHELGKITNRSRFVDGLNVDAPYTTTAHYWLIKQMVNADEW\n+RMISDDDFSIRNAFYRVFTKELRLSDAHHFICQVNKTKSRKQCLKEFGQAKAELLDWGDI\n+RGFKTKFLRTLASHYLTELLTSHQFHEEAISKDGERYRKYADNPIKHPLATKDKGFYSVD\n+CRTDLSALEPNEIAKMLLNVNDHSTNSFIQQIRRYISSLERPLTTARGDKKSYIYANFNP\n+KYAQFAITILRTYYNFCRPFKSADKKVLTPAQRLGITDKQFDWKDIIYFK\n+>FODBOAIN_02935 hypothetical protein\n+MLKWLQFTKQKGVHFPMQFLEPKNKNAKSVDWEISEQVRVIVKQYAEYAERTESEAVDEF\n+LLNILDDKKFIEWIANKRSNKRIVEKMGIKDRVG\n+>FODBOAIN_02936 tetracycline efflux MFS transporter Tet(L)\n+MNTSYSQSNLRHNQILIWLCILSFFSVLNEMVLNVSLPDIANDFNKPPASTNWVNTAFML\n+TFSIGTAVYGKLSDQLGIKRLLLFGIIINCFGSVIGFVGHSFFSLLIMARFIQGAGAAAF\n+PALVMVVVARYIPKENRGKAFGLIGSIVAMGEGVGPAIGGMIAHYIHWSYLLLIPMITII\n+TVPFLMKLLKKEVRIKGHFDIKGIILMSVGIVFFMLFTTSYSISFLIVSVLSFLIFVKHI\n+RKVTDPFVDPGLGKNIPFMIGVLCGGIIFGTVAGFVSMVPYMMKDVHQLSTAEIGSVIIF\n+PGTMSVIIFGYIGGILVDRRGPLYVLNIGVTFLSVSFLTASFLLETTSWFMTIIIVFVLG\n+GLSFTKTVISTIVSSSLKQQEAGAGMSLLNFTSFLSEGTGIAIVGGLLSIPLLDQRLLPM\n+EVDQSTYLYSNLLLLFSGIIVISWLVTLNVYKHSQRDF\n+>FODBOAIN_02937 hypothetical protein\n+MKHGIQSQKVVAEVIKQKPTVRWLFLTLTVKNVYDGEELNKSLSDMAQGFRRMMQYKKIN\n+KNLVGFMRATEVTINNKDNSYNQHMHVLVCVEPTYFKNTENYVNQKQWIQFWKKAMKLDY\n+DPNVKVQMIRPKNKYKSDIQSAIDETAKYPVKDTDFMTDDEEKNLGSVAKF\n+>FODBOAIN_02938 hypothetical protein\n+MHLGVVPMRDGKLQGKNVFNRQELLWLQDKFPEHMKKQGFELKRGERGSDRKHIETAKFK\n+KQTLEKEIDFLEKNLAVKKDEWTAYSDKVKSDLEVPAKRHMKSVEVPTGEKSMFGLGKEI\n+MKTEKKPTKNVVISERDYKNLVTAARDNDRLKQHVRNLMSTDMAREYKKLSKEHGQVKEK\n+YSGLVERFNENVNDYNELLEENKSLKSKISDLKRDVSLIYESTKEFLKERTDGLKAFKNV\n+FKGFVDKVKDKTAQFQEKHDLEPKKNEFELTHNREVKKERSRDQGMSL\n+>FODBOAIN_02940 IS110 family transposase ISSpn10\n+MKLFVGLDVSSEKLDACFMTDDSTCSVLKEASYGNSQLGASQIKEYILEFSQKFEIESLV\n+IGMEATSLYSFHPAMFFKEDLELNQLNLMVSVEQPNKIKKYRDIFEENKNDQIDAFYIAD\n+YFRIQRQVNSIIKEEEYLALQHLTRTRYQLIKQLVRTKQHFIENIYYKCNTLSKELKAEG\n+GSVLSATLVTLMTEDYTMDQLAELSLEEFANLIQKLGKYRFKNPEGIAKAISKAIRSSYR\n+LGKVHQDSVDIVLGVLAKEIRSLEKLIKDLDKAIDDLVVVLPEYQCLTSIPGIGPVYAAG\n+ILAEIGPINRFSDESKLAKYAGLYWRQNQSGNSEYENTPMAKRGNRYLRYYLVEATNSVR\n+RYEPEYHAYYKKKYAETPKHKHKRAIVLTARKFTRLVDTLLRNHQLYMPPRSVIDK\n+>FODBOAIN_02944 ISL3 family transposase ISEfa5\n+MNNHIKKMLRITDEHLDLTNTEEYKIKGKNTLVIFGVYSPMPSACRNCGSTIVDNEGKSV\n+VVRNGKKEVTIQLDSYQNMPTILKLKKQRFHCKSCSHNWTAQCSIVEKNCHISKFITLKI\n+LELLTEKISMTFIAKQCHVSLTTVLRVLKSVESQLPQQLKPRSFPEVLMVDEFRSHASYE\n+DKMSFICADGETGELVDILPSRKLDKIIPYFNRSPLEEREKVKFLVTDMNAAYFQLTKNV\n+FPTAKLIIDRFHIVKHLNTAFNDFRVREMKRLITNKKKSKANKLKSNWKLLLKNQTNISI\n+SEFKTWRSFPSPKYHLLTESMVIDRLLSFSSELKEAYDIFHLLMYHFRNKDDRSFFELLK\n+NLPDSLDTQFRDKIENLISYEEGIRNALKYNFSNGKIEAKNTHIKTLKRVSYGFNSFTNM\n+RIRIFLINGLIKIK\n+>FODBOAIN_02945 IS3 family transposase ISEfa10\n+MYWQKRLDRTASTQIIEEEIQAIRKKHQHYGYRRITQELKRRGFQVNKKKVQRLIQKLKL\n+QVKAFTKKSRKYNSYKGIVGKIAKNLIRRRFKTSVPHQKITTDTTEFKYFEADNAGIFRQ\n+KKLYLDPFMDMYNSEILSYSLSTQPNGKTVMKGLKEAISQTNDCPYRRTFHSDQGWAYQM\n+NVYIQTLKDNNIFQSMSRKGTCLDNSPMENFFSILKQEVYYGKIYQSQNELIEAIENYIY\n+YYNHHRIKEKLNWKSPVEFRQFNQKTA\n+>FODBOAIN_02946 IS3 family transposase ISEfa10\n+MAKYSFEFKLKLVHDYLSGQGGLRFLAKKYGFKDSSQISKWINAYKELGEEGLLRSRKNK\n+NYSVQFKLDAIELYLTTELSYQEVANLLKMNNPSLIANWLRTYQKFGIEGLSKQKGRPPT\n+MSKKKRNEPQPLPSERSQVEKLEKENRMLKIENAYLKELRRLRLEDEQKMNESHESFTVS\n+EDAFD\n+>FODBOAIN_02947 IS30 family transposase IS1062\n+MTYTHLTTDELVMIESYFKINQSVAKTAHCLNRSRQTIHKVYLFFKQGKSALEYYQQYKK\n+NKSNCGRRPLVLPEEQSEYIQRKVVQGWTPDVIVGRAAFPIRCSARTIYRMFKKGLFNPS\n+DLPMKGKRKPNGHQERRGKQAFRRSIHEREKDYSQFSNEFGHLEGDTIVGLKHKSAVITL\n+VERLSKVIITLKPCGRQAIDIENKLNHWFESVPKNLFKSITFDCGKEFSNWKQISNANDI\n+AIYFADPGTPSQRGLNENSNGLLRRDGLLKSMDFNSVDESFIQSVASKRNNIPRKSLNYR\n+TPLEVFLSYVSIDDLSNLT\n+>FODBOAIN_02949 Toxin zeta\n+MANITDFTEKQFEDRLEKNVERLTKNRLAVESPTAFLLGGQPGSGKTSLRSAIFEETQGN\n+VIVIDNDTFKQQHPNFDELVKRFCCKVLNLLSNKVE\n' |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/PROKKA_05252023.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/PROKKA_05252023.gff Fri May 26 09:19:12 2023 +0000 |
| b |
| b'@@ -0,0 +1,3052 @@\n+##gff-version 3\n+##sequence-region contig_1 1 436224\n+##sequence-region contig_2 1 252900\n+##sequence-region contig_3 1 206370\n+##sequence-region contig_4 1 168397\n+##sequence-region contig_5 1 132811\n+##sequence-region contig_6 1 115359\n+##sequence-region contig_7 1 113419\n+##sequence-region contig_8 1 99915\n+##sequence-region contig_9 1 97190\n+##sequence-region contig_10 1 92075\n+##sequence-region contig_11 1 86662\n+##sequence-region contig_12 1 82418\n+##sequence-region contig_13 1 81741\n+##sequence-region contig_14 1 81694\n+##sequence-region contig_15 1 71911\n+##sequence-region contig_16 1 66886\n+##sequence-region contig_17 1 64537\n+##sequence-region contig_18 1 62649\n+##sequence-region contig_19 1 55461\n+##sequence-region contig_20 1 52826\n+##sequence-region contig_21 1 48115\n+##sequence-region contig_22 1 47790\n+##sequence-region contig_23 1 45935\n+##sequence-region contig_24 1 44497\n+##sequence-region contig_25 1 35306\n+##sequence-region contig_26 1 35051\n+##sequence-region contig_27 1 29358\n+##sequence-region contig_28 1 27780\n+##sequence-region contig_29 1 24296\n+##sequence-region contig_30 1 23952\n+##sequence-region contig_31 1 18776\n+##sequence-region contig_32 1 17346\n+##sequence-region contig_33 1 16026\n+##sequence-region contig_34 1 15602\n+##sequence-region contig_35 1 15587\n+##sequence-region contig_36 1 15306\n+##sequence-region contig_37 1 13750\n+##sequence-region contig_38 1 13168\n+##sequence-region contig_39 1 12357\n+##sequence-region contig_40 1 12074\n+##sequence-region contig_41 1 11206\n+##sequence-region contig_42 1 9892\n+##sequence-region contig_43 1 8939\n+##sequence-region contig_44 1 7812\n+##sequence-region contig_45 1 6929\n+##sequence-region contig_46 1 6828\n+##sequence-region contig_47 1 5969\n+##sequence-region contig_48 1 5336\n+##sequence-region contig_49 1 3276\n+##sequence-region contig_50 1 2262\n+##sequence-region contig_51 1 2083\n+##sequence-region contig_52 1 1817\n+##sequence-region contig_53 1 1775\n+##sequence-region contig_54 1 1642\n+##sequence-region contig_55 1 1578\n+##sequence-region contig_56 1 1526\n+##sequence-region contig_57 1 1515\n+##sequence-region contig_58 1 1299\n+##sequence-region contig_59 1 652\n+##sequence-region contig_60 1 607\n+##sequence-region contig_61 1 534\n+##sequence-region contig_62 1 525\n+##sequence-region contig_63 1 442\n+##sequence-region contig_64 1 412\n+##sequence-region contig_65 1 405\n+##sequence-region contig_66 1 398\n+##sequence-region contig_67 1 378\n+##sequence-region contig_68 1 372\n+##sequence-region contig_69 1 351\n+##sequence-region contig_70 1 332\n+##sequence-region contig_71 1 319\n+##sequence-region contig_72 1 280\n+##sequence-region contig_73 1 267\n+##sequence-region contig_74 1 256\n+##sequence-region contig_75 1 255\n+##sequence-region contig_76 1 255\n+##sequence-region contig_77 1 255\n+##sequence-region contig_78 1 255\n+##sequence-region contig_79 1 255\n+##sequence-region contig_80 1 255\n+##sequence-region contig_81 1 255\n+##sequence-region contig_82 1 255\n+##sequence-region contig_83 1 255\n+##sequence-region contig_84 1 255\n+##sequence-region contig_85 1 255\n+##sequence-region contig_86 1 254\n+##sequence-region contig_87 1 253\n+##sequence-region contig_88 1 253\n+##sequence-region contig_89 1 252\n+##sequence-region contig_90 1 250\n+##sequence-region contig_91 1 246\n+##sequence-region contig_92 1 235\n+##sequence-region contig_93 1 231\n+##sequence-region contig_94 1 206\n+##sequence-region contig_95 1 205\n+##sequence-region contig_96 1 161\n+##sequence-region contig_97 1 151\n+##sequence-region contig_98 1 138\n+##sequence-region contig_99 1 135\n+##sequence-region contig_100 1 128\n+contig_1\tProdigal:002006\tCDS\t289\t1581\t.\t+\t0\tID=FODBOAIN_00001;eC_number=2.5.1.7;Name=murA1_1;gene=murA1_1;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:A0A0H2ZNL3;locus_tag=FODBOAIN_00001;product=UDP-N-acetylglucosamine 1-carboxyvinyltransferase\n+contig_1\tProdigal:002006\tCDS\t1578\t2870\t.\t+\t0\tID=FODBOAIN_00002;eC_number=3.6.4.-;Na'..b'othetical protein\n+contig_48\tProdigal:002006\tCDS\t1568\t2776\t.\t-\t0\tID=FODBOAIN_02930;inference=ab initio prediction:Prodigal:002006;locus_tag=FODBOAIN_02930;product=hypothetical protein\n+contig_48\tProdigal:002006\tCDS\t3276\t4214\t.\t+\t0\tID=FODBOAIN_02931;Name=repD;gene=repD;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:P03065;locus_tag=FODBOAIN_02931;product=Replication initiation protein\n+contig_48\tProdigal:002006\tCDS\t4344\t4991\t.\t+\t0\tID=FODBOAIN_02932;eC_number=2.3.1.28;Name=cat;gene=cat;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:P06135;locus_tag=FODBOAIN_02932;product=Chloramphenicol acetyltransferase\n+contig_49\tProdigal:002006\tCDS\t275\t772\t.\t+\t0\tID=FODBOAIN_02933;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:ISfinder:ISSsu9;locus_tag=FODBOAIN_02933;product=IS1595 family transposase ISSsu9\n+contig_49\tProdigal:002006\tCDS\t844\t2796\t.\t-\t0\tID=FODBOAIN_02934;inference=ab initio prediction:Prodigal:002006;locus_tag=FODBOAIN_02934;product=hypothetical protein\n+contig_49\tProdigal:002006\tCDS\t2803\t3087\t.\t-\t0\tID=FODBOAIN_02935;inference=ab initio prediction:Prodigal:002006;locus_tag=FODBOAIN_02935;product=hypothetical protein\n+contig_50\tProdigal:002006\tCDS\t282\t1658\t.\t+\t0\tID=FODBOAIN_02936;Name=tet(L);gene=tet(L);inference=ab initio prediction:Prodigal:002006,similar to AA sequence:BARRGD:NG_048203.1;locus_tag=FODBOAIN_02936;product=tetracycline efflux MFS transporter Tet(L)\n+contig_51\tProdigal:002006\tCDS\t106\t621\t.\t-\t0\tID=FODBOAIN_02937;inference=ab initio prediction:Prodigal:002006;locus_tag=FODBOAIN_02937;product=hypothetical protein\n+contig_51\tProdigal:002006\tCDS\t1142\t2008\t.\t-\t0\tID=FODBOAIN_02938;inference=ab initio prediction:Prodigal:002006;locus_tag=FODBOAIN_02938;product=hypothetical protein\n+contig_52\tbarrnap:0.9\trRNA\t193\t1750\t0\t+\t.\tID=FODBOAIN_02939;locus_tag=FODBOAIN_02939;product=16S ribosomal RNA\n+contig_53\tProdigal:002006\tCDS\t385\t1635\t.\t+\t0\tID=FODBOAIN_02940;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:ISfinder:ISSpn10;locus_tag=FODBOAIN_02940;product=IS110 family transposase ISSpn10\n+contig_54\tbarrnap:0.9\trRNA\t97\t1621\t0\t+\t.\tID=FODBOAIN_02941;locus_tag=FODBOAIN_02941;note=aligned only 47 percent of the 23S ribosomal RNA;product=23S ribosomal RNA (partial)\n+contig_55\tbarrnap:0.9\trRNA\t12\t1362\t0\t+\t.\tID=FODBOAIN_02942;locus_tag=FODBOAIN_02942;note=aligned only 41 percent of the 23S ribosomal RNA;product=23S ribosomal RNA (partial)\n+contig_55\tbarrnap:0.9\trRNA\t1464\t1573\t2.9e-14\t+\t.\tID=FODBOAIN_02943;locus_tag=FODBOAIN_02943;product=5S ribosomal RNA\n+contig_56\tProdigal:002006\tCDS\t84\t1388\t.\t-\t0\tID=FODBOAIN_02944;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:ISfinder:ISEfa5;locus_tag=FODBOAIN_02944;product=ISL3 family transposase ISEfa5\n+contig_57\tProdigal:002006\tCDS\t58\t861\t.\t-\t0\tID=FODBOAIN_02945;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:ISfinder:ISEfa10;locus_tag=FODBOAIN_02945;product=IS3 family transposase ISEfa10\n+contig_57\tProdigal:002006\tCDS\t903\t1460\t.\t-\t0\tID=FODBOAIN_02946;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:ISfinder:ISEfa10;locus_tag=FODBOAIN_02946;product=IS3 family transposase ISEfa10\n+contig_58\tProdigal:002006\tCDS\t201\t1160\t.\t-\t0\tID=FODBOAIN_02947;db_xref=COG:COG2826;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:ISfinder:IS1062;locus_tag=FODBOAIN_02947;product=IS30 family transposase IS1062\n+contig_64\tAragorn:001002\ttRNA\t132\t204\t.\t+\t.\tID=FODBOAIN_02948;inference=COORDINATES:profile:Aragorn:001002;locus_tag=FODBOAIN_02948;product=tRNA-Ala(tgc)\n+contig_67\tProdigal:002006\tCDS\t9\t299\t.\t+\t0\tID=FODBOAIN_02949;eC_number=2.7.1.176;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:Q54944;locus_tag=FODBOAIN_02949;product=Toxin zeta\n+contig_69\tAragorn:001002\ttRNA\t132\t204\t.\t+\t.\tID=FODBOAIN_02950;inference=COORDINATES:profile:Aragorn:001002;locus_tag=FODBOAIN_02950;product=tRNA-Ala(tgc)\n' |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/amrfinderplus_database.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amrfinderplus_database.loc Fri May 26 09:19:12 2023 +0000 |
| b |
| @@ -0,0 +1,7 @@ +# this is a tab separated file describing the location of amrfinderplus database +# +# the columns are: +# value, name, path +# +# for example +amrfinderplus_V3.11.1_2023-04-17.1 V3.11.1-2023-04-17.1 ${__HERE__}/test-db |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/annotation_ncbi.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotation_ncbi.gff3 Fri May 26 09:19:12 2023 +0000 |
| b |
| @@ -0,0 +1,17 @@ +##gff-version 3 +##sequence-region contig1 1-50000 +contig01 . gene 101 961 . + . ID=gene1;Name=blaTEM-156 +contigX . gene 1 501 . + . ID=gene2;Name=nimIJ_hmm +contig02 . gene 1 1191 . + . ID=gene3;Name=blaPDC-114_blast +contig03 . gene 101 802 . + . ID=gene4;Name=blaOXA-436_partial +contig04 . gene 101 1147 . + . ID=gene5;Name=vanG +contig06 . gene 31 2616 . + . ID=gene6;Name=gyrA +contig07 . gene 101 526 . + . ID=gene7;Name=50S_L22 +contig09 . gene 1 675 . - . Name=aph3pp-Ib_partial_5p_neg +contig09 . gene 715 1377 . - . Name=sul2_partial_3p_neg +contig11 . gene 113 547 . + . Name=blaTEM-internal_stop +contig12 . gene 71 637 . + . Name=qacR-curated_blast +contig13 . gene 1 1137 . + . Name=emrD3-suppressed-in-vibrio +contig13 . gene 1141 1491 . + . Name=arsR-suppressed-in-escherichia +contig14 . gene 1093 2181 . + . Name=pmrB_C84R +contig16 . gene 1 423 . + . Name=nfsA_R15C_K141STOP |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/enterococcus_faecalis.faa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/enterococcus_faecalis.faa Fri May 26 09:19:12 2023 +0000 |
| b |
| @@ -0,0 +1,12 @@ +>IDOBJL_14770 aminoglycoside O-phosphotransferase APH(3')-IIIa +MAKMRISPELKKLIEKYRCVKDTEGMSPAKVYKLVGENENLYLKMTDSRYKGTTYDVEREKDMMLWLEGKLPVPKVLHFERHDGWSNLLMSEADGVLCSEEYEDEQSPEKIIELYAECIRLFHSIDISDCPYTNSLDSRLAELDYLLNNDLADVDCENWEEDTPFKDPRELYDFLKTEKPEEELVFSHGDLGDSNIFVKDGKVSGFIDLGRSGRADKWYDIAFCVRSIREDIGEEQYVELFFDLLGIKPDWEKIKYYILLDELF +>IDOBJL_14775 streptothricin N-acetyltransferase Sat4 +MITEMKAGHLKDIDKPSEPFEVIGKIIPRYENENWTFTELLYEAPYLKSYQDEEDEEDEEADCLEYIDNTDKIIYLYYQDDKCVGKVKLRKNWNRYAYIEDIAVCKDFRGQGIGSALINISIEWAKHKNLHGLMLETQDNNLIACKFYHNCGFKIGSVDTMLYANFENNFEKAVFWYLRF +>IDOBJL_14820 tetracycline resistance ribosomal protection protein Tet(M) +MKIINIGVLAHVDAGKTTLTESLLYNSGAITELGSVDKGTTRTDNTLLERQRGITIQTGITSFQWENTKVNIIDTPGHMDFLAEVYRSLSVLDGAILLISAKDGVQAQTRILFHALRKMGIPTIFFINKIDQNGIDLSTVYQDIKEKLSAEIVIKQKVELYPNMCVTNFTESEQWDTVIEGNDDLLEKYMSGKSLEALELEQEESIRFQNCSLFPVYHGSAKNNIGIDNLIEVITNKFYSSTHRGQSELCGNVFKIEYTKKRQRLAYIRLYSGVLHLRDSVRISEKEKIKITEMYTSINGELCKIDKAYSGEIVILQNEFLKLNSVLGDTKLLPQRERIENPLPLLQTTVEPSKPQQREMLLDALLEISDSDPLLRYYVDSTTHEIILSFLGKVQMEVISALLQEKYHVEIELKEPTVIYMERPLKNAEYTIHIEVPPNPFWASIGLSVSPLPLGSGVQYESSVSLGYLNQSFQNAVMEGIRYGCEQGLYGWNVTDCKICFKYGLYYSPVSTPADFRMLAPIVLEQVLKKAGTELLEPYLSFKIYAPQEYLSRAYNDAPKYCANIVDTQLKNNEVILSGEIPARCIQEYRSDLTFFTNGRSVCLTELKGYHVTTGEPVCQPRRPNSRIDKVRYMFNKIT +>IDOBJL_14830 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B) +MNKNIKYSQNFLTSEKVLNQIIKQLNLKETDTVYEIGTGKGHLTTKLAKISKQVTSIELDSHLFNLSSEKLKLNTRVTLIHQDILQFQFPNKQRYKIVGSIPYHLSTQIIKKVVFESHASDIYLIVEEGFYKRTLDIHRTLGLLLHTQVSIQQLLKLPAECFHPKPKVNSVLIKLTRHTTDVPDKYWKLYTYFVSKWVNREYRQLFTKNQFHQAMKHAKVNNLSTVTYEQVLSIFNSYLLFNGRK +>IDOBJL_14880 tetracycline efflux MFS transporter Tet(L) +MNTSYSQSNLRHNQILIWLCILSFFSVLNEMVLNVSLPDIANDFNKPPASTNWVNTAFMLTFSIGTAVYGKLSDQLGIKRLLLFGIIINCFGSVIGFVGHSFFSLLIMARFIQGAGAAAFPALVMVVVARYIPKENRGKAFGLIGSIVAMGEGVGPAIGGMIAHYIHWSYLLLIPMITIITVPFLMKLLKKEVRIKGHFDIKGIILMSVGIVFFMLFTTSYSISFLIVSVLSFLIFVKHIRKVTDPFVDPGLGKNIPFMIGVLCGGIIFGTVAGFVSMVPYMMKDVHQLSTAEIGSVIIFPGTMSVIIFGYIGGILVDRRGPLYVLNIGVTFLSVSFLTASFLLETTSWFMTIIIVFVLGGLSFTKTVISTIVSSSLKQQEAGAGMSLLNFTSFLSEGTGIAIVGGLLSIPLLDQRLLPMEVDQSTYLYSNLLLLFSGIIVISWLVTLNVYKHSQRDF +>IDOBJL_13105 ABC-F type ribosomal protection protein OptrA +MQYKIINGAVYYDGNMVLENIGIEINDNEKIAIVGRNGCGKTTLLKAIIGEIELEEGTGESEFQVIKTGNPYISYLRQMPFEDESISMVDEVRTVFKTLIDMENKMKQLIDKMENQYDDKIINEYSDISERYMALGGLTYQKEYETMIRSMGFTEADYKKPISEFSGGQRTKIAFIKILLTKPDILLLDEPTNHLDIETIQWLESYLRSYKSTLVIISHDRMFLNRIVDKVYEIEWGETKCYKGNYSAFEEQKRENHIKQQKDYDLQQIEIERITRLIERFRYKPTKAKMVQSKIKLLQRMQILNAPDQYDTKTYMSKFQPRISSSRQVLSASELVIGYDTPLAKVNFNLERGQKLGIVGSNGIGKSTLLKTLMGGVAALSGDFKFGYNVEISYFDQQLAQISGDDTLFEIFQSEYPELNDTEVRTALGSFQFSGDDVFRPVSSLSGGEKVRLTLCKLLYKRTNVLILDEPTNHMDIIGKENLENILCSYQGTIIFVSHDRYFTNKIADRLLVFDKDGVEFVQSTYGEYEKKRMNSEKPFNNIKVEQKVEKNNTVKGDRNSIEKEKVKKEKRIEKLEVLINQYDEELERLNKIISEPNNSSDYIVLTEIQKSIDDVKRCQGNYFNEWEQLMRELEVM |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/enterococcus_faecalis.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/enterococcus_faecalis.fna Fri May 26 09:19:12 2023 +0000 |
| [ |
| b'@@ -0,0 +1,11396 @@\n+>contig_2 [gcode=11]\n+TAAAAATGTTTGTTGTCTTGAATTGAATCAAGACGCCCTACACATTTGGTTCGTCTATTC\n+TTTGTTCAGTTTTCAAAGGTCTACGTTACCTCGCAGCAACTTTTATATCATAACAAACTT\n+TCGTTTGGATGTCAAGAACTTTTTTAAAAAAGTTTTTTTAAGTTGTTTTGCTCGGTTGTT\n+GTTGTCTGTTGTGACAACTTCTATATCTTATCATTATCTCAGTTGTTTGTCAACAACTTT\n+TTAAAACTTTTTTGTTATTTTATAACAAGTTTTTTTGATCAAATGATTGATTTAAAAGCA\n+ATCTCTTTAACGACTTTGTTATTCTAACATGTTATTTATCTTTTCGTCAAGAGAAATTTT\n+TAACTTTTTAAAACTTTTTTTCTTAACAAACTGTTTGTCAGAACAGATATTAATATACCA\n+AGGATTTTTCTAAAACGCAACTATTATTTTGCAGAAAAATAACATTTTTTTCAATTTCGA\n+ACGATGAATATTTTCTGCAAAGAAAACATTCGTTTCTTTATCTTATAATCCCTTTTCTCT\n+TACTTAAATGTTCGTTAATCATTCGTAAAAAAAGCAACGTACTTTATTGTACGTTGCTCT\n+CTTCTTTTATTCCAGCGATTGGAATAAAAATTCTAAAGATCGTTCCTTGATGCAATACGC\n+TTTCTGCATCAATACGTCCTTTATAGTTTTCGACTAATTGTTTTGCAATCGATAGTCCTA\n+AGCCATTACCGCCTTTATTTCTTGCACGGGCTTTATCTACTCGATAGAATCGATCAAATA\n+TTTTCTCCAAGTCTTCTTCAGTGATTCCTTCACCAAAATCTTGCACAGCTATTTCAAATT\n+CATTCATCGTTCGAGAAATGGAAATATGCACTTCTTTTCGATCTGTTGAATATTTAATCG\n+CATTATCTAATAGAATAATTAGCAATTGTTCAAAGTGATTACGATAGATTTTCAGTTCAA\n+CTTCGGTTGGTAAATCGTCATCTAACGTGATATGAAACTCAGGATAAACCAATTGGAAGT\n+TATTAAATACTTGGTAGACTACTTGTTTAGCATCTGTTCGTTCATTTGCATATTGGGTGT\n+CCACTTGTTCAGCGCGTGAAAGGTCAAGCATTTCTTGGACCAAACTCTTCATACGACTAA\n+TTTCTTGTAAACTGGCCTTTAATGATTCATCTAAAATTTCAGGATCGTCTTTCCCCCAAC\n+GATTTAAAAGGTTTAAATGGCCTTCCATAATCGCAACGGGCGTTCTTAATTCATGGGAAA\n+CATCTTCAACAAACTGCTCTTGTTGTTCGATATAGCGTCTCATACGATCTAACATTTCAT\n+TAAAGATTTCCGAGATATCTGCTAACTCATCTCTCGTATTAATCTCCGGCATGTGGACAT\n+CTGATTGCGGGTCTTTGCGGATTGTATCCATCGTGTCTCTCAATACTTTTAATGGTTTTA\n+AGAAATAAGAAGAGAGGATAAAGCCTAAGACACTACTTACAATCAGAGAAATCACTTCTA\n+AAACTACAAGTGTTAATAATAAATGATTACGAATTTCATAAAAAGAAGAAAGTTCATAAA\n+ACGCTTGAATATAGCCAATCTTTTCTCGTGTTTCTTTTGAAAAAATAGGTTCCACGGAAT\n+AAAAACCGGTTTTATCAAAAACAGTTCGAACAACAGGTAATTGTCGATCCAATTGTAATA\n+ACTTATCATATTCATTTTGTGTTTTAAAAACTAGCTTTTGGTTTGTGTCATACACAGATA\n+AATAAAGTTCTGGTTGTCCTAGTTCAGATATGAAACTGTCCATTTCCATAAACGAACCTT\n+CTACTGCTATATGCTTATTATAGTAGTTTTCATCTCTTTCACTCGGCGTTTTTAAATAGT\n+CAAAAACGTCTGTTACCGTTAAATTTTCATTGGCATTAGCTAATCGATTTGTTACTTCTG\n+CAATCGTTGCTTCGACATTTTCCTTTTCTTTGGCAACAATAAGACTGACAGAAGACTTAT\n+AGGTAATCACCGCAAAAATGGTAAAAACTACAAATATAAAGAAAGAACTTGCGAAAGCCC\n+ACTTTATAGTTAAAGATGGGCCTTCCAGTTCTTTTTTAATCGTTCTTTTCATTAATTAGT\n+TCTCACGAACGCATAACGTAGCCAGTTCCACGGACAGTTTGGATGTAGCTTTCTTCTCCA\n+GGTACGTCAATTTTATTTCGTAAGTAGCGGATATACACATCCACAACGTTTGTTTCTACT\n+TCTGTTTCATAGCCCCAAACTTTATTTAGTAACACATCACGTGCCAAGACAACATTCACG\n+TTTTCCATTAGCGTTAATAGTAATTCGTATTCGCGTTTTGTTAATTCAATCATTTCAGAA\n+TTACGACGAACGACACGATTTTCTTTTTCAATTGTTAAGTCACGATATGTAATCGTTGTT\n+TGTTTTGCAACGTTTTTATCGCCCTCAATATCAATACGACGAAGTAACGCACGTAAACGA\n+GCTAACAATTCTTCAATTGCAAATGGTTTAACAATATAATCATCCGCTCCATGGTCTAAG\n+CCAGAAACACGGTCAATTACTGAATCACGCGCAGTCATCATAATAATTGGTGTATTTTTC\n+ACTTGGCGAACACGGCGACATACTTCTAATCCATTTAATTCTGGTAACATCAAATCAAGA\n+AGGATAGCATCCCATTCGTTGTTAAGAGCGGCTTCCAATCCTGTACGACCATTGTAGTGT\n+ACTTCTGTCGTATACCCCTCATGTTTTAATTCAAGCTCAACGAATCTCGCTAAGTTCTTT\n+TCATCTTCAATAATTAAAATGTTGCTCATTTGATTAATTGTCCTTTCTCTTTAAAAGCTA\n+TACTCAAGCTCAACCTTTTTATTCCTTACTACTTATTAGAGAATTACTACTCAATCTATC\n+TGGTTCTTTTTTAAGCCACAGTAAAACCATGAGCATGGTGAGCCACACTCATGGTCTCCA\n+GCGTGTTTATTCTTCGTTGTACCAGCTGTAATGGTAGATTCCTTCTTTGTCTGTGCGTTC\n+GTACGTATGAGCACCGAAGTAATCACGTTGTGCTTGAATTAAATTCGCTGGTAAGCGATC\n+TGAACGATAAGAATCGTAATAAGCAATTGCAGATGAGAATGTTGGTACAGGAACACCTGC\n+TTGAACAGCAATCGCAACAACTTCACGAACGGCTTGTTGATATTTTTTCGTAATTTCTAC\n+AAAGTATTCATCTAACAACAAGTTTTCAAGTGCTGGATTTTTTTCATATGCATCGGTAAT\n+TTTTTGTAAGAATTGTGCACGGATAATACAACCTGCTCGCCAGATTTTTGCAATTTCACC\n+AAATGGTAAATCCCATCCGTATTCTTCAGAAGCTGCACGGAGTTGTGCAAAACCTTGCGC\n+ATAACTCATTAATTTACTAAAGTATAATGCTTCGCGAATTTTTTCAATCAATTCTTTTTT\n+ATCGCCTGCAAAGTTAAAGGCTGCAGGTTTTGATAAAATGCCACTTGCTTTTACGCGTTC\n+TTCTTTGTAAGCCGAAATAAAACGTGCAAATACTGATTCTGTAATTAATGGTAATGGTAC\n+ACCAAGATCTAACGCACTTTGGCTTGTCCATTTACCTGTTCCTTTGTTGCCTGCTGCATC\n+AAGAATAACATCAACGATTGGTTGGTCGGTTCCTTCATCATCTTTACGTGTCAAAATGTC\n+AGCCGTGATCTCGATAAGGTAACTGTCTAATTCGCCTTCGTTCCATTCTTTGAAAATCTC\n+TGCCATTTCATCAACAGATAAACCTAAGATTTGTTTCATTAAATCGTAGGATTCAGCAAT\n+TAATTGCATGTCCCCATATTCAATCCCATTATGAACCATTTTTACATAAT'..b'AGTTAAGAAAACTGTTTTTTATGGTCGTA\n+ATGGCAAGCCAGAAACAAAATATTTTGGTGTCCGTGATAGTGATAGATTTATTAGAATTT\n+ATAATAAAAAACAAGAACGTAAAGATAACGCAGATGTTGAAGTTGTGTCTGAACATTTAT\n+GGCGTGTAGAAGTTGAATTAAAAAGAGATATGGTTGATTACTGGAATGATTGTTTTAATG\n+ATTTACACATCTTGAAACCTGCGTGGGCTACTTTAGAAAAAATTAATGAGCAAGCTATGG\n+TTTATACTTTGTTGCATGAAGAAAGTATGTGGGGAAAGCTAAGTAAGAATACTAAGACTA\n+AATTTAAAAAATTGATTAGAGAAATATCTCCAATTGATTTAACGGAATTAATGAAATCGA\n+CTTTAAAAGCGAACGAAAAACAATTGCAAAAGCAGATTGATTTTTGGCAACGTGAATTTA\n+GGTTTTGGAAGTAAAATAAGTTTTATTTGATAAAAATTGCTAATTCAGTATAATTAATAT\n+TTACGAGGTGACATAACGTATGAAAAAATCAGAGGATTATTCCTCCTAAATATAAAAATT\n+TAAAATTTAGGAGGAAGTTATATATGACTTTTAATATTATTGAATTAGAAAATTGGGATA\n+GAAAAGAATATTTTGAACACTATTTTAATCAGCAAACTACTTATAGCATTACTAAAGAAA\n+TTGATATTACTTTGTTTAAAGATATGATAAAAAAGAAAGGATATGAAATTTATCCCTCTT\n+TAATTTATGCAATTATGGAAGTTGTAAATAAAAATAAAGTGTTTAGAACAGGAATTAATA\n+GTGAGAATAAATTAGGTTATTGGGATAAGTTAAATCCTTTGTATACAGTTTTTAATAAGC\n+AAACTGAAAAATTTACTAACATTTGGACTGAATCTGATAAAAACTTCATTTCTTTTTATA\n+ATAATTATAAAAATGACTTGCTTGAATATAAAGATAAAGAAGAAATGTTTCCTAAAAAAC\n+CGATACCTGAAAACACCATACCGATTTCAATGATTCCTTGGATTGATTTTAGTTCATTTA\n+ATTTAAATATTGGTAACAATAGCAGCTTTTTATTGCCTATTATTACGATAGGTAAATTTT\n+ATAGTGAGAATAATAAAATTTATATACCAGTTGCTCTGCAACTTCATCATTCTGTATGTG\n+ATGGTTACCATGCTTCACTATTTATGAATGAATTTCAAGATATAATTCATAGGGTAGATG\n+ATTGGATTTAGTTTTTAGATTTTGAAAGTGAATTTAATTTTATACACGTAAGTGATCATA\n+AAATTTATGAACGTATAACAACCACATTTTTTGGTTGCTTGTGGTTTTGATTTTGAATTT\n+GGTTTTGAACTTATGGACTGATTTATTCAGTCCATTTTTTGTGCTTGCACAAAAACTAGC\n+CTCGCAGAGCACACGCATTAATGACTTATGAAACGTAGTAAATAAGTCTAGTGTGTTATA\n+CTTTACTTGGAAGTGGTTGCCGGAAAGAGCGAAAATGCCTCACATTTGTGCCACCTAAAA\n+AGGAGCGATTTACATATGAGTTATGCAGTTTGTAGAATGCAAAAAGTGAAATCAGC\n+>contig_50 [gcode=11]\n+CGGCTACAATAATCACATCCTGCTGAAATTGCTTTCCTTTAAAATGATTCATCGTCATTC\n+CTCCTGCTATCTTTTTCTATTATTCTACCTTATTTGATAGTAGATTTAAAACTTTGCAAC\n+AGAACCATTTAAAACTTAGTTTATATGTGGTAAAATGTTTTAATCAAGTTTAGGAGGAAT\n+TAATTATGAAGTGTAATTAATGTAACAGGGTTCAATTAAAAGAGGGAAGCGTATCATTAA\n+CCCTATAAACTACGTCTGCCCTCATTATTGGAGGGTGAAATGTGAATACATCCTATTCAC\n+AATCGAATTTACGACACAACCAAATTTTAATTTGGCTTTGCATTTTATCTTTTTTTAGCG\n+TATTAAATGAAATGGTTTTGAACGTCTCATTACCTGATATTGCAAATGATTTTAATAAAC\n+CACCTGCGAGTACAAACTGGGTGAACACAGCCTTTATGTTAACCTTTTCCATTGGAACAG\n+CTGTATATGGAAAGCTATCTGATCAATTAGGCATCAAAAGGTTACTCCTATTTGGAATTA\n+TAATAAATTGTTTCGGGTCGGTAATTGGGTTTGTTGGCCATTCTTTCTTTTCCTTACTTA\n+TTATGGCTCGTTTTATTCAAGGGGCTGGTGCAGCTGCATTTCCAGCACTCGTAATGGTTG\n+TAGTTGCGCGCTATATTCCAAAGGAAAATAGGGGTAAAGCATTTGGTCTTATTGGATCGA\n+TAGTAGCCATGGGAGAAGGAGTCGGTCCAGCGATTGGTGGAATGATAGCCCATTATATTC\n+ATTGGTCCTATCTTCTACTCATTCCTATGATAACAATTATCACTGTTCCGTTTCTTATGA\n+AATTATTAAAGAAAGAAGTAAGGATAAAAGGTCATTTTGATATCAAAGGAATTATACTAA\n+TGTCTGTAGGCATTGTATTTTTTATGTTGTTTACAACATCATATAGCATTTCTTTTCTTA\n+TCGTTAGCGTGCTGTCATTCCTGATATTTGTAAAACATATCAGGAAAGTAACAGATCCTT\n+TTGTTGATCCCGGATTAGGGAAAAATATACCTTTTATGATTGGAGTTCTTTGTGGGGGAA\n+TTATATTTGGAACAGTAGCAGGGTTTGTCTCTATGGTTCCTTATATGATGAAAGATGTTC\n+ACCAGCTAAGTACTGCCGAAATCGGAAGTGTAATTATTTTCCCTGGAACAATGAGTGTCA\n+TTATTTTCGGCTACATTGGTGGGATACTTGTTGATAGAAGAGGTCCTTTATACGTGTTAA\n+ACATCGGAGTTACATTTCTTTCTGTTAGCTTTTTAACTGCTTCCTTTCTTTTAGAAACAA\n+CATCATGGTTCATGACAATTATAATCGTATTTGTTTTAGGTGGGCTTTCGTTCACCAAAA\n+CAGTTATATCAACAATTGTTTCAAGTAGCTTGAAACAGCAGGAAGCTGGTGCTGGAATGA\n+GTTTGCTTAACTTTACCAGCTTTTTATCAGAGGGAACAGGTATTGCAATTGTAGGTGGTT\n+TATTATCCATACCCTTACTTGATCAAAGGTTGTTACCTATGGAAGTTGATCAGTCAACTT\n+ATCTGTATAGTAATTTGTTATTACTTTTTTCAGGAATCATTGTCATTAGTTGGCTGGTTA\n+CCTTGAATGTATATAAACATTCTCAAAGGGATTTCTAAATCGTTAAGGGATCAACTTTGG\n+GAGAGAGTTCAAAATTGATCCTTTTTTTATAACAGGAATTCAAATCTTTTTGTTCCATTA\n+AAGGGCGCGATTGCTGAATAAAAGATACGAGAGACCTCTCTTGTATCTTTTTTATTTTGA\n+GTGGTTTTGTCCGTTACACTAGAAAACCGAAAGACAATAAAAATTTTATTCTTGCTGAGT\n+CTGGCTTTCGGTAAGCTAGACAAAACGGACAAAATAAAAATTGGCAAGGGTTTAAAGGTG\n+GAGATTTTTTGAGTGATCTTCTCAAAAAATACTACCTGTCCCTTGCTGATTTTTAAACGA\n+GCACGAGAGCAAAACCCCCCTTTGCTGAGGTGGCAGAGGGCAGGTTTTTTTGTTTCTTTT\n+TTCTCGTAAAAAAAAGAAAGGTCTTAAAGGTTTTATGGTTTTGGTCGGCACTGCCGACAG\n+CCTCGCAGAGCACACACTTTATGAATATAAAGTAAAGTGTGTTATACTTTACTTGGAAGT\n+GGTTGCCGGAAAGAGCGAAAATGCCTCACATTTGTGCCACCTAAAAAGGAGCGATTTACA\n+TATGAGTTATGCAGTTTGTAGAATGCAAAAAGTGAAATCAGC\n' |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/enterococcus_faecalis_bakta.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/enterococcus_faecalis_bakta.gff3 Fri May 26 09:19:12 2023 +0000 |
| b |
| b'@@ -0,0 +1,731 @@\n+##gff-version 3\n+##feature-ontology https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/v3.1/so.obo\n+# Annotated with Bakta\n+# Software: v1.6.1\n+# Database: v4.0\n+# DOI: 10.1099/mgen.0.000685\n+# URL: github.com/oschwengers/bakta\n+##sequence-region contig_2 1 252900\n+contig_2\tBakta\tregion\t1\t252900\t.\t+\t.\tID=contig_2;Name=contig_2\n+contig_2\tProdigal\tCDS\t584\t2092\t.\t-\t0\tID=IDOBJL_02050;Name=sensor histidine kinase;locus_tag=IDOBJL_02050;product=sensor histidine kinase;Dbxref=COG:COG0642,COG:T,SO:0001217,UniRef:UniRef50_A0A6L6HHT3,UniRef:UniRef90_A0A640MH20;gene=baeS\n+contig_2\tProdigal\tCDS\t2103\t2789\t.\t-\t0\tID=IDOBJL_02055;Name=DNA-binding response regulator;locus_tag=IDOBJL_02055;product=DNA-binding response regulator;Dbxref=COG:COG0745,COG:TK,RefSeq:WP_002355954.1,SO:0001217,UniParc:UPI000005C03A,UniRef:UniRef100_A0A640MKE0,UniRef:UniRef50_Q49XM7,UniRef:UniRef90_S0P072;gene=ompR\n+contig_2\tProdigal\tCDS\t2947\t4368\t.\t-\t0\tID=IDOBJL_02060;Name=NADP-dependent phosphogluconate dehydrogenase;locus_tag=IDOBJL_02060;product=NADP-dependent phosphogluconate dehydrogenase;Dbxref=COG:COG0362,COG:G,RefSeq:WP_002355953.1,SO:0001217,UniParc:UPI000005C039,UniRef:UniRef100_A0A640MFC2,UniRef:UniRef50_P00350,UniRef:UniRef90_A0A3N3PEX1;gene=gndA\n+contig_2\tProdigal\tCDS\t4573\t4752\t.\t-\t0\tID=IDOBJL_02065;Name=50S ribosomal protein L32;locus_tag=IDOBJL_02065;product=50S ribosomal protein L32;Dbxref=COG:COG0333,COG:J,GO:0003735,GO:0006412,GO:0015934,RefSeq:WP_002355952.1,SO:0001217,UniParc:UPI000005C038,UniRef:UniRef100_Q836R0,UniRef:UniRef50_Q836R0,UniRef:UniRef90_Q836R0;gene=rpmF\n+contig_2\tProdigal\tCDS\t4809\t5378\t.\t-\t0\tID=IDOBJL_02070;Name=Large ribosomal RNA subunit accumulation protein YceD;locus_tag=IDOBJL_02070;product=Large ribosomal RNA subunit accumulation protein YceD;Dbxref=COG:COG1399,COG:J,RefSeq:WP_002363429.1,SO:0001217,UniParc:UPI000005C037,UniRef:UniRef100_A0A640MG56,UniRef:UniRef50_G4L6Q2,UniRef:UniRef90_R3L1L8;gene=yceD\n+contig_2\tProdigal\tCDS\t5751\t7508\t.\t-\t0\tID=IDOBJL_02075;Name=pyruvate kinase;locus_tag=IDOBJL_02075;product=pyruvate kinase;Dbxref=COG:COG3848,COG:T,EC:2.7.1.40,KEGG:K00873,RefSeq:WP_002355949.1,SO:0001217,UniParc:UPI00019C6FB7,UniRef:UniRef100_X5NVK0,UniRef:UniRef50_P34038,UniRef:UniRef90_Q836R2;gene=pyk\n+contig_2\tProdigal\tCDS\t7573\t8535\t.\t-\t0\tID=IDOBJL_02080;Name=6-phosphofructokinase;locus_tag=IDOBJL_02080;product=6-phosphofructokinase;Dbxref=COG:COG0205,COG:G,EC:2.7.1.11,GO:0003872,GO:0005524,GO:0005737,GO:0006002,GO:0046872,KEGG:K00850,RefSeq:WP_002355947.1,SO:0001217,UniParc:UPI000005C035,UniRef:UniRef100_Q836R3,UniRef:UniRef50_P00512,UniRef:UniRef90_Q836R3;gene=pfkA\n+contig_2\tProdigal\tCDS\t8708\t12037\t.\t-\t0\tID=IDOBJL_02085;Name=DNA polymerase III subunit alpha;locus_tag=IDOBJL_02085;product=DNA polymerase III subunit alpha;Dbxref=COG:COG0587,COG:L,EC:2.7.7.7,KEGG:K02337,RefSeq:WP_024797152.1,SO:0001217,UniParc:UPI0003EA4690,UniRef:UniRef100_UPI0003EA4690,UniRef:UniRef50_G4L6P9,UniRef:UniRef90_A0A7H0FRP2;gene=dnaE\n+contig_2\tProdigal\tCDS\t12155\t12340\t.\t+\t0\tID=IDOBJL_02090;Name=DUF2929 domain-containing protein;locus_tag=IDOBJL_02090;product=DUF2929 domain-containing protein;Dbxref=RefSeq:WP_002355945.1,SO:0001217,UniParc:UPI000005C033,UniRef:UniRef100_A0A640MF69,UniRef:UniRef50_A0A1E5KZN2,UniRef:UniRef90_A0A640MF69\n+contig_2\tProdigal\tCDS\t12395\t13591\t.\t-\t0\tID=IDOBJL_02095;Name=MFS transporter;locus_tag=IDOBJL_02095;product=MFS transporter;Dbxref=COG:COG2814,COG:G,KEGG:K08161,RefSeq:WP_002381323.1,SO:0001217,UniParc:UPI000005C032,UniRef:UniRef100_C7CYK8,UniRef:UniRef50_P58120,UniRef:UniRef90_R3JVK9;gene=araJ\n+contig_2\tProdigal\tCDS\t13800\t15206\t.\t-\t0\tID=IDOBJL_02100;Name=guanine permease;locus_tag=IDOBJL_02100;product=guanine permease;Dbxref=COG:COG2252,COG:F,RefSeq:WP_156234463.1,SO:0001217,UniParc:UPI0012E0CE2A,UniRef:UniRef100_UPI0012E0CE2A,UniRef:UniRef50_A0A367CCI8,UniRef:UniRef90_A0A0M2AEN1;gene=nCS2\n+contig_2\tProdigal\tCDS\t15358\t15987\t.\t-\t0\tID=IDOBJL_02105;Name=Integral membrane protein;locus_tag=ID'..b'ame=Cis-regulator of HTH transcription factor;product=Cis-regulator of HTH transcription factor;Dbxref=RFAM:RF03532,SO:0005836\n+contig_47\tProdigal\tCDS\t3294\t3647\t.\t+\t0\tID=IDOBJL_14815;Name=XRE family transcriptional regulator;locus_tag=IDOBJL_14815;product=XRE family transcriptional regulator;Dbxref=COG:COG1476,COG:K,RefSeq:WP_001227347.1,SO:0001217,UniParc:UPI00000B1BC3,UniRef:UniRef100_A0A8B6B5W7,UniRef:UniRef50_K1LJU3,UniRef:UniRef90_K1LJU3;gene=xRE\n+contig_47\tProdigal\tCDS\t3993\t5912\t.\t-\t0\tID=IDOBJL_14820;Name=tetracycline resistance ribosomal protection protein Tet(M);locus_tag=IDOBJL_14820;product=tetracycline resistance ribosomal protection protein Tet(M);Dbxref=COG:COG0480,COG:J,GO:0003924,GO:0005525,GO:0006412,GO:0046677,NCBIProtein:WP_000691746.1,RefSeq:WP_000691746.1,SO:0001217,UniParc:UPI0000D79F4E,UniRef:UniRef100_A0A0D5C6L1,UniRef:UniRef50_P10952,UniRef:UniRef90_P21598;gene=tet(M)\n+##sequence-region contig_48 1 5336\n+contig_48\tBakta\tregion\t1\t5336\t.\t+\t.\tID=contig_48;Name=contig_48\n+contig_48\tProdigal\tCDS\t102\t194\t.\t-\t0\tID=IDOBJL_14825;Name=hypothetical protein;locus_tag=IDOBJL_14825;product=hypothetical protein\n+contig_48\tProdigal\tCDS\t199\t936\t.\t-\t0\tID=IDOBJL_14830;Name=23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B);locus_tag=IDOBJL_14830;product=23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B);Dbxref=COG:COG0030,COG:J,EC:2.1.1.184,GO:0000179,GO:0003723,GO:0046677,GO:0052910,NCBIProtein:WP_002292226.1,RefSeq:WP_002292226.1,SO:0001217,UniParc:UPI0000000CFD,UniRef:UniRef100_P0A4D6,UniRef:UniRef50_P21236,UniRef:UniRef90_P0A4D6;gene=erm(B)\n+contig_48\tBakta\tCDS\t1061\t1144\t.\t-\t0\tID=IDOBJL_14835;Name=23S rRNA methylase leader peptide;locus_tag=IDOBJL_14835;product=23S rRNA methylase leader peptide;Dbxref=GO:0046677,RefSeq:WP_001814874.1,SO:0001217,UniParc:UPI000000011E,UniRef:UniRef100_P23130,UniRef:UniRef50_P23130,UniRef:UniRef90_P23130;gene=ermC\n+contig_48\tProdigal\tCDS\t1165\t1428\t.\t-\t0\tID=IDOBJL_14840;Name=peptide-binding protein;locus_tag=IDOBJL_14840;product=peptide-binding protein;Dbxref=SO:0001217,UniRef:UniRef50_A0A8H9BZC3,UniRef:UniRef90_A0A8H9BZC3\n+contig_48\tProdigal\tCDS\t1568\t2776\t.\t-\t0\tID=IDOBJL_14845;Name=DNA topoisomerase III;locus_tag=IDOBJL_14845;product=DNA topoisomerase III;Dbxref=EC:5.6.2.1,KEGG:K03169,SO:0001217,UniParc:UPI00000B31A1,UniRef:UniRef100_A0A4D6PEZ9,UniRef:UniRef50_E6LIS5,UniRef:UniRef90_E6LIS5;gene=topB\n+contig_48\tProdigal\tCDS\t3276\t4214\t.\t+\t0\tID=IDOBJL_14850;Name=replication initiation protein;locus_tag=IDOBJL_14850;product=replication initiation protein;Dbxref=RefSeq:WP_002331393.1,SO:0001217,UniParc:UPI00000B5057,UniRef:UniRef100_A0A1L5KST2,UniRef:UniRef50_P12053,UniRef:UniRef90_A0A1D4S1V7\n+contig_48\tBakta\tCDS\t4280\t4309\t.\t+\t0\tID=IDOBJL_14855;Name=Chloramphenicol resistance leader peptide;locus_tag=IDOBJL_14855;product=Chloramphenicol resistance leader peptide;Dbxref=GO:0046677,SO:0001217,UniParc:UPI00000004AB,UniRef:UniRef100_P0A061\n+contig_48\tProdigal\tCDS\t4344\t4991\t.\t+\t0\tID=IDOBJL_14860;Name=type A-7 chloramphenicol O-acetyltransferase;locus_tag=IDOBJL_14860;product=type A-7 chloramphenicol O-acetyltransferase;Dbxref=EC:2.3.1.28,GO:0008811,GO:0046677,NCBIProtein:WP_002331392.1,RefSeq:WP_002331392.1,SO:0001217,UniParc:UPI00000BD356,UniRef:UniRef100_Q03058,UniRef:UniRef50_P00485,UniRef:UniRef90_P06135;gene=catA\n+##sequence-region contig_50 1 2262\n+contig_50\tBakta\tregion\t1\t2262\t.\t+\t.\tID=contig_50;Name=contig_50\n+contig_50\tProdigal\tCDS\t282\t1658\t.\t+\t0\tID=IDOBJL_14880;Name=tetracycline efflux MFS transporter Tet(L);locus_tag=IDOBJL_14880;product=tetracycline efflux MFS transporter Tet(L);Dbxref=COG:COG2814,COG:G,GO:0005886,GO:0006811,GO:0015297,GO:0016021,GO:0046677,KEGG:K08168,NCBIProtein:WP_001574277.1,RefSeq:WP_001574277.1,SO:0001217,UniParc:UPI0000000365,UniRef:UniRef100_P0A4K7,UniRef:UniRef50_P02983,UniRef:UniRef90_P0A4K7;gene=tet(L)\n+contig_50\tBLAST+\toriC\t1659\t2221\t.\t?\t.\tID=IDOBJLBBGI_3041;Name=origin of replication;product=origin of replication;inference=similar to DNA sequence\n' |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/input_ncbi.faa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_ncbi.faa Fri May 26 09:19:12 2023 +0000 |
| [ |
| @@ -0,0 +1,74 @@ +>blaTEM-156 +MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLS +RVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNIGDHVTRL +DRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGS +RGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW +>blaPDC-114_blast BLAST (100% length, but 1 mismatch) +MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRV +TPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALVGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRD +YYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAG +PGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMAL +QPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR +>blaOXA-436_partial (Should be partial OXA-48 family +MRALALSAVLMVTTMIGMPAVAKEWQENKSWNAHFSEHKTQGVVVLWNENTQQGFTNDLKRANQAFLPASTFKIPNSLIA +LDLGVVKDEHQVFKWDGQTRDIAAWNRDHDLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNLDSFWLDG +GIRISATQQIAFLRKLYHNKLHVSERSQRIVKQAMLTEANADYIIRAKTGYSVRIEPKIGWWVGWIELDDNVW +>vanG +MQNKKIAVIFGGNSTEYEVSLQSASAVFENINTNKFDIIPIGITRSGEWYHYTGEKEKILNNTWFEDSKN +LCPVVVSQNRSVKGFLEIASDKYRIIKVDLVFPVLHGKNGENGTLQGIFELAGIPVVGCDTLSSALCMDK +DRAHKLVSLAGISVPKSVTFKRFNEEAAMKEIEANLTYPLFIKPVRAGSSFGITKVIEKQELDAAIELAF +EHDTEVIVEETINGFEVGCAVLGIDELIVGRVDEIELSSGFFDYTEKYTLKSSKIYMPARIDAEAEKRIQ +EAAVTIYKALGCSGFSRVDMFYTPSGEIVFNEVNTIPGFTSHSRYPNMMKGIGLSFSQMLDKLIGLYVE +>gyrA T86I Campylobacter +MENIFSKDSDIELVDIENSIKGSYLDYSMSVIIGRALPDARDGLKPVHRRILYAMQNDEAKSRTDFVKSARIVGAVIGRYHPHGDAAVYDALVRMAQDFSMRYPSITGQGNFGSIDGDSAAAMRYTEAKMSKLSHELLKD +IDKDTVDFVPNYDGSESEPDVLPSRVPNLLLNGSSGIAVGMATNIPPHSLNELIDGLLYLLDSKDASLEE +IMQFIKGPDFPTGGIIYGKKGIIEAYRTGRGRVKVRAKTHIEKKTNKDVIVIDELPYQTNKARLIEQIAE +LVKEKQIEGISEVRDESNKEGIRVVIELKREAMSEIVLNNLFKSTTMESTFGVIMLAIHNKEPKIFSLLE +LLNLFLTHRKTVIIRRTIFELQKARARAHILEGLKIALDNIDEVIALIKNSSDNNTARDSLVAKFGLSEL +QANAILDMKLGRLTGLEREKIENELAELMKEIARLEEILKSETLLENLIRDELKEIRSKFDVPRITQIED +DYDDIDIEDLIPNENMVVTITHRGYIKRVPSKQYEKQKRGGKGKLAVTTYDDDFIESFFTANTHDTLMFV +TDRGQLYWLKVYKIPEGSRTAKGKAVVNLINLQAEEKIMAIIPTTDFDESKSLCFFTKNGIVKRTNLSEY +QNIRSVGVRAINLDENDELVTAIIVQRDEDEIFATGGEENLENQEIENLDDENLENEESVSTQGKMLFAV +TKKGMCIKFPLAKVREIGRVSRGVTAIKFKEKNDELVGAVVIENDEQEILSISAKGIGKRTNAGEYRLQS +RGGKGVICMKLTEKTKDLISVVIVDETMDLMALTSSGKMIRVDMQSIRKAGRNTSGVIVVNVENDEVVSI +AKCPKEENDEDELSDENFGLDL +>50S_L22 Campylobacter 50S_L22:A103V +MSKALIKFIRLSSTKARLIAREVQGMNAELAMASLKFMPNKGAKYIANAISSAVANGGFEANEVIVKSCRVDAAAVLKRF +RPRARGSASRIRKPTSHILVEVVKAEVKAEEKKTVAKKTTTTKAPAKKTTSTKKATAKKES + +>nimIJ_hmm WP_027455679.1 NimIJ family nitroimidazole resistance protein [Prevotella brevis] +MSEFREMRRKRQQLTDADSIAVLQKATSGTLALLGDNDYPYAVPISYVYDNGKLYFHSAMAGHKVDAIRR +CNKASFCVIEKDDVRPEKYTTYFRSVIAFGRIEIVEDEAEKRTIMHMMGNRFNPNHDDALQKELESGLAH +MLAIRMDIEHLTGKEAIELVRQRGGN + +>aph3pp-Ib_partial_5p_neg NZ_QKNQ01000001.1 Providencia rettgeri strain Pret_2032, whole genome shotgun sequence 2160922-2162737 150-1527 704-137 +IRKLKEPPLNRTNIFFGESHSDWLPVRGGESGDFVFRRGDGHAFAKIAPASRRGELAGERDRLIWLKGRGVACPEVINWQEEQEGACLVITAIPGVPAADLSGADLLKAWPSMGQQLGAVHSLSVDQCPFERRLSRMFGRAVDVVSRNAVNPDFLPDEDKSTPQLDLLARVERELPVRLDQERTDMVVCHGDPCMPNFMVDPKTLQCTGLIDLGRLGTADRYADL + +>sul2_partial_3p_neg NZ_QKNQ01000001.1 Providencia rettgeri strain Pret_2032, whole genome shotgun sequence 2160922-2162737 150-1377 2-667 +SSNPDAAPVSSDTEIERIAPVLDALKADGIPVSLDSYQPATQAYALSRGVAYLNDIRGFPDAAFYPQLAKSSAKLVVMHSVQDGQADRREAPAGDIMDHIAAFFDARIAALTGAGIKRNRLVLDPGMGFFLGAAPETSLSVLARFDELRLRFDLPVLLSVSRKSFLRALTGRGPGDVGAATLAAELAAAAGGADFIRTHEPRPLRDGLAVLAALKETARIR + +>blaTEM-internal_stop +HFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVNYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSCVDAG +QEQLGRSIHYSQNDLVEYSPVTEKHLTDGMTLRELCSAAITMSDNTAANLLLTTIGGPKELTA + +>qacR-curated_blast (ADK23698.1) +MKLKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIEESKWQEQWKKEQI +KCKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKMNKLENKYIDAYHVIFKEGNLNGEW +CINDVNAVSKIAANAVNGIVTFTHEQNINERIKLMNKFSQIFLNGLSK + +>arsR-suppressed-in-escherichia BAE77793.1 arsR_K-12 As(III)-sensing_metalloregulatory_transcriptional_repressor_ArsR +MSFLLPIQLFKILADETRLGIVLLLSELGELCVCDLCTALDQSQPKISRHLALLRESGLLLDRKQGKWVHYRLSPHIPAW +AAKIIDEAWRCEQEKVQAIVRNLARQNCSGDSKNICS + +>emrD3-suppressed-in-vibrio ABQ18953.1 +MKTKPSLWLMVIMLMFPQIVETIYSPVLGSIARSFSVSDAQAAQTLSVYFLAFALGVVIWGVLADKWGRRPTMLVGLLIY +GSATFIAMQTDSFTILMLARVFSAFGIAVGSVVTQTILRDVFSGHELRKVFSLMGIGISISPVLGMLLGGQLAFAGGHQL +VFLALFFIALVLFVYNLCQLPETQQVKPKIALGCLVARMFKDRQVLLSALLVALYNVALFSYYQLGAFIFSDLGLDAEQF +GYSGIALGLGSLIGSFLNKTLLAKQVPQRALLLLAALLLIMGTIGVSLTLDSIGFVAAMILVVIAYGMAIPNILSTALVE +YKSQAGSAGALFGLLYYLLIGSGLALTGLVQRLGVVLLMCAGITLLATLARSSHIARLP + +>pmrB_C84R +MHFLRRPISLRQRLILTIGAILLVFELISVFWLWHESTEQIQLFEQALRDNRNNDRHIMREIREAVASLIVPGVFMVSLTLFIRYQAVRRITRPLAELQKELEARTADNLTPIAIHSATLEIEAVVSALNDLVSRLTSTLDNERLFTADVAHELRTPLAGVRLHLELLAKTHHIDVAPLVARLDQMMESVSQLLQLARAGQSFSSGNYQHVKLLEDVILPSYDELSTMLDQRQQTLLLPESAADITVQGDATLLRMLLRNLVENAHRYSPQGSNIMIKLQEDDGAVMAVEDEGPGIDESKCGELSKAFVRMDSRYGGIGLGLSIVSRITQLHHGQFFLQNRQETSGTRAWVRLKKDQYVANQI + +>nfsA_R15C_K141STOP +MTPTIELICGHRSICHFTDEPISEAQREAIINSARATSSSSFLQYSSIIRITDKALREELVTLTGGQKHVAQAAEFWVFCADFNRHLQICPDAQLGLAEQLLLGVVDTAMMAQNALIAAESLGLGGVYIGGLRNNIEAVT |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test-db/AMR.LIB --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/AMR.LIB Fri May 26 09:19:12 2023 +0000 |
| [ |
| b'@@ -0,0 +1,6500 @@\n+HMMER3/f [3.1b2 | February 2015]\n+NAME tet_ABC_46_A-NCBIFAM\n+ACC NF000474.1\n+DESC NCBIFAM: tetracycline efflux ABC transporter Tet(46) subunit A\n+LENG 574\n+ALPH amino\n+RF no\n+MM no\n+CONS yes\n+CS no\n+MAP yes\n+DATE Tue Aug 27 12:39:42 2019\n+NSEQ 5\n+EFFN 0.405273\n+CKSUM 3622448626\n+GA 1250 1250\n+TC 1250 1250\n+NC 1250 1250\n+STATS LOCAL MSV -11.9374 0.69736\n+STATS LOCAL VITERBI -12.7561 0.69736\n+STATS LOCAL FORWARD -6.3343 0.69736\n+HMM A C D E F G H I K L M N P Q R S T V W Y\n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 2.55881 4.49993 2.93380 2.79370 3.15097 2.79672 3.88777 2.66977 2.78373 2.28694 3.58134 3.28220 3.63499 3.01909 2.94342 2.68638 2.91336 2.54646 4.47664 3.36127\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.03386 3.79821 4.52056 0.61958 0.77255 0.00000 *\n+ 1 2.91318 4.47450 3.97049 3.55992 3.17917 3.77862 4.31234 2.34751 3.33143 1.78660 1.52825 3.84610 4.24023 3.71911 3.54516 3.25380 3.21778 2.34458 5.00913 3.76340 1 m - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.03386 3.79821 4.52056 0.61958 0.77255 0.48576 0.95510\n+ 2 2.97337 4.41526 4.22623 3.84078 3.32614 3.98301 4.58395 1.17512 3.66729 1.92971 3.27541 4.09660 4.42309 4.02442 3.87247 3.47271 3.27462 1.84971 5.20019 3.93072 2 i - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.03386 3.79821 4.52056 0.61958 0.77255 0.48576 0.95510\n+ 3 2.92484 4.76558 3.40824 2.93741 4.10136 3.42467 3.77613 3.63946 2.21581 3.16909 4.17302 3.30193 3.93250 3.00174 1.09842 3.01366 3.19695 3.36708 5.21564 4.04667 3 r - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.03386 3.79821 4.52056 0.61958 0.77255 0.48576 0.95510\n+ 4 1.12649 4.15831 3.38969 3.17968 3.98066 2.98437 4.21016 3.09535 3.19405 2.98009 4.02182 3.34729 3.71677 3.54255 3.44855 2.51011 2.78241 2.76278 5.41537 4.20774 4 a - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.03386 3.79821 4.52056 0.61958 0.77255 0.48576 0.95510\n+ 5 2.97337 4.41526 4.22623 3.84078 3.32614 3.98301 4.58395 1.17512 3.66729 1.92971 3.27541 4.09660 4.42309 4.02442 3.87247 3.47271 3.27462 1.84971 5.20019 3.93072 5 i - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.03386 3.79821 4.52056 0.61958 0.77255 0.48576 0.95510\n+ 6 2.99964 4.50080 4.00607 3.53243 2.44313 3.84920 3.70593 2.75832 3.23546 1.92151 3.40968 3.71304 4.23894 3.59102 3.42742 3.24662 3.24963 2.68949 1.89475 2.50247 6 w - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.03386 3.79821 4.52056 0.61958 0.77255 0.4857'..b' 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.03150 3.86924 4.59158 0.61958 0.77255 0.48576 0.95510\n+ 69 3.00176 4.84118 3.49207 3.00377 4.19494 3.49042 3.82184 3.73640 2.23595 3.25291 4.25315 3.36377 3.99313 3.04230 0.98334 3.08607 3.26792 3.46048 5.27927 4.12297 69 r - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.03150 3.86924 4.59158 0.61958 0.77255 0.48576 0.95510\n+ 70 3.06303 4.43114 4.56086 4.00550 2.29264 4.26987 4.49404 1.76885 3.89021 1.37484 2.93679 4.24143 4.52117 4.04233 4.04916 3.59690 3.29171 2.02951 4.90105 3.65166 70 l - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.03150 3.86924 4.59158 0.61958 0.77255 0.48576 0.95510\n+ 71 2.65042 4.97394 2.37397 2.19864 4.29764 3.25354 3.52746 3.75233 2.48616 3.31296 4.12641 2.21008 2.87483 2.78288 2.97899 2.40564 2.91436 3.37837 5.51475 4.12630 71 e - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.03150 3.86924 4.59158 0.61958 0.77255 0.48576 0.95510\n+ 72 2.82684 4.88742 2.87978 2.57959 4.09001 3.37774 3.71718 3.66771 2.31091 3.17751 4.14238 3.04321 3.89612 1.44141 2.52973 2.86017 3.09908 3.37580 5.32568 4.00751 72 q - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.03150 3.86924 4.59158 0.61958 0.77255 0.48576 0.95510\n+ 73 2.92668 4.90873 3.33473 2.80010 4.09553 3.52772 3.41052 3.72365 2.03412 3.22001 4.14409 3.19096 3.96785 2.83868 1.26161 2.97224 3.14928 3.42956 5.22372 3.95221 73 r - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.03150 3.86924 4.59158 0.61958 0.77255 0.48576 0.95510\n+ 74 1.76274 4.21184 3.24777 2.84993 4.03533 2.69407 3.93978 3.42446 2.85365 3.10422 3.94125 3.14352 3.67086 3.18028 3.07071 2.06815 2.26336 2.99396 5.37683 4.13523 74 a - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.03150 3.86924 4.59158 0.61958 0.77255 0.48576 0.95510\n+ 75 3.02858 4.44817 4.33114 3.94679 3.37197 4.06309 4.67549 1.08191 3.77487 1.95864 3.30780 4.19259 4.49458 4.12347 3.97181 3.55805 3.32779 1.84575 5.26216 4.00020 75 i - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.03150 3.86924 4.59158 0.61958 0.77255 0.48576 0.95510\n+ 76 3.04189 4.44450 4.41667 3.97756 3.31747 4.17934 4.68449 1.15539 3.78471 1.83984 3.23210 4.23183 4.55416 4.12248 3.98786 3.60498 3.32259 1.79603 5.24865 3.97929 76 i - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.03150 3.86924 4.59158 0.61958 0.77255 0.48576 0.95510\n' |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test-db/AMR.LIB.h3f |
| b |
| Binary file test-data/test-db/AMR.LIB.h3f has changed |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test-db/AMR.LIB.h3i |
| b |
| Binary file test-data/test-db/AMR.LIB.h3i has changed |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test-db/AMR.LIB.h3m |
| b |
| Binary file test-data/test-db/AMR.LIB.h3m has changed |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test-db/AMR.LIB.h3p |
| b |
| Binary file test-data/test-db/AMR.LIB.h3p has changed |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test-db/AMRProt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/AMRProt Fri May 26 09:19:12 2023 +0000 |
| b |
| b'@@ -0,0 +1,10000 @@\n+>0|EAC4468893.1|1|1|emrC_Lis|emrC_Lis||1|QUATERNARY_AMMONIUM|QUATERNARY_AMMONIUM|multidrug_efflux_transporter_outer_membrane_subunit_EmrC\n+MSYLYLTLAIIGELIGSSMLKASEGFSKLYPTIGVIIAFISAFFFLSLAMKTIPLNTAYAIWSGIGIVATTIISVLIWKE\n+KVNAASVTGIALILIGVVILNLFGPGHGEASNNEKVNESTIIASNKME\n+>0|EGO5141043.1|1|1|arsR_LGI2_1|arsR_LGI2_1||1|ARSENITE|ARSENIC|As(III)-sensing_metalloregulatory_transcriptional_repressor_ArsR\n+MDYLGLSKIMKAIAEPNRLQILDMISTGEKCACDILDNFDFTQPTLSHHMKVLIEAGVVTARKEGKWQYYSLVTENIEEF\n+QELIHQILNIKQKEGVM\n+>0|MBO4175406.1|1|1|mcr-9.2|mcr-9||1|COLISTIN|COLISTIN|phosphoethanolamine--lipid_A_transferase_MCR-9.2\n+MPVLFRVKVIPLVLLLAMIFAFLLNWPILLHFYEILSHLEHVKIGFVISIPFVLVAALNVVFMPFSVRFLLKPFFALLFI\n+TGSLVSYSTLKYKVMFDQTMIQNIIETNPQEAHSYLNGSIIIWFVFTGILPAILLFSIKIQYPEKWYKGIAYRLLSVLAS\n+LSLIAGVAALYYQDYASVGRNNSTLNKEIIPANYAYSTFQYVKDTYFTTKVPFQTLGNDAKRVVAHEKPTLMFLVIGETA\n+RSQNFSMNGYSRDTNAFTSKSGGVISFKNMHSCGTATAISVPCMFSNMNRTEYDSKKASNSENFLDIVQKTGVSLLWKEN\n+DGGCKGVCSRIPTVEIKPSDNPKLCDGKTCHDEVMLENLDDEIAKMPGDKLVAFHIIGSHGPTYYLRYPAEHRHFMPECA\n+RSDIENCTQEQLVNTYDNTLRYTDYVLAEMIEKLKNYSDQYNTVLLYVSDHGESLGESGLYLHGTPYKLAPDQQTHIPMQ\n+VWMSPGFIAGKHINMSCLENNAAKKSYSHDNLFSSILGLWDVSTSVYNPDRDLFRECRGW\n+>0|MBY0597968.1|1|1|entFM|entFM||1|||enterotoxin_EntFM\n+MKKVLAGLAAASVAGVAVPGMDTAHAQVSADALKEINGQTQEQTVETNVTETNAVETNSELKYTVTADVLNVRSGAGTGH\n+NIISKVTEGQVLQVTGQENGWFKVNVNGQTGYVSGDFVTTGGKQGTAVQQGTGTYTVNVSSLNVRTGPSASHTVVGTVNK\n+GQTVQVVGEVQDWFKINRDGGTGYVSKDFVTKGGTTTNVNTETEKPSNNEMTIRKDGSYVVDTGALRVRTGPATYNPVIG\n+GVVKGQTLQVISGENGWYKINHQGKTGYVSADLVKFVKGGTANVTTPSRPTTGGEQGNTQTEKPTTPSANGSSIVSIAQS\n+LNGSPYTWGGTTPNGFDCSGFIYYVLKEAGHSGGRQNVAGYWSSKQHTSNPQPGDLVYFSNTTGAGGMTHMGIYLGNGQF\n+ISAETEKTGVRVQSVNSSYWSQHLAGYTKA\n+>0|NDR16746.1|1|1|sel27|sel27||1|||staphylococcal_enterotoxin_type_27\n+MKLFFIFNFILNTIMSQTDYSDPTSNQLNKTSQYEGLMYNMKALYESDPVSIEKIKSYDQFLSFDLIYFYQTSQYNRIKT\n+ELTNDLSNYYKDKDVDLFGVKYFVNCYFSDNKDIKENSPSNDKVCMYGGVTEHEGNRTKLFGYTIVVSVYIDNRNSRSFT\n+LSTNKDHITAQELDYKVRNRLIKDVRLYEFESSRFETGYIKFIENGKAGFWYDLMPPANFSQSKYLMIYKDNKTLLSSKT\n+AIEVHLTKKK\n+>0|NDR16747.1|1|1|sel28|sel28||1|||staphylococcal_enterotoxin_type_28\n+MKKLYIFLIAISLHMLTNSEEAYADVGVQNLRNYYGSYEFIDLKNQSDKNNPQSHQLEYEVEGKALYSQLSSEHDVKRLK\n+SQKVDIFGIPYTGITQNVEYIYGGITLSNDYLDNARNIPINLWINGQHKTISTDRVSTNKKQVTAQEIDVKLRRYLQEEY\n+NIYGHNKTNKGREYGNESKFNSGFDKGNVIFHLNNGTQFSYDLFYTGHGQPEDFLKVYNDNKTIDSENFHLDVDLSLSKT\n+I\n+>1000903631|WP_061154665.1|1|1|blaLEN-42|blaLEN|hydrolase|2|BETA-LACTAM|BETA-LACTAM|class_A_beta-lactamase_LEN-42\n+MRYVRLCVISLLATLPLAVYAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARV\n+DAGVEQLDRRIHYRQQDLVDYSPVSEKHLVDGMTIGELCAAAITMSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDR\n+WETALNEALPGDMRDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGARG\n+IVALLGPDGKAERIVVIYLRDTPASMAERNQHIAGIGAALIEHWQR\n+>1000909371|WP_061158039.1|1|1|blaTEM-156|blaTEM|hydrolase|2|BETA-LACTAM|BETA-LACTAM|class_A_beta-lactamase_TEM-156\n+MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLS\n+RVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNIGDHVTRL\n+DRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGS\n+RGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW\n+>1001043515|WP_061189306.1|1|1|blaPDC-114|blaPDC|hydrolase|2|CEPHALOSPORIN|BETA-LACTAM|class_C_beta-lactamase_PDC-114\n+MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRV\n+TPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRD\n+YYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAG\n+PGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMAL\n+QPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR\n+>1001044756|WP_061190338.1|1|1|blaPDC-226|blaPDC|hydrolase|2|CEPHALOSPORIN|BETA-LACTAM|class_C_beta-lactamase_PDC-226\n+MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRV\n+TPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRD\n+YYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLM'..b'IGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNAS\n+ALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGE\n+FSTFDWRAANFTHCDLTNSELGGLDIRGVDLQGVKLDNYQASLLMERLGIAIIG\n+>1028111930|WP_063866135.1|1|1|qnrB49|qnrB|target_protection|2|QUINOLONE|QUINOLONE|quinolone_resistance_pentapeptide_repeat_protein_QnrB49\n+MALALVGEKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNAS\n+ALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGE\n+FSTFDWRAANFTHCDLTNSELGDLDIRRVDLQGVKLDNYQASLLMERLGIAIIG\n+>1028111939|WP_063866143.1|1|1|qnrB5|qnrB|target_protection|2|QUINOLONE|QUINOLONE|quinolone_resistance_pentapeptide_repeat_protein_QnrB5\n+MTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVS\n+ALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGE\n+FSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDSYQASLLMERLGIAIIG\n+>1028111946|WP_063866150.1|1|1|qnrB50|qnrB|target_protection|2|QUINOLONE|QUINOLONE|quinolone_resistance_pentapeptide_repeat_protein_QnrB50\n+MTLALVGEKIDRKRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVS\n+ALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGE\n+FSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG\n+>1028111955|WP_063866158.1|1|1|qnrB52|qnrB|target_protection|2|QUINOLONE|QUINOLONE|quinolone_resistance_pentapeptide_repeat_protein_QnrB52\n+MALALVGEKINRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNAS\n+ALGIEISHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGE\n+FSTFDWRAANFTHCDLTNSELGDLDIRRVDLQGVKLDNYQASLLMERLGIAIIG\n+>1028111959|WP_063866162.1|1|1|qnrB53|qnrB|target_protection|2|QUINOLONE|QUINOLONE|quinolone_resistance_pentapeptide_repeat_protein_QnrB53\n+MALALVGEKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNAS\n+ALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKAVLEKCELWENRWMGAQVLGATFSGSDLSGGE\n+FSTFDWRAANFTHCDLTNSELGDLDIRRVDLQGVKLDNYQASLLMERLGIAIIG\n+>1028111966|WP_063866168.1|1|1|qnrB54|qnrB|target_protection|2|QUINOLONE|QUINOLONE|quinolone_resistance_pentapeptide_repeat_protein_QnrB54\n+MALALVSEKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNAS\n+ALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGE\n+FSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAIIG\n+>1028111975|WP_063866176.1|1|1|qnrB55|qnrB|target_protection|2|QUINOLONE|QUINOLONE|quinolone_resistance_pentapeptide_repeat_protein_QnrB55\n+MTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQLYDRESQKGCNFSRANLKDAIFKSCDLSMADFRNIN\n+ALGIEIRHCRAQGSDFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGE\n+FSSFDWRAANVTHCDLTNSELGDLDIRGVDLQGVKLDSYQASLLLERLGIAVMG\n+>1028111984|WP_063866184.1|1|1|qnrB56|qnrB|target_protection|2|QUINOLONE|QUINOLONE|quinolone_resistance_pentapeptide_repeat_protein_QnrB56\n+MTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVS\n+ALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGE\n+FSTFDWRAGNFTHCDLTNSELGDLDIRGVDLQGVKLDSYQASLLMERLGIAIIG\n+>1028111988|WP_063866188.1|1|1|qnrB57|qnrB|target_protection|2|QUINOLONE|QUINOLONE|quinolone_resistance_pentapeptide_repeat_protein_QnrB57\n+MALALVGEKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNAS\n+ALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGE\n+FSTFDWRAANFTHCDLTNSELGNLDIRGVDLQGVKLDNYQASLLMERLGIAIIG\n+>1028111993|WP_063866193.1|1|1|qnrB58|qnrB|target_protection|2|QUINOLONE|QUINOLONE|quinolone_resistance_pentapeptide_repeat_protein_QnrB58\n+MALALVGEKIDRNRFTGEKIDNSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNAS\n+ALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGE\n+FSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAIIG\n+>1028111999|WP_063866199.1|1|1|qnrB59|qnrB|target_protection|2|QUINOLONE|QUINOLONE|quinolone_resistance_pentapeptide_repeat_protein_QnrB59\n+MTLALVGEKIDRNRFTSEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVS\n' |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test-db/AMRProt-mutation.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/AMRProt-mutation.tab Fri May 26 09:19:12 2023 +0000 |
| b |
| b'@@ -0,0 +1,1056 @@\n+#taxgroup\taccession_version\tmutation_position\tmutation_symbol\tclass\tsubclass\tmutated_protein_name\n+Escherichia\tWP_000019358.1\t12\tsoxS_A12S\tMULTIDRUG\tAMPICILLIN/CHLORAMPHENICOL/QUINOLONE/RIFAMPIN/TETRACYCLINE\tEscherichia_ampicillin/chloramphenicol/quinolone/rifampin/tetracycline_resistant_SoxS\n+Salmonella\tWP_000019483.1\t52\tsoxS_E52K\tMULTIDRUG\tAMPICILLIN/CHLORAMPHENICOL/QUINOLONE/RIFAMPIN/TETRACYCLINE\tSalmonella_ampicillin/chloramphenicol/quinolone/rifampin/tetracycline_resistant_SoxS\n+Escherichia\tWP_000031783.1\t121\ttufA_L121Q\tPOLYKETIDE\tKIRROMYCIN\tEscherichia_kirromycin_resistant_TufA\n+Escherichia\tWP_000031783.1\t125\ttufA_Q125E\tPOLYKETIDE\tKIRROMYCIN\tEscherichia_kirromycin_resistant_TufA\n+Escherichia\tWP_000031783.1\t125\ttufA_Q125K\tPOLYKETIDE\tKIRROMYCIN\tEscherichia_kirromycin_resistant_TufA\n+Escherichia\tWP_000031783.1\t125\ttufA_Q125R\tPOLYKETIDE\tKIRROMYCIN\tEscherichia_kirromycin_resistant_TufA\n+Escherichia\tWP_000031783.1\t161\ttufA_Y161C\tPOLYKETIDE\tKIRROMYCIN\tEscherichia_kirromycin_resistant_TufA\n+Escherichia\tWP_000031783.1\t161\ttufA_Y161D\tPOLYKETIDE\tKIRROMYCIN\tEscherichia_kirromycin_resistant_TufA\n+Escherichia\tWP_000031783.1\t161\ttufA_Y161N\tPOLYKETIDE\tKIRROMYCIN\tEscherichia_kirromycin_resistant_TufA\n+Escherichia\tWP_000031783.1\t231\ttufA_R231C\tPOLYKETIDE\tPULVOMYCIN\tEscherichia_pulvomycin_resistant_TufA\n+Escherichia\tWP_000031783.1\t231\ttufA_R231V\tPOLYKETIDE\tPULVOMYCIN\tEscherichia_pulvomycin_resistant_TufA\n+Escherichia\tWP_000031783.1\t234\ttufA_R234F\tPOLYKETIDE\tPULVOMYCIN\tEscherichia_pulvomycin_resistant_TufA\n+Escherichia\tWP_000031783.1\t234\ttufA_R234S\tPOLYKETIDE\tPULVOMYCIN\tEscherichia_pulvomycin_resistant_TufA\n+Escherichia\tWP_000031783.1\t317\ttufA_G317D\tPOLYKETIDE\tKIRROMYCIN\tEscherichia_kirromycin_resistant_TufA\n+Escherichia\tWP_000031783.1\t330\ttufA_Q330H\tPOLYKETIDE\tKIRROMYCIN\tEscherichia_kirromycin_resistant_TufA\n+Escherichia\tWP_000031783.1\t334\ttufA_R334C\tPOLYKETIDE\tPULVOMYCIN\tEscherichia_pulvomycin_resistant_TufA\n+Escherichia\tWP_000031783.1\t335\ttufA_T335A\tPOLYKETIDE\tPULVOMYCIN\tEscherichia_pulvomycin_resistant_TufA\n+Escherichia\tWP_000031783.1\t376\ttufA_A376S\tPOLYKETIDE\tKIRROMYCIN\tEscherichia_kirromycin_resistant_TufA\n+Escherichia\tWP_000031783.1\t376\ttufA_A376T\tPOLYKETIDE\tKIRROMYCIN\tEscherichia_kirromycin_resistant_TufA\n+Escherichia\tWP_000031783.1\t376\ttufA_A376V\tPOLYKETIDE\tKIRROMYCIN\tEscherichia_kirromycin_resistant_TufA\n+Escherichia\tWP_000031783.1\t379\ttufA_E379K\tPOLYKETIDE\tKIRROMYCIN\tEscherichia_kirromycin_resistant_TufA\n+Acinetobacter_baumannii\tWP_000064875.1\t68\tlpxA_G68D\tCOLISTIN\tCOLISTIN\tAcinetobacter_baumannii_colistin_resistant_LpxA\n+Acinetobacter_baumannii\tWP_000064875.1\t72\tlpxA_Q72K\tCOLISTIN\tCOLISTIN\tAcinetobacter_baumannii_colistin_resistant_LpxA\n+Acinetobacter_baumannii\tWP_000064875.1\t159\tlpxA_H159D\tCOLISTIN\tCOLISTIN\tAcinetobacter_baumannii_colistin_resistant_LpxA\n+Acinetobacter_baumannii\tWP_000064875.1\t233\tlpxA_D233STOP\tCOLISTIN\tCOLISTIN\tAcinetobacter_baumannii_colistin_resistant_LpxA\n+Salmonella\tWP_000072047.1\t421\tgyrB_Y421C\tQUINOLONE\tQUINOLONE\tSalmonella_quinolone_resistant_GyrB\n+Salmonella\tWP_000072047.1\t438\tgyrB_R438L\tQUINOLONE\tQUINOLONE\tSalmonella_quinolone_resistant_GyrB\n+Salmonella\tWP_000072047.1\t464\tgyrB_S464F\tQUINOLONE\tCIPROFLOXACIN\tSalmonella_ciprofloxacin_resistant_GyrB\n+Salmonella\tWP_000072047.1\t464\tgyrB_S464T\tQUINOLONE\tCIPROFLOXACIN\tSalmonella_ciprofloxacin_resistant_GyrB\n+Salmonella\tWP_000072047.1\t464\tgyrB_S464Y\tQUINOLONE\tCIPROFLOXACIN\tSalmonella_ciprofloxacin_resistant_GyrB\n+Salmonella\tWP_000072047.1\t466\tgyrB_E466D\tQUINOLONE\tQUINOLONE\tSalmonella_quinolone_resistant_GyrB\n+Escherichia\tWP_000072067.1\t136\tgyrB_R136C\tAMINOCOUMARIN\tAMINOCOUMARIN\tEscherichia_aminocoumarin_resistant_GyrB\n+Escherichia\tWP_000072067.1\t136\tgyrB_R136E\tAMINOCOUMARIN\tAMINOCOUMARIN\tEscherichia_aminocoumarin_resistant_GyrB\n+Escherichia\tWP_000072067.1\t136\tgyrB_R136G\tAMINOCOUMARIN\tAMINOCOUMARIN\tEscherichia_aminocoumarin_resistant_GyrB\n+Escherichia\tWP_000072067.1\t136\tgyrB_R136H\tAMINOCOUMARIN\tAMINOCOUMARIN\tEscherichia_aminocoumarin_resist'..b'OMYCIN\tStaphylococcus_aureus_daptomycin_resistant_MprF\n+Staphylococcus_aureus\tWP_111724484.1\t347\tmprF_M347R\tLIPOPEPTIDE\tDAPTOMYCIN\tStaphylococcus_aureus_daptomycin_resistant_MprF\n+Staphylococcus_aureus\tWP_111724484.1\t351\tmprF_V351E\tLIPOPEPTIDE\tDAPTOMYCIN\tStaphylococcus_aureus_daptomycin_resistant_MprF\n+Staphylococcus_aureus\tWP_111724484.1\t420\tmprF_I420N\tLIPOPEPTIDE\tDAPTOMYCIN\tStaphylococcus_aureus_daptomycin_resistant_MprF\n+Staphylococcus_aureus\tWP_111724484.1\t472\tmprF_T472K\tLIPOPEPTIDE\tDAPTOMYCIN\tStaphylococcus_aureus_daptomycin_resistant_MprF\n+Staphylococcus_aureus\tWP_111724484.1\t826\tmprF_L826F\tLIPOPEPTIDE\tDAPTOMYCIN\tStaphylococcus_aureus_daptomycin_resistant_MprF\n+Enterococcus_faecium\tWP_115256011.1\t82\tparC_S80I\tQUINOLONE\tQUINOLONE\tEnterococcus_faecium_quinolone_resistant_ParC\n+Enterococcus_faecium\tWP_115256011.1\t82\tparC_S80R\tQUINOLONE\tQUINOLONE\tEnterococcus_faecium_quinolone_resistant_ParC\n+Enterococcus_faecium\tWP_115256011.1\t86\tparC_E84A\tQUINOLONE\tQUINOLONE\tEnterococcus_faecium_quinolone_resistant_ParC\n+Enterococcus_faecium\tWP_115256011.1\t86\tparC_E84K\tQUINOLONE\tQUINOLONE\tEnterococcus_faecium_quinolone_resistant_ParC\n+Enterococcus_faecium\tWP_115256011.1\t86\tparC_E84T\tQUINOLONE\tQUINOLONE\tEnterococcus_faecium_quinolone_resistant_ParC\n+Klebsiella_pneumoniae\tWP_117036963.1\t83\tgyrA_S83F\tQUINOLONE\tQUINOLONE\tKlebsiella_pneumoniae_quinolone_resistant_GyrA\n+Klebsiella_pneumoniae\tWP_117036963.1\t83\tgyrA_S83I\tQUINOLONE\tQUINOLONE\tKlebsiella_pneumoniae_quinolone_resistant_GyrA\n+Klebsiella_pneumoniae\tWP_117036963.1\t83\tgyrA_S83L\tQUINOLONE\tQUINOLONE\tKlebsiella_pneumoniae_quinolone_resistant_GyrA\n+Klebsiella_pneumoniae\tWP_117036963.1\t83\tgyrA_S83T\tQUINOLONE\tQUINOLONE\tKlebsiella_pneumoniae_quinolone_resistant_GyrA\n+Klebsiella_pneumoniae\tWP_117036963.1\t83\tgyrA_S83Y\tQUINOLONE\tQUINOLONE\tKlebsiella_pneumoniae_quinolone_resistant_GyrA\n+Klebsiella_pneumoniae\tWP_117036963.1\t87\tgyrA_D87A\tQUINOLONE\tQUINOLONE\tKlebsiella_pneumoniae_quinolone_resistant_GyrA\n+Klebsiella_pneumoniae\tWP_117036963.1\t87\tgyrA_D87G\tQUINOLONE\tQUINOLONE\tKlebsiella_pneumoniae_quinolone_resistant_GyrA\n+Klebsiella_pneumoniae\tWP_117036963.1\t87\tgyrA_D87H\tQUINOLONE\tQUINOLONE\tKlebsiella_pneumoniae_quinolone_resistant_GyrA\n+Klebsiella_pneumoniae\tWP_117036963.1\t87\tgyrA_D87N\tQUINOLONE\tQUINOLONE\tKlebsiella_pneumoniae_quinolone_resistant_GyrA\n+Klebsiella_pneumoniae\tWP_117036963.1\t87\tgyrA_D87Y\tQUINOLONE\tQUINOLONE\tKlebsiella_pneumoniae_quinolone_resistant_GyrA\n+Staphylococcus_aureus\tWP_123090655.1\t183\tpbp4_E183A\tBETA-LACTAM\tCEPHALOSPORIN\tStaphylococcus_aureus_cephalosporin_resistant_Pbp4\n+Staphylococcus_aureus\tWP_123090655.1\t200\tpbp4_R200L\tBETA-LACTAM\tCEPHALOSPORIN\tStaphylococcus_aureus_cephalosporin_resistant_Pbp4\n+Staphylococcus_aureus\tWP_123090655.1\t218\tpbp4_E218K\tBETA-LACTAM\tCEPHALOSPORIN\tStaphylococcus_aureus_cephalosporin_resistant_Pbp4\n+Staphylococcus_aureus\tWP_123090655.1\t241\tpbp4_F241R\tBETA-LACTAM\tCEPHALOSPORIN\tStaphylococcus_aureus_cephalosporin_resistant_Pbp4\n+Enterococcus_faecium\tWP_137277832.1\t84\tgyrA_S83I\tQUINOLONE\tQUINOLONE\tEnterococcus_faecium_quinolone_resistant_GyrA\n+Enterococcus_faecium\tWP_137277832.1\t84\tgyrA_S83L\tQUINOLONE\tQUINOLONE\tEnterococcus_faecium_quinolone_resistant_GyrA\n+Enterococcus_faecium\tWP_137277832.1\t84\tgyrA_S83N\tQUINOLONE\tQUINOLONE\tEnterococcus_faecium_quinolone_resistant_GyrA\n+Enterococcus_faecium\tWP_137277832.1\t84\tgyrA_S83R\tQUINOLONE\tQUINOLONE\tEnterococcus_faecium_quinolone_resistant_GyrA\n+Enterococcus_faecium\tWP_137277832.1\t84\tgyrA_S83Y\tQUINOLONE\tQUINOLONE\tEnterococcus_faecium_quinolone_resistant_GyrA\n+Enterococcus_faecium\tWP_137277832.1\t88\tgyrA_E87G\tQUINOLONE\tQUINOLONE\tEnterococcus_faecium_quinolone_resistant_GyrA\n+Enterococcus_faecium\tWP_137277832.1\t88\tgyrA_E87K\tQUINOLONE\tQUINOLONE\tEnterococcus_faecium_quinolone_resistant_GyrA\n+Enterococcus_faecium\tWP_137277832.1\t88\tgyrA_E87L\tQUINOLONE\tQUINOLONE\tEnterococcus_faecium_quinolone_resistant_GyrA\n+Enterococcus_faecium\tWP_137277832.1\t98\tgyrA_S97N\tQUINOLONE\tQUINOLONE\tEnterococcus_faecium_quinolone_resistant_GyrA\n' |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test-db/AMRProt-suppress --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/AMRProt-suppress Fri May 26 09:19:12 2023 +0000 |
| b |
| @@ -0,0 +1,17 @@ +#taxgroup protein_accession protein_gi +Escherichia AAA21095.1 151858 +Escherichia AAA21096.1 151859 +Escherichia AAB09628.1 1061418 +Escherichia BAA24823.1 2879920 +Escherichia BAA24824.1 2879921 +Escherichia BAA15331.2 85675040 +Escherichia BAE77395.1 85676145 +Escherichia BAE77620.1 85676370 +Escherichia BAE77793.1 85676543 +Klebsiella_oxytoca BAA24824.1 2879921 +Klebsiella_oxytoca BAB89353.1 20152201 +Klebsiella_pneumoniae ABR76310.1 150954280 +Salmonella BAE77395.1 85676145 +Staphylococcus_pseudintermedius AAA25637.1 150728 +Staphylococcus_pseudintermedius AAA27588.1 155345 +Vibrio_cholerae ABQ18953.1 146314413 |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test-db/AMRProt-susceptible.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/AMRProt-susceptible.tab Fri May 26 09:19:12 2023 +0000 |
| b |
| @@ -0,0 +1,27 @@ +#taxgroup gene_symbol accession_version resistance_cutoff class subclass resistance_protein_name +Neisseria_gonorrhoeae pbp2 WP_003703066.1 94.000000 BETA-LACTAM BETA-LACTAM Neisseria_gonorrhoeae_beta-lactam_resistant_PBP2 +Streptococcus_pneumoniae pbp1a WP_001039998.1 99.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP1A +Streptococcus_pneumoniae pbp1a WP_001040004.1 99.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP1A +Streptococcus_pneumoniae pbp1a WP_001040010.1 99.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP1A +Streptococcus_pneumoniae pbp1a WP_001040013.1 99.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP1A +Streptococcus_pneumoniae pbp1a WP_050078510.1 99.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP1A +Streptococcus_pneumoniae pbp1a WP_050208712.1 99.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP1A +Streptococcus_pneumoniae pbp1a WP_054370471.1 99.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP1A +Streptococcus_pneumoniae pbp2b WP_001224867.1 99.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP2B +Streptococcus_pneumoniae pbp2b WP_001224871.1 99.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP2B +Streptococcus_pneumoniae pbp2b WP_001224884.1 99.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP2B +Streptococcus_pneumoniae pbp2b WP_001224885.1 99.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP2B +Streptococcus_pneumoniae pbp2b WP_001224886.1 99.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP2B +Streptococcus_pneumoniae pbp2b WP_061634854.1 99.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP2B +Streptococcus_pneumoniae pbp2x WP_000872264.1 98.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP2X +Streptococcus_pneumoniae pbp2x WP_000872267.1 98.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP2X +Streptococcus_pneumoniae pbp2x WP_000872270.1 98.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP2X +Streptococcus_pneumoniae pbp2x WP_000872271.1 98.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP2X +Streptococcus_pneumoniae pbp2x WP_000872273.1 98.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP2X +Streptococcus_pneumoniae pbp2x WP_000872275.1 98.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP2X +Streptococcus_pneumoniae pbp2x WP_000872277.1 98.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP2X +Streptococcus_pneumoniae pbp2x WP_000872282.1 98.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP2X +Streptococcus_pneumoniae pbp2x WP_033707918.1 98.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP2X +Streptococcus_pneumoniae pbp2x WP_050293540.1 98.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP2X +Streptococcus_pneumoniae pbp2x WP_054364452.1 98.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP2X +Streptococcus_pneumoniae pbp2x WP_061745305.1 98.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP2X |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test-db/AMRProt.pdb |
| b |
| Binary file test-data/test-db/AMRProt.pdb has changed |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test-db/AMRProt.phr |
| b |
| Binary file test-data/test-db/AMRProt.phr has changed |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test-db/AMRProt.pin |
| b |
| Binary file test-data/test-db/AMRProt.pin has changed |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test-db/AMRProt.pjs --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/AMRProt.pjs Fri May 26 09:19:12 2023 +0000 |
| [ |
| @@ -0,0 +1,22 @@ +{ + "version": "1.2", + "dbname": "AMRProt", + "dbtype": "Protein", + "db-version": 5, + "description": "AMRProt", + "number-of-letters": 585748, + "number-of-sequences": 1848, + "last-updated": "2023-05-12T11:10:00", + "number-of-volumes": 1, + "bytes-total": 1038796, + "bytes-to-cache": 602469, + "files": [ + "AMRProt.pdb", + "AMRProt.phr", + "AMRProt.pin", + "AMRProt.pot", + "AMRProt.psq", + "AMRProt.ptf", + "AMRProt.pto" + ] +} |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test-db/AMRProt.psq |
| b |
| Binary file test-data/test-db/AMRProt.psq has changed |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test-db/AMRProt.ptf |
| b |
| Binary file test-data/test-db/AMRProt.ptf has changed |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test-db/AMRProt.pto |
| b |
| Binary file test-data/test-db/AMRProt.pto has changed |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test-db/AMR_CDS --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/AMR_CDS Fri May 26 09:19:12 2023 +0000 |
| b |
| b'@@ -0,0 +1,1000 @@\n+>0|EAC4468893.1|AAAIJS010000026.1|1|1|emrC_Lis|emrC_Lis|multidrug_efflux_transporter_outer_membrane_subunit_EmrC AAAIJS010000026.1:2413-2027\n+atgtcgtatttatatttaacactagccataataggagaacttattggttcgtctatgctcaaagcttctgaaggattttc\n+aaaactctatcctactattggtgtaataattgcttttataagcgcatttttctttttatcactagcaatgaagactattc\n+cacttaataccgcctatgccatttggtctggaataggaatcgttgctacaaccattatttccgttctaatttggaaagag\n+aaagtcaatgctgccagtgttacaggaatcgcattaattcttataggtgttgtaatattgaatctatttggtccagggca\n+cggtgaagcaagtaataatgaaaaagtaaatgaatccacaatcattgccagtaataaaatggaataa\n+>0|EGO5141043.1|AAXDBA010000092.1|1|1|arsR_LGI2_1|arsR_LGI2_1|As(III)-sensing_metalloregulatory_transcriptional_repressor_ArsR AAXDBA010000092.1:1754-2047\n+atggattatttaggattatcaaaaattatgaaggcaattgcagagcctaatagacttcaaatattagatatgatttcaac\n+tggtgaaaagtgtgcatgtgatattttggataattttgattttactcagccgacactatcacatcatatgaaggttttaa\n+ttgaggcgggagtagtaaccgcacgtaaggaaggcaaatggcaatattattctctggtaacagagaacattgaagaattt\n+caagaattaatacatcagatattgaatataaaacaaaaagaaggagttatgtaa\n+>0|MBO4175406.1|JAGFWX010000027.1|1|1|mcr-9.2|mcr-9|phosphoethanolamine--lipid_A_transferase_MCR-9.2 JAGFWX010000027.1:224-1846\n+atgcctgtacttttcagggtgaaagttattccgctggttttacttctggcaatgatctttgcgtttttacttaactggcc\n+aatattgctgcatttttacgagattttgtcgcatttagagcatgtcaaaattggttttgtcatttctattccctttgttc\n+tggttgcggcgcttaacgttgtttttatgcctttctcagttcgttttctgctgaaacctttctttgctttactgtttatc\n+actggctcactggtcagttattcgacactaaaatataaagtaatgtttgatcaaacgatgattcaaaacattattgaaac\n+taacccccaggaagcgcattcctatcttaatggctcaattattatatggttcgtctttaccggtatccttcctgccatcc\n+tccttttttcaataaaaattcaatatcctgaaaaatggtataaaggcattgcttaccgtttgctctccgtgctggcatcg\n+ttgagtttgattgcaggtgttgccgcactttattatcaggattatgcctctgtcggccgcaataactcgacattgaataa\n+agagatcatcccggcgaactacgcttacagcactttccagtatgttaaggatacgtactttacgactaaagtgcctttcc\n+agacgctggggaatgatgctaaacgcgtcgtcgctcacgaaaaacccacgctgatgttcctggtgattggcgaaacggca\n+cgcagccagaatttctcgatgaacggttattcgcgtgataccaatgcctttaccagcaaatccggcggcgttatttcgtt\n+taaaaatatgcattcctgcggtaccgctaccgcaatatccgttccgtgcatgttctcgaatatgaatcgcaccgagtacg\n+acagtaaaaaagcatctaacagtgaaaatttcctcgacatcgtgcagaaaaccggtgtctcgctgttatggaaagagaac\n+gatggcggttgtaaaggcgtatgtagccgcatcccgactgtcgaaattaagcctagtgataacccgaaactgtgcgatgg\n+caaaacgtgccatgacgaggtgatgctggaaaaccttgatgatgaaatcgccaaaatgccaggtgataagcttgtcgcct\n+tccatatcattggcagccatggaccgacttattacctgcgttatccggctgagcatcgccacttcatgcccgaatgtgca\n+cgtagcgatatcgaaaactgtactcaggaacaattggtcaacacctacgacaacacccttcgttatacagactatgtatt\n+agctgagatgattgaaaagctaaaaaattacagcgatcagtacaacaccgtgctgctttatgtgtccgatcatggtgaat\n+cattgggcgaaagcgggctatatctgcacggcacgccgtacaaactggcaccggatcagcagacgcatattccgatgcag\n+gtctggatgtcaccgggctttatcgccgggaaacacatcaacatgtcttgccttgaaaataatgcggcgaaaaaatcata\n+ttcccacgacaacctgttctcatcgattttggggctgtgggacgtaagcaccagcgtctataatcctgaccgcgatttgt\n+tccgcgaatgccgtggctggtaa\n+>0|MBY0597968.1|JAIKLI010000168.1|1|1|entFM|entFM|enterotoxin_EntFM JAIKLI010000168.1:169310-168018\n+atgaaaaaagtactagcaggtttagcagcagcatctgtagctggcgtagcagttcctggaatggatactgctcatgcaca\n+agtttcagctgatgcactaaaagaaatcaatggacaaactcaagaacaaacggttgaaacaaatgtaactgaaacaaatg\n+cagtagaaacaaattctgaactaaaatatacagtaacagctgatgtattaaatgttcgttcaggtgctggcacaggacat\n+aacattatttctaaagtaacagaaggccaagtgctacaagtaactggtcaagaaaatggctggtttaaagtaaatgtaaa\n+cggtcaaacaggctatgtaagcggcgacttcgtaacaactggtggaaaacaaggaactgctgttcaacaaggaacaggta\n+catatacagtaaatgtttcttcacttaacgtacgtacaggccctagcgcttctcatacagttgtaggtactgtaaacaaa\n+ggacaaactgtacaagttgtcggtgaagtacaagactggtttaaaattaaccgcgatggcggaactggctatgtaagtaa\n+agactttgtaacaaaaggcggcacaactacaaatgtaaatacagaaacagaaaagcctagcaacaatgaaatgacaatcc\n+gaaaagatggttcatatgttgttgatacaggtgctttacgtgtacgtacaggcccagctacatataatcctgtaattggt\n+ggcgtagtgaaaggtcaaacattacaagttattagtggggaaaacggttggtataaaattaaccaccaaggaaaaacagg\n+ttatgtaagtgcagatcttgttaagtttgtaaaaggtggtacagcaaatgtaactacgccttctcgtccaactactggcg\n+gtgagcaaggaaatacacaaacagaaaaaccgacaacaccatctgctaatggatcatcaattgtgtctattgcacaatca\n+ttaaatggttcaccatatacatggggaggtacaacacctaatggctttgactgcagtggtttcatttactatgtattaaa\n+agaagcaggtcattctggtgg'..b"atacattattaaaattaggggtatgtgttagtttactaggaataactccatttgttagtacaatttcttctgt\n+acaagcagaacgaaaggtagagcataaagtaataaaaaatgagacaggaactatttcaatttctcagttaaacaaaaatg\n+tttgggttcatacggagttaggttgttttaacggagaagcagttccttcgaacggtttaatccttaatacttctaaagga\n+ttagtacttgtcgattcttcttgggatgataagttaacgaaggaattaatagagatggcagaaaagaaatttaagaagag\n+tgtaacggatgttattattacacatgcacacgctgatcggattggtggaataaaaacgttgaaagaaagaggcattaaag\n+cgcatagtacaacgttaactgcggaactagcaaagaaaaatggatatgaagaaccacttggagacttacaagcaattacg\n+aaattgaagtttggaaatatgaaagtagaaacgttttatccagggaaaggacatacagaagataatatcgtcgtatggtt\n+accacaatacaacatgttagttggaggctgtttagtgaagtctgcgtccgcgaaagatttaggaaatattactgatgctt\n+atgtaaatgaatggtctacatcgattgagaatgtgctgaagcgatatgaaaatataaattttgtagtacctggtcatgga\n+gaagtaggggacaaaggattacttttacatacattggatttgttaaaataa\n+>1028079000|WP_063839881.1|NG_047225.1|1|1|aac(2')-IIa|aac(2')-IIa|kasugamycin_N-acetyltransferase_AAC(2')-IIa NG_047225.1:101-883\n+atgaaagacagatcccatgacgactcaatggccgaggtctgtcggaacacctctgagaaccactggctgaagaccgatta\n+tcggacgttgtttcggctgtgccccgacggtcggatcgagcgcgagaatgatccggactgctcgccggggccgcgtttct\n+ggttggctggctgttcggaaggcaacgtgttcggcgtacgtgccgatgtgcccgatgacatagcactaaagctcgaagaa\n+ctcgccagcgtcgagcctccgttcacacccccggcgataccgaagcatcttgaacgttatctttcactgctcggcagtga\n+tggccctgttacccacgatcttggtctgatttacgagttgccgcacgcgcagcagtacccgagcaaggcccggctcatcg\n+gcagcggttccgaggagggcgagagtctgatgcagtcttgggcggaggacagagtaccggaagctttgtttgagcttggc\n+ttccgtgaggtggcggacttctggacgccttggtgcgcggcagttgtcgatggtgaagtcgcttcaatcgcctttgcagc\n+gcgtctcgcggatgccggtgccgaactcgggttggtaacggcgaaggcattcagaggacaggggttcgccgccgctgcga\n+cggctggttggtcccggctctccgctcttcgttcccgcacgctgttctacagcacggaccgagacaacatttcatcgcag\n+cgcgttgccgcccgccttggtctccggcttcgtggagccagcttgcgaatatcacgcgcctga\n+>1028080873|WP_063840256.1|NG_047235.1|1|1|aac(3)-I|aac(3)-I|AAC(3)-I_family_aminoglycoside_3-N-acetyltransferase NG_047235.1:101-565\n+atgggcatcattcgcacatgtaggctcggccctgaccaagtccaatccatgcgggctgctcttgatcttttcggtcgtga\n+gttcggagacgtagccacctactcccaacatcagccggactccgattacctcgggaacttgctccgtagtaggacattca\n+tcgcgcttgctgccttcgagcaagaagcggttgttggcgctctcgcggcttacgttctgcccaagtttgagcaggcgcgt\n+agtgagatctatatctatgatctcgcagtctccggcgagcaccgccggcagggcattgccaccgcgctcatcaatctcct\n+caagcatgaggccaacgcgcttggtgcttacgtgatctacgtgcaagcggattacggtgacgatcccgcagtggctctct\n+atacaaagttgggcatacgggaagacgtgatgcactttgatatcgacccaagttccgccacctaa\n+>1028080874|WP_063840257.1|NG_047236.1|1|1|aac(3)-Ia|aac(3)-Ia|aminoglycoside_N-acetyltransferase_AAC(3)-Ia NG_047236.1:101-565\n+atgggcatcattcgcacatgtaggctcggccctgaccaagtcaaatccatgcgggctgctcttgatcttttcggtcgtga\n+gttcggagacgtagccacctactcccaacatcagccggactccgattacctcgggaacttgctccgtagtaagacattca\n+tcgcgcttgctgccttcgaccaagaagcggttgttggcgctctcgcggcttacgttctgcccaagtttgagcaggcgcgt\n+agtgagatctatatctatgatctcgcagtctccggcgagcaccggaggcagggcattgccaccgcgctcatcaatcccct\n+caagcatgaggccaacgcgcttggtgcttatgtgatctacgtgcaagcagattacggtgacgatcccgcagtggctctct\n+atacaaagttgggcatacgggaagaagtgatgcactttgatatcgacccaagtaccgccacctaa\n+>1028080875|WP_063840258.1|NG_047238.1|1|1|aac(3)-Ia|aac(3)-Ia|aminoglycoside_N-acetyltransferase_AAC(3)-Ia NG_047238.1:101-565\n+atgggcatcattcgcacatgtaggctcggccctgaccaagtcaaatccatgcgggctgctcttgatcttttcggtcgtga\n+gttcggagacgtagccacctactcccaacatcagccggactccgattacctcgggaacttgctccgtagtaagacattca\n+tcgcgctcgctgccttcgaccaagaagcggttgttggcgctctcgcggcttacgttctgcccaagtttgagcaggcgcgt\n+agtgagatctatatctatgatctcgcagtctccggcgagcaccggcggcagggcattgccaccgcgctcatcaatctcct\n+caagcatgaggccaacgcgcttggtgcttatgtgatctacgtgcaagcagattacggtgacgatcccgcagtggctctct\n+atacaaagttgggcatacgggaagacgtgatgcactttgatatcgacccaagtaccgccacctaa\n+>1028080876|WP_063840259.1|NG_047239.1|1|1|aac(3)-Ia|aac(3)-Ia|aminoglycoside_N-acetyltransferase_AAC(3)-Ia NG_047239.1:101-565\n+atgggcatcattcgcacatgtaggctcggccctgaccaagtcaaatccatgagggctgctcttgatcttttcggtcgtga\n+gttcggaggcgtagccacctactcccaacatcagccggactccgattacctcgggaacttgctccgtagtaagacattca\n+tcgcgcttgctgccttcgaccaagaagcggttgttggcgctctcgcggcttacgttctgccaaagtttgagcaggcgcgt\n+agtgagatctatatctatgatctcgcagtctccggcgagcaccggaggcaaggcattgccaccgcgctcatcaatctcct\n" |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test-db/AMR_DNA-Enterococcus_faecium --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/AMR_DNA-Enterococcus_faecium Fri May 26 09:19:12 2023 +0000 |
| b |
| @@ -0,0 +1,38 @@ +>NZ_CP041261.2@23S_ribosomal_RNA@23S:423530-426430 +ggcgcacggtggatgccttggcactaggagccgatgaaggacgggactaacaccgatatgctttggggagctgtacgtaa +gctatgatccagagatttccgaatgggggaacccaacatctttaataggatgttacgattgtgtgaatacatagcacatt +cgaggtagacgcagagaactgaaacatctaagtacctgcaggaagagaaagaaaattcgattccctgagtagcggcgagc +gaaacgggaaaagcccaaaccagcaagcttgcttgttggggttgtaggactccaatatggtagttctttcagatagtcga +atgacttggaaaagtcagtcaaagagggtaaaaaccccgtagacgaaatgtggaagacacctaggaggatcctgagtacg +gcggaacacgagaaattccgtcggaatccgggaggaccatctcccaaggctaaatactccctagtgaccgatagtgaacc +agtaccgtgagggaaaggtgaaaagcaccccggaaggggagtgaaatagaacctgaaaccgtgtgcctacaacaagtcaa +agcccgttaatgggtgatggcgtgccttttgtagaatgaaccggcgagttacgattgcatgcgaggttaagttgaagaga +cggagccgcagcgaaagcgagtctgaatagggcgtttgagtatgtagtcgtagacccgaaaccatgtgatctacccatgt +ccaggttgaaggtgcggtaaaacgcactggaggaccgaacccacgtacgttgaaaagtgcggggatgaggtgtgggtagc +ggagaaattccaaacgaacttggagatagctggttctctccgaaatagctttagggctagcctcggaattgagaatgatg +gaggtagagcactgtttggactaggggcccatctcgggttaccgaattcagataaactccgaatgccattcattcatatc +cgggagtcagactgtgagtgataagatccatagtcgaaagggaaacagcccagaccaccagctaaggtcccaaaatatat +gttaagtggaaaaggatgtggggttgcacagacaactaggatgttggcttagaagcagccaccatttaaagagtgcgtaa +tagctcactagtcgagtgaccctgcgccgaaaatgtaccggggctaaacatattaccgaagctgtggagtacacctttag +gtgtattggtaggagagcgttctaagggcgttgaaggcagatcgtgaggactgctggagcgcttagaagtgagaatgccg +gtatgagtagcgaaagacaggtgagaatcctgtccaccgaatgactaaggtttcctggggaaggctcgtccgcccagggt +tagtcgggacctaagccgaggccgacaggcgtaggcgatggataacaggttgatattcctgtacccgttgtttttgtttg +agcaatggagggacgcaggaggctaaggaatgcagacgatcggaaatgtctgtccaagcagtaagtctgaagaggagtca +aatgcttcttttcttaaggacaagctgtgatggggagggaaataatagtaccgaagttcctgatgtcacactgccgagaa +aagcttctagtgagaaaacagcggcccgtaccgcaaaccgacacaggtagtcgaggagagaatcctaaggtgagcgagag +aactctcgttaaggaactcggcaaaatgaccccgtaacttcgggagaaggggtgctgatcatacgatcagccgcagtgaa +taggcccaagcgactgtttatcaaaaacacaggtctctgcaaaatcgtaagatgaagtataggggctgacgcctgcccgg +tgctggaaggttaagaggagtgcttagcgcaagcgaaggtacgaattgaagccccagtaaacggcggccgtaactataac +ggtcctaaggtagcgaaattccttgtcgggtaagttccgacccgcacgaaaggcgtaacgatttgggcactgtctcaacg +agagactcggtgaaattttagtacctgtgaagatgcaggttacccgcgacaggacggaaagaccccatggagctttactg +tagtttgatattgagtgtctgtaccgcatgtacaggataggtaggagccgtagaaatcggaacgctagtttcgatggagg +cgctggtgggatactacccctgcgttatggccactctaacccgcaccactaatcgtggtgggagacagtgtcagatgggc +agtttgactggggcggtcgcctcctaaaaggtaacggaggcgcccaaaggttccctcagaatggttggaaatcattcgaa +gagtgtaaaggcagaagggagcttgactgcgagaccaacaagtcgagcagggacgaaagtcgggcttagtgatccggtgg +ttccgcatggaagggccatcgctcaacggataaaagctaccctggggataacaggcttatctcccccaagagtccacatc +gacggggaggtttggcacctcgatgtcggctcgtcgcatcctggggctgtagtcggtcccaagggttgggctgttcgccc +attaaagcggcacgcgagctgggttcagaacgtcgtgagacagttcggtccctatccgtcgcgggcgttggaaatttgag +aggagctgtccttagtacgagaggaccgggatggacttaccgctggtgtaccagttgttctgccaagggcattgctgggt +agctatgtagggaagggataaacgctgaaagcatctaagtgtgaagcccacctcaagatgagatttcccatttctttaag +aaagtaagatccctgagagatgatcaggtagataggtcaggagtggaagtacagtgatgtatggagcggactgatactaa +tcgatcgaggacttaaccaat |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test-db/AMR_DNA-Enterococcus_faecium.ndb |
| b |
| Binary file test-data/test-db/AMR_DNA-Enterococcus_faecium.ndb has changed |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test-db/AMR_DNA-Enterococcus_faecium.nhr |
| b |
| Binary file test-data/test-db/AMR_DNA-Enterococcus_faecium.nhr has changed |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test-db/AMR_DNA-Enterococcus_faecium.nin |
| b |
| Binary file test-data/test-db/AMR_DNA-Enterococcus_faecium.nin has changed |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test-db/AMR_DNA-Enterococcus_faecium.njs --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/AMR_DNA-Enterococcus_faecium.njs Fri May 26 09:19:12 2023 +0000 |
| [ |
| @@ -0,0 +1,22 @@ +{ + "version": "1.2", + "dbname": "AMR_DNA-Enterococcus_faecium", + "dbtype": "Nucleotide", + "db-version": 5, + "description": "AMR_DNA-Enterococcus_faecium", + "number-of-letters": 2901, + "number-of-sequences": 1, + "last-updated": "2023-05-12T11:11:00", + "number-of-volumes": 1, + "bytes-total": 37883, + "bytes-to-cache": 879, + "files": [ + "AMR_DNA-Enterococcus_faecium.ndb", + "AMR_DNA-Enterococcus_faecium.nhr", + "AMR_DNA-Enterococcus_faecium.nin", + "AMR_DNA-Enterococcus_faecium.not", + "AMR_DNA-Enterococcus_faecium.nsq", + "AMR_DNA-Enterococcus_faecium.ntf", + "AMR_DNA-Enterococcus_faecium.nto" + ] +} |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test-db/AMR_DNA-Enterococcus_faecium.not |
| b |
| Binary file test-data/test-db/AMR_DNA-Enterococcus_faecium.not has changed |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test-db/AMR_DNA-Enterococcus_faecium.nsq |
| b |
| Binary file test-data/test-db/AMR_DNA-Enterococcus_faecium.nsq has changed |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test-db/AMR_DNA-Enterococcus_faecium.ntf |
| b |
| Binary file test-data/test-db/AMR_DNA-Enterococcus_faecium.ntf has changed |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test-db/AMR_DNA-Enterococcus_faecium.nto |
| b |
| Binary file test-data/test-db/AMR_DNA-Enterococcus_faecium.nto has changed |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test-db/AMR_DNA-Enterococcus_faecium.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/AMR_DNA-Enterococcus_faecium.tab Fri May 26 09:19:12 2023 +0000 |
| b |
| @@ -0,0 +1,3 @@ +#accesion_version@gene_name@gene_symbol:start-stop mutation_position mutation_symbol class subclass mutated_gene_name +NZ_CP041261.2@23S_ribosomal_RNA@23S:423530-426430 2505 23S_G2505A OXAZOLIDINONE LINEZOLID Enterococcus_faecium_linezolid_resistant_23S +NZ_CP041261.2@23S_ribosomal_RNA@23S:423530-426430 2576 23S_G2576T OXAZOLIDINONE LINEZOLID Enterococcus_faecium_linezolid_resistant_23S |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test-db/database_format_version.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/database_format_version.txt Fri May 26 09:19:12 2023 +0000 |
| b |
| @@ -0,0 +1,1 @@ +3.11.1 |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test-db/fam.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/fam.tab Fri May 26 09:19:12 2023 +0000 |
| b |
| b'@@ -0,0 +1,1905 @@\n+#node_id\tparent_node_id\tgene_symbol\thmm_id\thmm_tc1\thmm_tc2\tblastrule_complete_ident\tblastrule_complete_wp_coverage\tblastrule_complete_br_coverage\tblastrule_partial_ident\tblastrule_partial_wp_coverage\tblastrule_partial_br_coverage\treportable\ttype\tsubtype\tclass\tsubclass\tfamily_name\n+ACID\tSTRESS\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tACID\t\t\t\n+ALL\t\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\t\t\t\t\t\n+AME\tAMR\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\taminoglycoside modifying enzymes\n+AMR\tALL\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\t\n+BIOCIDE\tSTRESS\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tBIOCIDE\t\t\t\n+BcII\tbla-B1\tbla2\tNF033095.1\t500.00\t500.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tBETA-LACTAM\tCARBAPENEM\tBcII family subclass B1 metallo-beta-lactamase\n+CDF_efflux\tMETAL\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tMETAL\t\t\tCDF family cation efflux transporter\n+CMY2-MIR-ACT-EC\tbla-C\tampC\tNF012173.1\t680.00\t680.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tBETA-LACTAM\tBETA-LACTAM\tCMY2/MIR/ACT/EC family class C beta-lactamase\n+EFFLUX\tAMR\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\tefflux\n+HARLDQ_not_B3\tbla-B3\t-\tNF000405.1\t350.00\t350.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\tHARLDQ motif MBL-fold protein\n+HEAT\tSTRESS\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tHEAT\t\t\t\n+HTH_5\tMETAL\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tMETAL\t\t\tArsR/SmtB family metalloregulatory transcriptional repressor\n+LHR_hdeD\tHEAT\thdeD-GI\t-\t0.00\t0.00\t90.00\t90.00\t90.00\t93.00\t90.00\t25.00\t1\tSTRESS\tHEAT\t\t\theat resistance membrane protein HdeD-GI\n+LHR_hsp20A\tHEAT\thsp20\t-\t0.00\t0.00\t94.00\t90.00\t90.00\t96.00\t90.00\t25.00\t1\tSTRESS\tHEAT\t\t\tsmall heat shock protein sHSP20\n+LHR_hsp20B\tHEAT\tshsP\t-\t0.00\t0.00\t93.00\t90.00\t90.00\t94.00\t90.00\t25.00\t1\tSTRESS\tHEAT\t\t\tsmall heat shock protein sHSP20-GI\n+LHR_kefB\tHEAT\tkefB-GI\t-\t0.00\t0.00\t86.00\t90.00\t90.00\t90.00\t90.00\t25.00\t1\tSTRESS\tHEAT\t\t\theat resistance system K+/H+ antiporter KefB-GI\n+LHR_psiE\tHEAT\tpsi-GI\t-\t0.00\t0.00\t88.00\t90.00\t90.00\t90.00\t90.00\t25.00\t1\tSTRESS\tHEAT\t\t\theat resistance protein PsiE-GI\n+LHR_trx\tHEAT\ttrxLHR\t-\t0.00\t0.00\t85.00\t90.00\t90.00\t90.00\t90.00\t25.00\t1\tSTRESS\tHEAT\t\t\theat resistance system thioredoxin Trx-GI\n+LHR_yfdX1\tHEAT\tyfdX1\t-\t0.00\t0.00\t88.00\t90.00\t90.00\t90.00\t90.00\t25.00\t1\tSTRESS\tHEAT\t\t\theat resistance protein YfdX1\n+LHR_yfdX2\tHEAT\tyfdX2\t-\t0.00\t0.00\t90.00\t90.00\t90.00\t90.00\t90.00\t25.00\t1\tSTRESS\tHEAT\t\t\theat resistance protein YfdX2\n+MATE_efflux\tEFFLUX\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\tmultidrug efflux MATE transporter\n+METAL-RND-IM\tMETAL\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tMETAL\t\t\tcation efflux RND transporter permease subunit\n+METAL\tSTRESS\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tMETAL\t\t\tMetal Resistance\n+MFS_efflux_CHL\tMFS_efflux\tcml\t-\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tPHENICOL\tCHLORAMPHENICOL\tchloramphenicol efflux MFS transporter\n+MFS_efflux_qac\tBIOCIDE\tqac\tNF000089.1\t900.00\t900.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tSTRESS\tBIOCIDE\tQUATERNARY AMMONIUM\tQUATERNARY AMMONIUM\tQacA/B family quaternary ammonium compound efflux MFS transporter\n+MFS_efflux\tEFFLUX\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\tmultidrug efflux MFS transporter\n+MerP_Gneg\tmerP\tmerP\tTIGR02052.1\t92.55\t92.55\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t1\tSTRESS\tMETAL\tMERCURY\tMERCURY\tmercury resistance system periplasmic binding protein MerP\n+OM_sidero\tVIRULENCE_Ecoli\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tVIRULENCE\tVIRULENCE\t\t\tTonB-dependent siderophore receptor\n+P-type_ATPase\tMETAL\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tMETAL\t\t\tmetal-translocating P-type ATPase\n+PERI-SENSOR\tMETAL\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tMETAL\t\t\tperiplasmic heavy metal sensor\n+RESPONSE_REG\tAMR\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\tDNA-binding response regulator\n+RND-IM\tEFFLUX\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\tmultidrug efflux RND transporter permease subunit\n+RND-OM\tEFFLUX\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\tmultidrug'..b'ily ABC-F type ribosomal protection protein\n+vgb(A)\tvgb\tvgb(A)\tNF000022.1\t600.00\t600.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin B lyase Vgb(A)\n+vgb(B)\tvgb\tvgb(B)\tNF000096.1\t600.00\t600.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin B lyase Vgb(B)\n+vgb(C)\tvgb\tvgbC\t-\t0.00\t0.00\t84.00\t90.00\t90.00\t88.00\t90.00\t25.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin B lyase Vgb(C)\n+vgb\tAMR\tvgb\t-\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin B lyase\n+virF_Yersin\tVIRULENCE_Yersi\tvirF\t-\t0.00\t0.00\t90.00\t90.00\t90.00\t93.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\tvirulence regulon transcriptional activator VirF\n+virF\tVIRULENCE_Ecoli\tvirF\t-\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t1\tVIRULENCE\tVIRULENCE\t\t\tAraC family invasion system transcriptional regulator VirF\n+vmlR\tabc-f\tvmlR\t-\t0.00\t0.00\t90.00\t90.00\t90.00\t96.00\t90.00\t25.00\t2\tAMR\tAMR\tMACROLIDE/PLEUROMUTILIN\tLINCOSAMIDE/STREPTOGRAMIN/TIAMULIN\tABC-F type ribosomal protection protein VmlR\n+vph\tAMR\tvph\tNF000088.1\t400.00\t400.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tTUBERACTINOMYCIN\tVIOMYCIN\tviomycin phosphotransferase\n+yadA\tVIRULENCE_Yersi\tyadA\tNF033478.1\t750.00\t425.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t1\tVIRULENCE\tVIRULENCE\t\t\ttrimeric autotransporter adhesin YadA\n+ybtP\tVIRULENCE\tybtP\t-\t0.00\t0.00\t85.00\t90.00\t90.00\t96.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\tyersiniabactin ABC transporter ATP-binding/permease protein YbtP\n+ybtQ\tVIRULENCE\tybtQ\t-\t0.00\t0.00\t85.00\t90.00\t90.00\t96.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\tyersiniabactin ABC transporter ATP-binding/permease protein YbtQ\n+yfeA\tVIRULENCE\tyfeA\t-\t0.00\t0.00\t83.00\t90.00\t90.00\t88.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\tiron/manganese ABC transporter substrate-binding protein YfeA\n+yfeB\tVIRULENCE\tyfeB\t-\t0.00\t0.00\t86.00\t90.00\t90.00\t96.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\tiron/manganese ABC transporter ATP-binding protein YfeB\n+yfeD\tVIRULENCE\tyfeD\t-\t0.00\t0.00\t88.00\t90.00\t90.00\t92.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\tiron/manganese ABC transporter permease subunit YfeD\n+ymoA\tVIRULENCE_Yersi\tymoA\t-\t0.00\t0.00\t94.00\t90.00\t90.00\t96.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\texpression modulating protein YmoA\n+yopB\tVIRULENCE_Yersi\tyopB\t-\t0.00\t0.00\t90.00\t90.00\t90.00\t93.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\ttype III secretion system translocon subunit YopB\n+yopD\tVIRULENCE_Yersi\tyopD\t-\t0.00\t0.00\t90.00\t90.00\t90.00\t93.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\ttype III secretion system translocon subunit YopD\n+yopE\tVIRULENCE_Yersi\tyopE\t-\t0.00\t0.00\t92.00\t90.00\t90.00\t96.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\ttype III secretion system effector GTPase activator YopE\n+yopH\tVIRULENCE_Yersi\tyopH\t-\t0.00\t0.00\t94.00\t90.00\t90.00\t96.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\tT3SS effector protein-tyrosine-phosphatase YopH\n+yopJ_gen\tVIRULENCE_Yersi\tyopJ\tNF040632.1\t610.00\t610.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t1\tVIRULENCE\tVIRULENCE\t\t\tYopJ/YopP family T3SS effector serine/threonine acetyltransferase\n+yopM\tVIRULENCE_Yersi\tyopM\t-\t0.00\t0.00\t85.00\t90.00\t90.00\t90.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\ttype III secretion system effector YopM\n+yopO\tVIRULENCE_Yersi\tyopO\t-\t0.00\t0.00\t94.00\t90.00\t90.00\t96.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\ttype III secretion system effector protein kinase YopO/YpkA\n+yopT\tVIRULENCE_Yersi\tyopT\t-\t0.00\t0.00\t92.00\t90.00\t90.00\t96.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\tT3SS effector cysteine protease YopT\n+ystA\tVIRULENCE_Yersi\tystA\t-\t0.00\t0.00\t94.00\t90.00\t90.00\t96.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\tST-I family heat-stable enterotoxin YstA\n+ystB\tVIRULENCE_Yersi\tystB\t-\t0.00\t0.00\t94.00\t90.00\t90.00\t96.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\tST-I family heat-stable enterotoxin YstB\n+ystC\tVIRULENCE_Yersi\tystC\t-\t0.00\t0.00\t94.00\t90.00\t90.00\t96.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\tST-I family heat-stable enterotoxin YstC\n+zbmA\tble\tzbmA\tNF000479.1\t280.00\t280.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tBLEOMYCIN\tZORBAMYCIN\tzorbamycin binding protein ZbmA\n' |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test-db/taxgroup.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/taxgroup.tab Fri May 26 09:19:12 2023 +0000 |
| b |
| @@ -0,0 +1,25 @@ +#taxgroup gpipe_taxgroup number_of_nucl_ref_genes +Acinetobacter_baumannii Acinetobacter 0 +Burkholderia_cepacia Burkholderia_cepacia_complex 0 +Burkholderia_pseudomallei Burkholderia_pseudomallei 0 +Campylobacter Campylobacter 2 +Citrobacter_freundii Citrobacter_freundii 0 +Clostridioides_difficile Clostridioides_difficile 1 +Enterobacter_cloacae Enterobacter_cloacae 0 +Enterococcus_faecalis Enterococcus_faecalis 1 +Enterococcus_faecium Enterococcus_faecium 1 +Escherichia Escherichia_coli_Shigella 5 +Klebsiella_aerogenes Klebsiella 0 +Klebsiella_oxytoca Klebsiella_oxytoca 1 +Klebsiella_pneumoniae Klebsiella 0 +Neisseria_gonorrhoeae Neisseria_gonorrhoeae 6 +Neisseria_meningitidis Neisseria_meningitidis 0 +Pseudomonas_aeruginosa Pseudomonas_aeruginosa 0 +Salmonella Salmonella 1 +Serratia_marcescens Serratia 0 +Staphylococcus_aureus Staphylococcus_aureus 2 +Staphylococcus_pseudintermedius Staphylococcus_pseudintermedius 0 +Streptococcus_agalactiae Streptococcus_agalactiae 0 +Streptococcus_pneumoniae Streptococcus_pneumoniae 1 +Streptococcus_pyogenes Streptococcus_pyogenes 0 +Vibrio_cholerae Vibrio_cholerae 0 |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test-db/version.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/version.txt Fri May 26 09:19:12 2023 +0000 |
| b |
| @@ -0,0 +1,1 @@ +2023-04-17.1 |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test_1/amrfinderplus_mutation_all_report.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_1/amrfinderplus_mutation_all_report.tsv Fri May 26 09:19:12 2023 +0000 |
| b |
| b"@@ -0,0 +1,142 @@\n+>contig_26:6581-8545 strand:+ optrA ABC-F type ribosomal protection protein OptrA\n+TTGTCCAAAGCCACCTTTGCAATTGCTAGTACTAACGCAAAGGAGGATATGAAAATGCAA\n+TACAAAATAATTAATGGTGCCGTTTACTATGATGGTAATATGGTGTTGGAAAACATCGGT\n+ATTGAAATCAATGATAATGAAAAGATTGCTATTGTTGGTAGAAATGGATGTGGAAAAACA\n+ACCTTGCTAAAAGCTATTATAGGCGAAATTGAATTAGAAGAAGGAACTGGTGAAAGTGAG\n+TTTCAAGTAATAAAGACCGGTAACCCTTATATTAGCTATTTAAGACAGATGCCTTTTGAA\n+GATGAAAGTATATCAATGGTGGATGAAGTCCGTACGGTATTTAAGACGCTTATTGATATG\n+GAAAACAAGATGAAACAGCTGATAGATAAAATGGAGAATCAATATGATGATAAAATCATC\n+AATGAATACTCTGATATCAGTGAAAGGTATATGGCTCTTGGAGGTCTAACCTACCAAAAA\n+GAATATGAAACGATGATTCGTAGTATGGGTTTTACTGAAGCAGATTATAAAAAACCCATT\n+TCTGAATTTTCAGGTGGTCAGCGAACTAAGATAGCTTTTATAAAAATACTTTTAACAAAG\n+CCAGACATTCTATTACTTGATGAACCTACTAACCACCTTGATATAGAAACAATACAATGG\n+TTGGAGAGTTATTTGAGAAGTTATAAATCTACATTGGTTATTATTTCCCATGATAGAATG\n+TTTCTTAATCGAATTGTGGATAAGGTTTATGAAATCGAATGGGGAGAGACCAAATGTTAT\n+AAAGGTAATTATTCAGCCTTTGAGGAGCAAAAACGAGAAAATCATATCAAACAGCAAAAA\n+GATTACGACTTGCAACAGATAGAAATTGAAAGGATTACACGCTTGATTGAACGTTTTCGT\n+TATAAACCTACGAAAGCTAAAATGGTGCAATCTAAAATTAAATTATTACAGCGTATGCAA\n+ATATTAAATGCACCAGACCAATACGATACAAAAACTTATATGTCTAAATTTCAACCGAGA\n+ATCAGTAGTTCAAGGCAAGTATTAAGTGCTTCAGAACTTGTGATAGGCTATGATACTCCT\n+CTTGCAAAGGTTAATTTCAACCTTGAAAGGGGACAGAAGCTTGGAATTGTTGGGAGTAAT\n+GGTATTGGTAAATCCACGTTGCTTAAAACACTTATGGGTGGTGTGGCAGCATTGTCTGGA\n+GATTTTAAATTCGGATACAATGTTGAAATTAGCTATTTTGACCAACAGCTTGCTCAAATC\n+AGTGGAGATGATACACTATTCGAAATTTTTCAAAGCGAATACCCTGAGCTAAATGACACA\n+GAGGTCAGAACTGCTCTTGGCTCATTTCAGTTTAGTGGAGATGATGTTTTTAGACCGGTG\n+TCCTCTTTGTCAGGTGGAGAAAAGGTTAGATTGACATTATGTAAATTATTATATAAACGT\n+ACTAATGTTTTAATCTTAGATGAACCGACAAACCACATGGATATTATTGGAAAAGAGAAT\n+TTAGAGAATATCTTATGCAGTTATCAAGGTACAATTATTTTTGTGTCACATGATAGATAT\n+TTTACTAATAAGATTGCTGACAGATTACTTGTTTTTGATAAGGATGGTGTAGAGTTTGTA\n+CAATCTACTTATGGTGAGTACGAGAAAAAAAGGATGAATTCTGAAAAGCCATTTAATAAC\n+ATTAAAGTTGAGCAGAAAGTAGAGAAAAATAACACAGTAAAAGGCGATCGTAACTCCATT\n+GAGAAGGAGAAGGTTAAGAAGGAGAAACGAATTGAAAAGCTTGAAGTGTTAATAAATCAA\n+TATGATGAAGAATTAGAAAGATTGAATAAAATCATTTCTGAACCAAACAATTCTTCTGAT\n+TATATAGTACTGACGGAAATACAAAAATCAATTGATGATGTTAAAAGGTGTCAGGGTAAT\n+TATTTTAATGAATGGGAACAGTTGATGAGAGAATTGGAAGTTATG\n+>contig_46:2438-3229 strand:- aph(3')-IIIa aminoglycoside O-phosphotransferase APH(3')-IIIa\n+ATGGCTAAAATGAGAATATCACCGGAATTGAAAAAACTGATCGAAAAATACCGCTGCGTA\n+AAAGATACGGAAGGAATGTCTCCTGCTAAGGTATATAAGCTGGTGGGAGAAAATGAAAAC\n+CTATATTTAAAAATGACGGACAGCCGGTATAAAGGGACCACCTATGATGTGGAACGGGAA\n+AAGGACATGATGCTATGGCTGGAAGGAAAGCTGCCTGTTCCAAAGGTCCTGCACTTTGAA\n+CGGCATGATGGCTGGAGCAATCTGCTCATGAGTGAGGCCGATGGCGTCCTTTGCTCGGAA\n+GAGTATGAAGATGAACAAAGCCCTGAAAAGATTATCGAGCTGTATGCGGAGTGCATCAGG\n+CTCTTTCACTCCATCGACATATCGGATTGTCCCTATACGAATAGCTTAGACAGCCGCTTA\n+GCCGAATTGGATTACTTACTGAATAACGATCTGGCCGATGTGGATTGCGAAAACTGGGAA\n+GAAGACACTCCATTTAAAGATCCGCGCGAGCTGTATGATTTTTTAAAGACGGAAAAGCCC\n+GAAGAGGAACTTGTCTTTTCCCACGGCGACCTGGGAGACAGCAACATCTTTGTGAAAGAT\n+GGCAAAGTAAGTGGCTTTATTGATCTTGGGAGAAGCGGCAGGGCGGACAAGTGGTATGAC\n+ATTGCCTTCTGCGTCCGGTCGATCAGGGAGGATATCGGGGAAGAACAGTATGTCGAGCTA\n+TTTTTTGACTTACTGGGGATCAAGCCTGATTGGGAGAAAATAAAATATTATATTTTACTG\n+GATGAATTGTTT\n+>contig_46:3325-3864 strand:- sat4 streptothricin N-acetyltransferase Sat4\n+GTGATTACAGAAATGAAAGCAGGGCACCTGAAAGATATCGATAAACCCAGCGAACCATTT\n+GAGGTGATAGGTAAGATTATACCGAGGTATGAAAACGAGAATTGGACCTTTACAGAATTA\n+CTCTATGAAGCGCCATATTTAAAAAGCTACCAAGACGAAGAGGATGAAGAGGATGAGGAG\n+GCAGATTGCCTTGAATATATTGACAATACTGATAAGATAATATATCTTTACTACCAAGAC\n+GATAAATGCGTCGGAAAAGTTAAACTGCGAAAAAATTGGAACCGGTACGCTTATATAGAA\n+GATATCGCCGTATGTAAGGATTTCAGGGGGCAAGGCATAGGCAGCGCGCTTATCAATATA\n+TCTATAGAATGGGCAAAGCATAAAAACTTGCATGGACTAATGCTTGAAACCCAGGACAAT\n+AACCTTATAGCTTGTAAATTCTATCATAATTGTGGTTTCAAAATCGGCTCCGTCGATACT\n+ATGTTATACGCCAACTTTGAAAACAACTTTGAAAAAGCTGTTTTCTGGTATTTAAGGTTT\n+>contig_47:3996-5912 strand:- tet(M) tetracycline resistance ribosomal protection protein Tet(M)\n+ATGAAAATTATTAATATTGGAGTTTTAGCTCATGTTGATGCGGGAAAAACTACCTTAACA\n+GAAAGCTTATTATATAACAGTGGAGCGATTACAGAATTAGGAAGCGTGGACAAAGGTACA\n+ACGAGGACGGATAATACGCTTTTAGAACGTCAGAGAGGAATTACAATTCAGACAGGAATA\n+ACCTCTTTTCAGTGGGAAAATACGAAGGTGAACAT"..b'GTTGAACCGAGCAAACCTCAACAAAGGGAAATG\n+TTGCTTGATGCCCTTTTGGAAATCTCAGATAGTGATCCGCTTCTACGATATTACGTGGAT\n+TCTACGACACATGAAATTATACTTTCTTTCTTAGGGAAAGTACAAATGGAAGTGATTAGT\n+GCACTGTTGCAAGAAAAGTATCATGTGGAGATAGAACTAAAAGAGCCTACAGTCATTTAT\n+ATGGAGAGACCGTTAAAAAATGCAGAATATACCATTCACATCGAAGTGCCGCCAAATCCT\n+TTCTGGGCTTCCATTGGTTTATCTGTATCACCGCTTCCATTAGGGAGCGGAGTGCAGTAT\n+GAGAGCTCGGTTTCTCTTGGATACTTAAATCAATCGTTTCAAAATGCAGTTATGGAGGGG\n+ATACGCTATGGCTGTGAACAAGGATTGTATGGTTGGAATGTGACGGACTGTAAAATCTGT\n+TTTAAGTATGGCTTATACTATAGCCCTGTTAGTACCCCAGCAGATTTTCGGATGCTTGCT\n+CCTATTGTATTGGAACAAGTCTTAAAAAAAGCTGGAACAGAATTGTTAGAGCCATATCTT\n+AGTTTTAAAATTTATGCGCCACAGGAATATCTTTCACGAGCATACAACGATGCTCCTAAA\n+TATTGTGCGAACATCGTAGACACTCAATTGAAAAATAATGAGGTCATTCTTAGTGGAGAA\n+ATCCCTGCTCGGTGTATTCAAGAATATCGTAGTGATTTAACTTTCTTTACAAATGGACGT\n+AGTGTTTGTTTAACAGAGTTAAAAGGGTACCATGTTACTACCGGTGAACCTGTTTGCCAG\n+CCCCGTCGTCCAAATAGTCGGATAGATAAAGTACGATATATGTTCAATAAAATAACT\n+>contig_48:202-936 strand:- erm(B) 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B)\n+ATGAACAAAAATATAAAATATTCTCAAAACTTTTTAACGAGTGAAAAAGTACTCAACCAA\n+ATAATAAAACAATTGAATTTAAAAGAAACCGATACCGTTTACGAAATTGGAACAGGTAAA\n+GGGCATTTAACGACGAAACTGGCTAAAATAAGTAAACAGGTAACGTCTATTGAATTAGAC\n+AGTCATCTATTCAACTTATCGTCAGAAAAATTAAAACTGAATACTCGTGTCACTTTAATT\n+CACCAAGATATTCTACAGTTTCAATTCCCTAACAAACAGAGGTATAAAATTGTTGGGAGT\n+ATTCCTTACCATTTAAGCACACAAATTATTAAAAAAGTGGTTTTTGAAAGCCATGCGTCT\n+GACATCTATCTGATTGTTGAAGAAGGATTCTACAAGCGTACCTTGGATATTCACCGAACA\n+CTAGGGTTGCTCTTGCACACTCAAGTCTCGATTCAGCAATTGCTTAAGCTGCCAGCGGAA\n+TGCTTTCATCCTAAACCAAAAGTAAACAGTGTCTTAATAAAACTTACCCGCCATACCACA\n+GATGTTCCAGATAAATATTGGAAGCTATATACGTACTTTGTTTCAAAATGGGTCAATCGA\n+GAATATCGTCAACTGTTTACTAAAAATCAGTTTCATCAAGCAATGAAACACGCCAAAGTA\n+AACAATTTAAGTACCGTTACTTATGAGCAAGTATTGTCTATTTTTAATAGTTATCTATTA\n+TTTAACGGGAGGAAA\n+>contig_48:4344-4988 strand:+ catA type A-7 chloramphenicol O-acetyltransferase\n+ATGACTTTTAATATTATTGAATTAGAAAATTGGGATAGAAAAGAATATTTTGAACACTAT\n+TTTAATCAGCAAACTACTTATAGCATTACTAAAGAAATTGATATTACTTTGTTTAAAGAT\n+ATGATAAAAAAGAAAGGATATGAAATTTATCCCTCTTTAATTTATGCAATTATGGAAGTT\n+GTAAATAAAAATAAAGTGTTTAGAACAGGAATTAATAGTGAGAATAAATTAGGTTATTGG\n+GATAAGTTAAATCCTTTGTATACAGTTTTTAATAAGCAAACTGAAAAATTTACTAACATT\n+TGGACTGAATCTGATAAAAACTTCATTTCTTTTTATAATAATTATAAAAATGACTTGCTT\n+GAATATAAAGATAAAGAAGAAATGTTTCCTAAAAAACCGATACCTGAAAACACCATACCG\n+ATTTCAATGATTCCTTGGATTGATTTTAGTTCATTTAATTTAAATATTGGTAACAATAGC\n+AGCTTTTTATTGCCTATTATTACGATAGGTAAATTTTATAGTGAGAATAATAAAATTTAT\n+ATACCAGTTGCTCTGCAACTTCATCATTCTGTATGTGATGGTTACCATGCTTCACTATTT\n+ATGAATGAATTTCAAGATATAATTCATAGGGTAGATGATTGGATT\n+>contig_50:282-1655 strand:+ tet(L) tetracycline efflux MFS transporter Tet(L)\n+GTGAATACATCCTATTCACAATCGAATTTACGACACAACCAAATTTTAATTTGGCTTTGC\n+ATTTTATCTTTTTTTAGCGTATTAAATGAAATGGTTTTGAACGTCTCATTACCTGATATT\n+GCAAATGATTTTAATAAACCACCTGCGAGTACAAACTGGGTGAACACAGCCTTTATGTTA\n+ACCTTTTCCATTGGAACAGCTGTATATGGAAAGCTATCTGATCAATTAGGCATCAAAAGG\n+TTACTCCTATTTGGAATTATAATAAATTGTTTCGGGTCGGTAATTGGGTTTGTTGGCCAT\n+TCTTTCTTTTCCTTACTTATTATGGCTCGTTTTATTCAAGGGGCTGGTGCAGCTGCATTT\n+CCAGCACTCGTAATGGTTGTAGTTGCGCGCTATATTCCAAAGGAAAATAGGGGTAAAGCA\n+TTTGGTCTTATTGGATCGATAGTAGCCATGGGAGAAGGAGTCGGTCCAGCGATTGGTGGA\n+ATGATAGCCCATTATATTCATTGGTCCTATCTTCTACTCATTCCTATGATAACAATTATC\n+ACTGTTCCGTTTCTTATGAAATTATTAAAGAAAGAAGTAAGGATAAAAGGTCATTTTGAT\n+ATCAAAGGAATTATACTAATGTCTGTAGGCATTGTATTTTTTATGTTGTTTACAACATCA\n+TATAGCATTTCTTTTCTTATCGTTAGCGTGCTGTCATTCCTGATATTTGTAAAACATATC\n+AGGAAAGTAACAGATCCTTTTGTTGATCCCGGATTAGGGAAAAATATACCTTTTATGATT\n+GGAGTTCTTTGTGGGGGAATTATATTTGGAACAGTAGCAGGGTTTGTCTCTATGGTTCCT\n+TATATGATGAAAGATGTTCACCAGCTAAGTACTGCCGAAATCGGAAGTGTAATTATTTTC\n+CCTGGAACAATGAGTGTCATTATTTTCGGCTACATTGGTGGGATACTTGTTGATAGAAGA\n+GGTCCTTTATACGTGTTAAACATCGGAGTTACATTTCTTTCTGTTAGCTTTTTAACTGCT\n+TCCTTTCTTTTAGAAACAACATCATGGTTCATGACAATTATAATCGTATTTGTTTTAGGT\n+GGGCTTTCGTTCACCAAAACAGTTATATCAACAATTGTTTCAAGTAGCTTGAAACAGCAG\n+GAAGCTGGTGCTGGAATGAGTTTGCTTAACTTTACCAGCTTTTTATCAGAGGGAACAGGT\n+ATTGCAATTGTAGGTGGTTTATTATCCATACCCTTACTTGATCAAAGGTTGTTACCTATG\n+GAAGTTGATCAGTCAACTTATCTGTATAGTAATTTGTTATTACTTTTTTCAGGAATCATT\n+GTCATTAGTTGGCTGGTTACCTTGAATGTATATAAACATTCTCAAAGGGATTTC\n' |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test_1/amrfinderplus_nucleotide_output.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_1/amrfinderplus_nucleotide_output.fasta Fri May 26 09:19:12 2023 +0000 |
| b |
| b"@@ -0,0 +1,142 @@\n+>contig_26:6581-8545 strand:+ optrA ABC-F type ribosomal protection protein OptrA\n+TTGTCCAAAGCCACCTTTGCAATTGCTAGTACTAACGCAAAGGAGGATATGAAAATGCAA\n+TACAAAATAATTAATGGTGCCGTTTACTATGATGGTAATATGGTGTTGGAAAACATCGGT\n+ATTGAAATCAATGATAATGAAAAGATTGCTATTGTTGGTAGAAATGGATGTGGAAAAACA\n+ACCTTGCTAAAAGCTATTATAGGCGAAATTGAATTAGAAGAAGGAACTGGTGAAAGTGAG\n+TTTCAAGTAATAAAGACCGGTAACCCTTATATTAGCTATTTAAGACAGATGCCTTTTGAA\n+GATGAAAGTATATCAATGGTGGATGAAGTCCGTACGGTATTTAAGACGCTTATTGATATG\n+GAAAACAAGATGAAACAGCTGATAGATAAAATGGAGAATCAATATGATGATAAAATCATC\n+AATGAATACTCTGATATCAGTGAAAGGTATATGGCTCTTGGAGGTCTAACCTACCAAAAA\n+GAATATGAAACGATGATTCGTAGTATGGGTTTTACTGAAGCAGATTATAAAAAACCCATT\n+TCTGAATTTTCAGGTGGTCAGCGAACTAAGATAGCTTTTATAAAAATACTTTTAACAAAG\n+CCAGACATTCTATTACTTGATGAACCTACTAACCACCTTGATATAGAAACAATACAATGG\n+TTGGAGAGTTATTTGAGAAGTTATAAATCTACATTGGTTATTATTTCCCATGATAGAATG\n+TTTCTTAATCGAATTGTGGATAAGGTTTATGAAATCGAATGGGGAGAGACCAAATGTTAT\n+AAAGGTAATTATTCAGCCTTTGAGGAGCAAAAACGAGAAAATCATATCAAACAGCAAAAA\n+GATTACGACTTGCAACAGATAGAAATTGAAAGGATTACACGCTTGATTGAACGTTTTCGT\n+TATAAACCTACGAAAGCTAAAATGGTGCAATCTAAAATTAAATTATTACAGCGTATGCAA\n+ATATTAAATGCACCAGACCAATACGATACAAAAACTTATATGTCTAAATTTCAACCGAGA\n+ATCAGTAGTTCAAGGCAAGTATTAAGTGCTTCAGAACTTGTGATAGGCTATGATACTCCT\n+CTTGCAAAGGTTAATTTCAACCTTGAAAGGGGACAGAAGCTTGGAATTGTTGGGAGTAAT\n+GGTATTGGTAAATCCACGTTGCTTAAAACACTTATGGGTGGTGTGGCAGCATTGTCTGGA\n+GATTTTAAATTCGGATACAATGTTGAAATTAGCTATTTTGACCAACAGCTTGCTCAAATC\n+AGTGGAGATGATACACTATTCGAAATTTTTCAAAGCGAATACCCTGAGCTAAATGACACA\n+GAGGTCAGAACTGCTCTTGGCTCATTTCAGTTTAGTGGAGATGATGTTTTTAGACCGGTG\n+TCCTCTTTGTCAGGTGGAGAAAAGGTTAGATTGACATTATGTAAATTATTATATAAACGT\n+ACTAATGTTTTAATCTTAGATGAACCGACAAACCACATGGATATTATTGGAAAAGAGAAT\n+TTAGAGAATATCTTATGCAGTTATCAAGGTACAATTATTTTTGTGTCACATGATAGATAT\n+TTTACTAATAAGATTGCTGACAGATTACTTGTTTTTGATAAGGATGGTGTAGAGTTTGTA\n+CAATCTACTTATGGTGAGTACGAGAAAAAAAGGATGAATTCTGAAAAGCCATTTAATAAC\n+ATTAAAGTTGAGCAGAAAGTAGAGAAAAATAACACAGTAAAAGGCGATCGTAACTCCATT\n+GAGAAGGAGAAGGTTAAGAAGGAGAAACGAATTGAAAAGCTTGAAGTGTTAATAAATCAA\n+TATGATGAAGAATTAGAAAGATTGAATAAAATCATTTCTGAACCAAACAATTCTTCTGAT\n+TATATAGTACTGACGGAAATACAAAAATCAATTGATGATGTTAAAAGGTGTCAGGGTAAT\n+TATTTTAATGAATGGGAACAGTTGATGAGAGAATTGGAAGTTATG\n+>contig_46:2438-3229 strand:- aph(3')-IIIa aminoglycoside O-phosphotransferase APH(3')-IIIa\n+ATGGCTAAAATGAGAATATCACCGGAATTGAAAAAACTGATCGAAAAATACCGCTGCGTA\n+AAAGATACGGAAGGAATGTCTCCTGCTAAGGTATATAAGCTGGTGGGAGAAAATGAAAAC\n+CTATATTTAAAAATGACGGACAGCCGGTATAAAGGGACCACCTATGATGTGGAACGGGAA\n+AAGGACATGATGCTATGGCTGGAAGGAAAGCTGCCTGTTCCAAAGGTCCTGCACTTTGAA\n+CGGCATGATGGCTGGAGCAATCTGCTCATGAGTGAGGCCGATGGCGTCCTTTGCTCGGAA\n+GAGTATGAAGATGAACAAAGCCCTGAAAAGATTATCGAGCTGTATGCGGAGTGCATCAGG\n+CTCTTTCACTCCATCGACATATCGGATTGTCCCTATACGAATAGCTTAGACAGCCGCTTA\n+GCCGAATTGGATTACTTACTGAATAACGATCTGGCCGATGTGGATTGCGAAAACTGGGAA\n+GAAGACACTCCATTTAAAGATCCGCGCGAGCTGTATGATTTTTTAAAGACGGAAAAGCCC\n+GAAGAGGAACTTGTCTTTTCCCACGGCGACCTGGGAGACAGCAACATCTTTGTGAAAGAT\n+GGCAAAGTAAGTGGCTTTATTGATCTTGGGAGAAGCGGCAGGGCGGACAAGTGGTATGAC\n+ATTGCCTTCTGCGTCCGGTCGATCAGGGAGGATATCGGGGAAGAACAGTATGTCGAGCTA\n+TTTTTTGACTTACTGGGGATCAAGCCTGATTGGGAGAAAATAAAATATTATATTTTACTG\n+GATGAATTGTTT\n+>contig_46:3325-3864 strand:- sat4 streptothricin N-acetyltransferase Sat4\n+GTGATTACAGAAATGAAAGCAGGGCACCTGAAAGATATCGATAAACCCAGCGAACCATTT\n+GAGGTGATAGGTAAGATTATACCGAGGTATGAAAACGAGAATTGGACCTTTACAGAATTA\n+CTCTATGAAGCGCCATATTTAAAAAGCTACCAAGACGAAGAGGATGAAGAGGATGAGGAG\n+GCAGATTGCCTTGAATATATTGACAATACTGATAAGATAATATATCTTTACTACCAAGAC\n+GATAAATGCGTCGGAAAAGTTAAACTGCGAAAAAATTGGAACCGGTACGCTTATATAGAA\n+GATATCGCCGTATGTAAGGATTTCAGGGGGCAAGGCATAGGCAGCGCGCTTATCAATATA\n+TCTATAGAATGGGCAAAGCATAAAAACTTGCATGGACTAATGCTTGAAACCCAGGACAAT\n+AACCTTATAGCTTGTAAATTCTATCATAATTGTGGTTTCAAAATCGGCTCCGTCGATACT\n+ATGTTATACGCCAACTTTGAAAACAACTTTGAAAAAGCTGTTTTCTGGTATTTAAGGTTT\n+>contig_47:3996-5912 strand:- tet(M) tetracycline resistance ribosomal protection protein Tet(M)\n+ATGAAAATTATTAATATTGGAGTTTTAGCTCATGTTGATGCGGGAAAAACTACCTTAACA\n+GAAAGCTTATTATATAACAGTGGAGCGATTACAGAATTAGGAAGCGTGGACAAAGGTACA\n+ACGAGGACGGATAATACGCTTTTAGAACGTCAGAGAGGAATTACAATTCAGACAGGAATA\n+ACCTCTTTTCAGTGGGAAAATACGAAGGTGAACAT"..b'GTTGAACCGAGCAAACCTCAACAAAGGGAAATG\n+TTGCTTGATGCCCTTTTGGAAATCTCAGATAGTGATCCGCTTCTACGATATTACGTGGAT\n+TCTACGACACATGAAATTATACTTTCTTTCTTAGGGAAAGTACAAATGGAAGTGATTAGT\n+GCACTGTTGCAAGAAAAGTATCATGTGGAGATAGAACTAAAAGAGCCTACAGTCATTTAT\n+ATGGAGAGACCGTTAAAAAATGCAGAATATACCATTCACATCGAAGTGCCGCCAAATCCT\n+TTCTGGGCTTCCATTGGTTTATCTGTATCACCGCTTCCATTAGGGAGCGGAGTGCAGTAT\n+GAGAGCTCGGTTTCTCTTGGATACTTAAATCAATCGTTTCAAAATGCAGTTATGGAGGGG\n+ATACGCTATGGCTGTGAACAAGGATTGTATGGTTGGAATGTGACGGACTGTAAAATCTGT\n+TTTAAGTATGGCTTATACTATAGCCCTGTTAGTACCCCAGCAGATTTTCGGATGCTTGCT\n+CCTATTGTATTGGAACAAGTCTTAAAAAAAGCTGGAACAGAATTGTTAGAGCCATATCTT\n+AGTTTTAAAATTTATGCGCCACAGGAATATCTTTCACGAGCATACAACGATGCTCCTAAA\n+TATTGTGCGAACATCGTAGACACTCAATTGAAAAATAATGAGGTCATTCTTAGTGGAGAA\n+ATCCCTGCTCGGTGTATTCAAGAATATCGTAGTGATTTAACTTTCTTTACAAATGGACGT\n+AGTGTTTGTTTAACAGAGTTAAAAGGGTACCATGTTACTACCGGTGAACCTGTTTGCCAG\n+CCCCGTCGTCCAAATAGTCGGATAGATAAAGTACGATATATGTTCAATAAAATAACT\n+>contig_48:202-936 strand:- erm(B) 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B)\n+ATGAACAAAAATATAAAATATTCTCAAAACTTTTTAACGAGTGAAAAAGTACTCAACCAA\n+ATAATAAAACAATTGAATTTAAAAGAAACCGATACCGTTTACGAAATTGGAACAGGTAAA\n+GGGCATTTAACGACGAAACTGGCTAAAATAAGTAAACAGGTAACGTCTATTGAATTAGAC\n+AGTCATCTATTCAACTTATCGTCAGAAAAATTAAAACTGAATACTCGTGTCACTTTAATT\n+CACCAAGATATTCTACAGTTTCAATTCCCTAACAAACAGAGGTATAAAATTGTTGGGAGT\n+ATTCCTTACCATTTAAGCACACAAATTATTAAAAAAGTGGTTTTTGAAAGCCATGCGTCT\n+GACATCTATCTGATTGTTGAAGAAGGATTCTACAAGCGTACCTTGGATATTCACCGAACA\n+CTAGGGTTGCTCTTGCACACTCAAGTCTCGATTCAGCAATTGCTTAAGCTGCCAGCGGAA\n+TGCTTTCATCCTAAACCAAAAGTAAACAGTGTCTTAATAAAACTTACCCGCCATACCACA\n+GATGTTCCAGATAAATATTGGAAGCTATATACGTACTTTGTTTCAAAATGGGTCAATCGA\n+GAATATCGTCAACTGTTTACTAAAAATCAGTTTCATCAAGCAATGAAACACGCCAAAGTA\n+AACAATTTAAGTACCGTTACTTATGAGCAAGTATTGTCTATTTTTAATAGTTATCTATTA\n+TTTAACGGGAGGAAA\n+>contig_48:4344-4988 strand:+ catA type A-7 chloramphenicol O-acetyltransferase\n+ATGACTTTTAATATTATTGAATTAGAAAATTGGGATAGAAAAGAATATTTTGAACACTAT\n+TTTAATCAGCAAACTACTTATAGCATTACTAAAGAAATTGATATTACTTTGTTTAAAGAT\n+ATGATAAAAAAGAAAGGATATGAAATTTATCCCTCTTTAATTTATGCAATTATGGAAGTT\n+GTAAATAAAAATAAAGTGTTTAGAACAGGAATTAATAGTGAGAATAAATTAGGTTATTGG\n+GATAAGTTAAATCCTTTGTATACAGTTTTTAATAAGCAAACTGAAAAATTTACTAACATT\n+TGGACTGAATCTGATAAAAACTTCATTTCTTTTTATAATAATTATAAAAATGACTTGCTT\n+GAATATAAAGATAAAGAAGAAATGTTTCCTAAAAAACCGATACCTGAAAACACCATACCG\n+ATTTCAATGATTCCTTGGATTGATTTTAGTTCATTTAATTTAAATATTGGTAACAATAGC\n+AGCTTTTTATTGCCTATTATTACGATAGGTAAATTTTATAGTGAGAATAATAAAATTTAT\n+ATACCAGTTGCTCTGCAACTTCATCATTCTGTATGTGATGGTTACCATGCTTCACTATTT\n+ATGAATGAATTTCAAGATATAATTCATAGGGTAGATGATTGGATT\n+>contig_50:282-1655 strand:+ tet(L) tetracycline efflux MFS transporter Tet(L)\n+GTGAATACATCCTATTCACAATCGAATTTACGACACAACCAAATTTTAATTTGGCTTTGC\n+ATTTTATCTTTTTTTAGCGTATTAAATGAAATGGTTTTGAACGTCTCATTACCTGATATT\n+GCAAATGATTTTAATAAACCACCTGCGAGTACAAACTGGGTGAACACAGCCTTTATGTTA\n+ACCTTTTCCATTGGAACAGCTGTATATGGAAAGCTATCTGATCAATTAGGCATCAAAAGG\n+TTACTCCTATTTGGAATTATAATAAATTGTTTCGGGTCGGTAATTGGGTTTGTTGGCCAT\n+TCTTTCTTTTCCTTACTTATTATGGCTCGTTTTATTCAAGGGGCTGGTGCAGCTGCATTT\n+CCAGCACTCGTAATGGTTGTAGTTGCGCGCTATATTCCAAAGGAAAATAGGGGTAAAGCA\n+TTTGGTCTTATTGGATCGATAGTAGCCATGGGAGAAGGAGTCGGTCCAGCGATTGGTGGA\n+ATGATAGCCCATTATATTCATTGGTCCTATCTTCTACTCATTCCTATGATAACAATTATC\n+ACTGTTCCGTTTCTTATGAAATTATTAAAGAAAGAAGTAAGGATAAAAGGTCATTTTGAT\n+ATCAAAGGAATTATACTAATGTCTGTAGGCATTGTATTTTTTATGTTGTTTACAACATCA\n+TATAGCATTTCTTTTCTTATCGTTAGCGTGCTGTCATTCCTGATATTTGTAAAACATATC\n+AGGAAAGTAACAGATCCTTTTGTTGATCCCGGATTAGGGAAAAATATACCTTTTATGATT\n+GGAGTTCTTTGTGGGGGAATTATATTTGGAACAGTAGCAGGGTTTGTCTCTATGGTTCCT\n+TATATGATGAAAGATGTTCACCAGCTAAGTACTGCCGAAATCGGAAGTGTAATTATTTTC\n+CCTGGAACAATGAGTGTCATTATTTTCGGCTACATTGGTGGGATACTTGTTGATAGAAGA\n+GGTCCTTTATACGTGTTAAACATCGGAGTTACATTTCTTTCTGTTAGCTTTTTAACTGCT\n+TCCTTTCTTTTAGAAACAACATCATGGTTCATGACAATTATAATCGTATTTGTTTTAGGT\n+GGGCTTTCGTTCACCAAAACAGTTATATCAACAATTGTTTCAAGTAGCTTGAAACAGCAG\n+GAAGCTGGTGCTGGAATGAGTTTGCTTAACTTTACCAGCTTTTTATCAGAGGGAACAGGT\n+ATTGCAATTGTAGGTGGTTTATTATCCATACCCTTACTTGATCAAAGGTTGTTACCTATG\n+GAAGTTGATCAGTCAACTTATCTGTATAGTAATTTGTTATTACTTTTTTCAGGAATCATT\n+GTCATTAGTTGGCTGGTTACCTTGAATGTATATAAACATTCTCAAAGGGATTTC\n' |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test_1/amrfinderplus_results.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_1/amrfinderplus_results.tsv Fri May 26 09:19:12 2023 +0000 |
| b |
| @@ -0,0 +1,8 @@ +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 +NA contig_26 6581 8545 + optrA ABC-F type ribosomal protection protein OptrA core AMR AMR PHENICOL/OXAZOLIDINONE FLORFENICOL/OXAZOLIDINONE EXACTX 655 655 100.00 100.00 655 WP_063854496.1 ABC-F type ribosomal protection protein OptrA NA NA +NA contig_46 2438 3229 - aph(3')-IIIa aminoglycoside O-phosphotransferase APH(3')-IIIa core AMR AMR AMINOGLYCOSIDE AMIKACIN/KANAMYCIN BLASTX 264 264 100.00 99.62 264 WP_063841495.1 aminoglycoside O-phosphotransferase APH(3')-IIIa NA NA +NA contig_46 3325 3864 - sat4 streptothricin N-acetyltransferase Sat4 core AMR AMR STREPTOTHRICIN STREPTOTHRICIN BLASTX 180 180 100.00 99.44 180 WP_063854934.1 streptothricin N-acetyltransferase Sat4 NA NA +NA contig_47 3996 5912 - tet(M) tetracycline resistance ribosomal protection protein Tet(M) core AMR AMR TETRACYCLINE TETRACYCLINE BLASTX 639 639 100.00 99.84 639 WP_063856395.1 tetracycline resistance ribosomal protection protein Tet(M) NA NA +NA contig_48 202 936 - erm(B) 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B) core AMR AMR MACROLIDE MACROLIDE BLASTX 245 245 100.00 99.59 245 WP_063844601.1 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B) NA NA +NA contig_48 4344 4988 + catA type A-7 chloramphenicol O-acetyltransferase core AMR AMR PHENICOL CHLORAMPHENICOL BLASTX 215 215 100.00 96.28 215 WP_063843211.1 type A-7 chloramphenicol O-acetyltransferase NA NA +NA contig_50 282 1655 + tet(L) tetracycline efflux MFS transporter Tet(L) core AMR AMR TETRACYCLINE TETRACYCLINE BLASTX 458 458 100.00 99.78 458 WP_063856080.1 tetracycline efflux MFS transporter Tet(L) NA NA |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test_2/amrfinderplus_flanking_output.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_2/amrfinderplus_flanking_output.fasta Fri May 26 09:19:12 2023 +0000 |
| b |
| @@ -0,0 +1,37 @@ +>contig_26:6431-8545 strand:+ optrA ABC-F type ribosomal protection protein OptrA +GCGCTAGCGACTTGGTACAATAAGGTGGCAATTGAATTATATTAATAATCGATAGGAGGT +AGAAGCAAATGAAATCTACAACTATAGTAACATTTAAAGAACTCCATGTATAGGTGGCTG +TGACAAGCTTTACATGGAGTAGAATAATTATTGTCCAAAGCCACCTTTGCAATTGCTAGT +ACTAACGCAAAGGAGGATATGAAAATGCAATACAAAATAATTAATGGTGCCGTTTACTAT +GATGGTAATATGGTGTTGGAAAACATCGGTATTGAAATCAATGATAATGAAAAGATTGCT +ATTGTTGGTAGAAATGGATGTGGAAAAACAACCTTGCTAAAAGCTATTATAGGCGAAATT +GAATTAGAAGAAGGAACTGGTGAAAGTGAGTTTCAAGTAATAAAGACCGGTAACCCTTAT +ATTAGCTATTTAAGACAGATGCCTTTTGAAGATGAAAGTATATCAATGGTGGATGAAGTC +CGTACGGTATTTAAGACGCTTATTGATATGGAAAACAAGATGAAACAGCTGATAGATAAA +ATGGAGAATCAATATGATGATAAAATCATCAATGAATACTCTGATATCAGTGAAAGGTAT +ATGGCTCTTGGAGGTCTAACCTACCAAAAAGAATATGAAACGATGATTCGTAGTATGGGT +TTTACTGAAGCAGATTATAAAAAACCCATTTCTGAATTTTCAGGTGGTCAGCGAACTAAG +ATAGCTTTTATAAAAATACTTTTAACAAAGCCAGACATTCTATTACTTGATGAACCTACT +AACCACCTTGATATAGAAACAATACAATGGTTGGAGAGTTATTTGAGAAGTTATAAATCT +ACATTGGTTATTATTTCCCATGATAGAATGTTTCTTAATCGAATTGTGGATAAGGTTTAT +GAAATCGAATGGGGAGAGACCAAATGTTATAAAGGTAATTATTCAGCCTTTGAGGAGCAA +AAACGAGAAAATCATATCAAACAGCAAAAAGATTACGACTTGCAACAGATAGAAATTGAA +AGGATTACACGCTTGATTGAACGTTTTCGTTATAAACCTACGAAAGCTAAAATGGTGCAA +TCTAAAATTAAATTATTACAGCGTATGCAAATATTAAATGCACCAGACCAATACGATACA +AAAACTTATATGTCTAAATTTCAACCGAGAATCAGTAGTTCAAGGCAAGTATTAAGTGCT +TCAGAACTTGTGATAGGCTATGATACTCCTCTTGCAAAGGTTAATTTCAACCTTGAAAGG +GGACAGAAGCTTGGAATTGTTGGGAGTAATGGTATTGGTAAATCCACGTTGCTTAAAACA +CTTATGGGTGGTGTGGCAGCATTGTCTGGAGATTTTAAATTCGGATACAATGTTGAAATT +AGCTATTTTGACCAACAGCTTGCTCAAATCAGTGGAGATGATACACTATTCGAAATTTTT +CAAAGCGAATACCCTGAGCTAAATGACACAGAGGTCAGAACTGCTCTTGGCTCATTTCAG +TTTAGTGGAGATGATGTTTTTAGACCGGTGTCCTCTTTGTCAGGTGGAGAAAAGGTTAGA +TTGACATTATGTAAATTATTATATAAACGTACTAATGTTTTAATCTTAGATGAACCGACA +AACCACATGGATATTATTGGAAAAGAGAATTTAGAGAATATCTTATGCAGTTATCAAGGT +ACAATTATTTTTGTGTCACATGATAGATATTTTACTAATAAGATTGCTGACAGATTACTT +GTTTTTGATAAGGATGGTGTAGAGTTTGTACAATCTACTTATGGTGAGTACGAGAAAAAA +AGGATGAATTCTGAAAAGCCATTTAATAACATTAAAGTTGAGCAGAAAGTAGAGAAAAAT +AACACAGTAAAAGGCGATCGTAACTCCATTGAGAAGGAGAAGGTTAAGAAGGAGAAACGA +ATTGAAAAGCTTGAAGTGTTAATAAATCAATATGATGAAGAATTAGAAAGATTGAATAAA +ATCATTTCTGAACCAAACAATTCTTCTGATTATATAGTACTGACGGAAATACAAAAATCA +ATTGATGATGTTAAAAGGTGTCAGGGTAATTATTTTAATGAATGGGAACAGTTGATGAGA +GAATTGGAAGTTATG |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test_2/amrfinderplus_mutation_all.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_2/amrfinderplus_mutation_all.tsv Fri May 26 09:19:12 2023 +0000 |
| b |
| @@ -0,0 +1,1 @@ +Name 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 |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test_2/amrfinderplus_nucleotide_output.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_2/amrfinderplus_nucleotide_output.fasta Fri May 26 09:19:12 2023 +0000 |
| b |
| @@ -0,0 +1,34 @@ +>contig_26:6581-8545 strand:+ optrA ABC-F type ribosomal protection protein OptrA +TTGTCCAAAGCCACCTTTGCAATTGCTAGTACTAACGCAAAGGAGGATATGAAAATGCAA +TACAAAATAATTAATGGTGCCGTTTACTATGATGGTAATATGGTGTTGGAAAACATCGGT +ATTGAAATCAATGATAATGAAAAGATTGCTATTGTTGGTAGAAATGGATGTGGAAAAACA +ACCTTGCTAAAAGCTATTATAGGCGAAATTGAATTAGAAGAAGGAACTGGTGAAAGTGAG +TTTCAAGTAATAAAGACCGGTAACCCTTATATTAGCTATTTAAGACAGATGCCTTTTGAA +GATGAAAGTATATCAATGGTGGATGAAGTCCGTACGGTATTTAAGACGCTTATTGATATG +GAAAACAAGATGAAACAGCTGATAGATAAAATGGAGAATCAATATGATGATAAAATCATC +AATGAATACTCTGATATCAGTGAAAGGTATATGGCTCTTGGAGGTCTAACCTACCAAAAA +GAATATGAAACGATGATTCGTAGTATGGGTTTTACTGAAGCAGATTATAAAAAACCCATT +TCTGAATTTTCAGGTGGTCAGCGAACTAAGATAGCTTTTATAAAAATACTTTTAACAAAG +CCAGACATTCTATTACTTGATGAACCTACTAACCACCTTGATATAGAAACAATACAATGG +TTGGAGAGTTATTTGAGAAGTTATAAATCTACATTGGTTATTATTTCCCATGATAGAATG +TTTCTTAATCGAATTGTGGATAAGGTTTATGAAATCGAATGGGGAGAGACCAAATGTTAT +AAAGGTAATTATTCAGCCTTTGAGGAGCAAAAACGAGAAAATCATATCAAACAGCAAAAA +GATTACGACTTGCAACAGATAGAAATTGAAAGGATTACACGCTTGATTGAACGTTTTCGT +TATAAACCTACGAAAGCTAAAATGGTGCAATCTAAAATTAAATTATTACAGCGTATGCAA +ATATTAAATGCACCAGACCAATACGATACAAAAACTTATATGTCTAAATTTCAACCGAGA +ATCAGTAGTTCAAGGCAAGTATTAAGTGCTTCAGAACTTGTGATAGGCTATGATACTCCT +CTTGCAAAGGTTAATTTCAACCTTGAAAGGGGACAGAAGCTTGGAATTGTTGGGAGTAAT +GGTATTGGTAAATCCACGTTGCTTAAAACACTTATGGGTGGTGTGGCAGCATTGTCTGGA +GATTTTAAATTCGGATACAATGTTGAAATTAGCTATTTTGACCAACAGCTTGCTCAAATC +AGTGGAGATGATACACTATTCGAAATTTTTCAAAGCGAATACCCTGAGCTAAATGACACA +GAGGTCAGAACTGCTCTTGGCTCATTTCAGTTTAGTGGAGATGATGTTTTTAGACCGGTG +TCCTCTTTGTCAGGTGGAGAAAAGGTTAGATTGACATTATGTAAATTATTATATAAACGT +ACTAATGTTTTAATCTTAGATGAACCGACAAACCACATGGATATTATTGGAAAAGAGAAT +TTAGAGAATATCTTATGCAGTTATCAAGGTACAATTATTTTTGTGTCACATGATAGATAT +TTTACTAATAAGATTGCTGACAGATTACTTGTTTTTGATAAGGATGGTGTAGAGTTTGTA +CAATCTACTTATGGTGAGTACGAGAAAAAAAGGATGAATTCTGAAAAGCCATTTAATAAC +ATTAAAGTTGAGCAGAAAGTAGAGAAAAATAACACAGTAAAAGGCGATCGTAACTCCATT +GAGAAGGAGAAGGTTAAGAAGGAGAAACGAATTGAAAAGCTTGAAGTGTTAATAAATCAA +TATGATGAAGAATTAGAAAGATTGAATAAAATCATTTCTGAACCAAACAATTCTTCTGAT +TATATAGTACTGACGGAAATACAAAAATCAATTGATGATGTTAAAAGGTGTCAGGGTAAT +TATTTTAATGAATGGGAACAGTTGATGAGAGAATTGGAAGTTATG |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test_2/amrfinderplus_results.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_2/amrfinderplus_results.tsv Fri May 26 09:19:12 2023 +0000 |
| b |
| @@ -0,0 +1,2 @@ +Name 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 +test_2 NA contig_26 6581 8545 + optrA ABC-F type ribosomal protection protein OptrA core AMR AMR PHENICOL/OXAZOLIDINONE FLORFENICOL/OXAZOLIDINONE EXACTX 655 655 100.00 100.00 655 WP_063854496.1 ABC-F type ribosomal protection protein OptrA NA NA optrA |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test_3/amrfinderplus_nucleotide_output.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_3/amrfinderplus_nucleotide_output.fasta Fri May 26 09:19:12 2023 +0000 |
| b |
| b"@@ -0,0 +1,142 @@\n+>contig_26:6581-8545 strand:+ optrA ABC-F type ribosomal protection protein OptrA\n+TTGTCCAAAGCCACCTTTGCAATTGCTAGTACTAACGCAAAGGAGGATATGAAAATGCAA\n+TACAAAATAATTAATGGTGCCGTTTACTATGATGGTAATATGGTGTTGGAAAACATCGGT\n+ATTGAAATCAATGATAATGAAAAGATTGCTATTGTTGGTAGAAATGGATGTGGAAAAACA\n+ACCTTGCTAAAAGCTATTATAGGCGAAATTGAATTAGAAGAAGGAACTGGTGAAAGTGAG\n+TTTCAAGTAATAAAGACCGGTAACCCTTATATTAGCTATTTAAGACAGATGCCTTTTGAA\n+GATGAAAGTATATCAATGGTGGATGAAGTCCGTACGGTATTTAAGACGCTTATTGATATG\n+GAAAACAAGATGAAACAGCTGATAGATAAAATGGAGAATCAATATGATGATAAAATCATC\n+AATGAATACTCTGATATCAGTGAAAGGTATATGGCTCTTGGAGGTCTAACCTACCAAAAA\n+GAATATGAAACGATGATTCGTAGTATGGGTTTTACTGAAGCAGATTATAAAAAACCCATT\n+TCTGAATTTTCAGGTGGTCAGCGAACTAAGATAGCTTTTATAAAAATACTTTTAACAAAG\n+CCAGACATTCTATTACTTGATGAACCTACTAACCACCTTGATATAGAAACAATACAATGG\n+TTGGAGAGTTATTTGAGAAGTTATAAATCTACATTGGTTATTATTTCCCATGATAGAATG\n+TTTCTTAATCGAATTGTGGATAAGGTTTATGAAATCGAATGGGGAGAGACCAAATGTTAT\n+AAAGGTAATTATTCAGCCTTTGAGGAGCAAAAACGAGAAAATCATATCAAACAGCAAAAA\n+GATTACGACTTGCAACAGATAGAAATTGAAAGGATTACACGCTTGATTGAACGTTTTCGT\n+TATAAACCTACGAAAGCTAAAATGGTGCAATCTAAAATTAAATTATTACAGCGTATGCAA\n+ATATTAAATGCACCAGACCAATACGATACAAAAACTTATATGTCTAAATTTCAACCGAGA\n+ATCAGTAGTTCAAGGCAAGTATTAAGTGCTTCAGAACTTGTGATAGGCTATGATACTCCT\n+CTTGCAAAGGTTAATTTCAACCTTGAAAGGGGACAGAAGCTTGGAATTGTTGGGAGTAAT\n+GGTATTGGTAAATCCACGTTGCTTAAAACACTTATGGGTGGTGTGGCAGCATTGTCTGGA\n+GATTTTAAATTCGGATACAATGTTGAAATTAGCTATTTTGACCAACAGCTTGCTCAAATC\n+AGTGGAGATGATACACTATTCGAAATTTTTCAAAGCGAATACCCTGAGCTAAATGACACA\n+GAGGTCAGAACTGCTCTTGGCTCATTTCAGTTTAGTGGAGATGATGTTTTTAGACCGGTG\n+TCCTCTTTGTCAGGTGGAGAAAAGGTTAGATTGACATTATGTAAATTATTATATAAACGT\n+ACTAATGTTTTAATCTTAGATGAACCGACAAACCACATGGATATTATTGGAAAAGAGAAT\n+TTAGAGAATATCTTATGCAGTTATCAAGGTACAATTATTTTTGTGTCACATGATAGATAT\n+TTTACTAATAAGATTGCTGACAGATTACTTGTTTTTGATAAGGATGGTGTAGAGTTTGTA\n+CAATCTACTTATGGTGAGTACGAGAAAAAAAGGATGAATTCTGAAAAGCCATTTAATAAC\n+ATTAAAGTTGAGCAGAAAGTAGAGAAAAATAACACAGTAAAAGGCGATCGTAACTCCATT\n+GAGAAGGAGAAGGTTAAGAAGGAGAAACGAATTGAAAAGCTTGAAGTGTTAATAAATCAA\n+TATGATGAAGAATTAGAAAGATTGAATAAAATCATTTCTGAACCAAACAATTCTTCTGAT\n+TATATAGTACTGACGGAAATACAAAAATCAATTGATGATGTTAAAAGGTGTCAGGGTAAT\n+TATTTTAATGAATGGGAACAGTTGATGAGAGAATTGGAAGTTATG\n+>contig_46:2438-3229 strand:- aph(3')-IIIa aminoglycoside O-phosphotransferase APH(3')-IIIa\n+ATGGCTAAAATGAGAATATCACCGGAATTGAAAAAACTGATCGAAAAATACCGCTGCGTA\n+AAAGATACGGAAGGAATGTCTCCTGCTAAGGTATATAAGCTGGTGGGAGAAAATGAAAAC\n+CTATATTTAAAAATGACGGACAGCCGGTATAAAGGGACCACCTATGATGTGGAACGGGAA\n+AAGGACATGATGCTATGGCTGGAAGGAAAGCTGCCTGTTCCAAAGGTCCTGCACTTTGAA\n+CGGCATGATGGCTGGAGCAATCTGCTCATGAGTGAGGCCGATGGCGTCCTTTGCTCGGAA\n+GAGTATGAAGATGAACAAAGCCCTGAAAAGATTATCGAGCTGTATGCGGAGTGCATCAGG\n+CTCTTTCACTCCATCGACATATCGGATTGTCCCTATACGAATAGCTTAGACAGCCGCTTA\n+GCCGAATTGGATTACTTACTGAATAACGATCTGGCCGATGTGGATTGCGAAAACTGGGAA\n+GAAGACACTCCATTTAAAGATCCGCGCGAGCTGTATGATTTTTTAAAGACGGAAAAGCCC\n+GAAGAGGAACTTGTCTTTTCCCACGGCGACCTGGGAGACAGCAACATCTTTGTGAAAGAT\n+GGCAAAGTAAGTGGCTTTATTGATCTTGGGAGAAGCGGCAGGGCGGACAAGTGGTATGAC\n+ATTGCCTTCTGCGTCCGGTCGATCAGGGAGGATATCGGGGAAGAACAGTATGTCGAGCTA\n+TTTTTTGACTTACTGGGGATCAAGCCTGATTGGGAGAAAATAAAATATTATATTTTACTG\n+GATGAATTGTTT\n+>contig_46:3325-3864 strand:- sat4 streptothricin N-acetyltransferase Sat4\n+GTGATTACAGAAATGAAAGCAGGGCACCTGAAAGATATCGATAAACCCAGCGAACCATTT\n+GAGGTGATAGGTAAGATTATACCGAGGTATGAAAACGAGAATTGGACCTTTACAGAATTA\n+CTCTATGAAGCGCCATATTTAAAAAGCTACCAAGACGAAGAGGATGAAGAGGATGAGGAG\n+GCAGATTGCCTTGAATATATTGACAATACTGATAAGATAATATATCTTTACTACCAAGAC\n+GATAAATGCGTCGGAAAAGTTAAACTGCGAAAAAATTGGAACCGGTACGCTTATATAGAA\n+GATATCGCCGTATGTAAGGATTTCAGGGGGCAAGGCATAGGCAGCGCGCTTATCAATATA\n+TCTATAGAATGGGCAAAGCATAAAAACTTGCATGGACTAATGCTTGAAACCCAGGACAAT\n+AACCTTATAGCTTGTAAATTCTATCATAATTGTGGTTTCAAAATCGGCTCCGTCGATACT\n+ATGTTATACGCCAACTTTGAAAACAACTTTGAAAAAGCTGTTTTCTGGTATTTAAGGTTT\n+>contig_47:3996-5912 strand:- tet(M) tetracycline resistance ribosomal protection protein Tet(M)\n+ATGAAAATTATTAATATTGGAGTTTTAGCTCATGTTGATGCGGGAAAAACTACCTTAACA\n+GAAAGCTTATTATATAACAGTGGAGCGATTACAGAATTAGGAAGCGTGGACAAAGGTACA\n+ACGAGGACGGATAATACGCTTTTAGAACGTCAGAGAGGAATTACAATTCAGACAGGAATA\n+ACCTCTTTTCAGTGGGAAAATACGAAGGTGAACAT"..b'GTTGAACCGAGCAAACCTCAACAAAGGGAAATG\n+TTGCTTGATGCCCTTTTGGAAATCTCAGATAGTGATCCGCTTCTACGATATTACGTGGAT\n+TCTACGACACATGAAATTATACTTTCTTTCTTAGGGAAAGTACAAATGGAAGTGATTAGT\n+GCACTGTTGCAAGAAAAGTATCATGTGGAGATAGAACTAAAAGAGCCTACAGTCATTTAT\n+ATGGAGAGACCGTTAAAAAATGCAGAATATACCATTCACATCGAAGTGCCGCCAAATCCT\n+TTCTGGGCTTCCATTGGTTTATCTGTATCACCGCTTCCATTAGGGAGCGGAGTGCAGTAT\n+GAGAGCTCGGTTTCTCTTGGATACTTAAATCAATCGTTTCAAAATGCAGTTATGGAGGGG\n+ATACGCTATGGCTGTGAACAAGGATTGTATGGTTGGAATGTGACGGACTGTAAAATCTGT\n+TTTAAGTATGGCTTATACTATAGCCCTGTTAGTACCCCAGCAGATTTTCGGATGCTTGCT\n+CCTATTGTATTGGAACAAGTCTTAAAAAAAGCTGGAACAGAATTGTTAGAGCCATATCTT\n+AGTTTTAAAATTTATGCGCCACAGGAATATCTTTCACGAGCATACAACGATGCTCCTAAA\n+TATTGTGCGAACATCGTAGACACTCAATTGAAAAATAATGAGGTCATTCTTAGTGGAGAA\n+ATCCCTGCTCGGTGTATTCAAGAATATCGTAGTGATTTAACTTTCTTTACAAATGGACGT\n+AGTGTTTGTTTAACAGAGTTAAAAGGGTACCATGTTACTACCGGTGAACCTGTTTGCCAG\n+CCCCGTCGTCCAAATAGTCGGATAGATAAAGTACGATATATGTTCAATAAAATAACT\n+>contig_48:202-936 strand:- erm(B) 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B)\n+ATGAACAAAAATATAAAATATTCTCAAAACTTTTTAACGAGTGAAAAAGTACTCAACCAA\n+ATAATAAAACAATTGAATTTAAAAGAAACCGATACCGTTTACGAAATTGGAACAGGTAAA\n+GGGCATTTAACGACGAAACTGGCTAAAATAAGTAAACAGGTAACGTCTATTGAATTAGAC\n+AGTCATCTATTCAACTTATCGTCAGAAAAATTAAAACTGAATACTCGTGTCACTTTAATT\n+CACCAAGATATTCTACAGTTTCAATTCCCTAACAAACAGAGGTATAAAATTGTTGGGAGT\n+ATTCCTTACCATTTAAGCACACAAATTATTAAAAAAGTGGTTTTTGAAAGCCATGCGTCT\n+GACATCTATCTGATTGTTGAAGAAGGATTCTACAAGCGTACCTTGGATATTCACCGAACA\n+CTAGGGTTGCTCTTGCACACTCAAGTCTCGATTCAGCAATTGCTTAAGCTGCCAGCGGAA\n+TGCTTTCATCCTAAACCAAAAGTAAACAGTGTCTTAATAAAACTTACCCGCCATACCACA\n+GATGTTCCAGATAAATATTGGAAGCTATATACGTACTTTGTTTCAAAATGGGTCAATCGA\n+GAATATCGTCAACTGTTTACTAAAAATCAGTTTCATCAAGCAATGAAACACGCCAAAGTA\n+AACAATTTAAGTACCGTTACTTATGAGCAAGTATTGTCTATTTTTAATAGTTATCTATTA\n+TTTAACGGGAGGAAA\n+>contig_48:4344-4988 strand:+ catA type A-7 chloramphenicol O-acetyltransferase\n+ATGACTTTTAATATTATTGAATTAGAAAATTGGGATAGAAAAGAATATTTTGAACACTAT\n+TTTAATCAGCAAACTACTTATAGCATTACTAAAGAAATTGATATTACTTTGTTTAAAGAT\n+ATGATAAAAAAGAAAGGATATGAAATTTATCCCTCTTTAATTTATGCAATTATGGAAGTT\n+GTAAATAAAAATAAAGTGTTTAGAACAGGAATTAATAGTGAGAATAAATTAGGTTATTGG\n+GATAAGTTAAATCCTTTGTATACAGTTTTTAATAAGCAAACTGAAAAATTTACTAACATT\n+TGGACTGAATCTGATAAAAACTTCATTTCTTTTTATAATAATTATAAAAATGACTTGCTT\n+GAATATAAAGATAAAGAAGAAATGTTTCCTAAAAAACCGATACCTGAAAACACCATACCG\n+ATTTCAATGATTCCTTGGATTGATTTTAGTTCATTTAATTTAAATATTGGTAACAATAGC\n+AGCTTTTTATTGCCTATTATTACGATAGGTAAATTTTATAGTGAGAATAATAAAATTTAT\n+ATACCAGTTGCTCTGCAACTTCATCATTCTGTATGTGATGGTTACCATGCTTCACTATTT\n+ATGAATGAATTTCAAGATATAATTCATAGGGTAGATGATTGGATT\n+>contig_50:282-1655 strand:+ tet(L) tetracycline efflux MFS transporter Tet(L)\n+GTGAATACATCCTATTCACAATCGAATTTACGACACAACCAAATTTTAATTTGGCTTTGC\n+ATTTTATCTTTTTTTAGCGTATTAAATGAAATGGTTTTGAACGTCTCATTACCTGATATT\n+GCAAATGATTTTAATAAACCACCTGCGAGTACAAACTGGGTGAACACAGCCTTTATGTTA\n+ACCTTTTCCATTGGAACAGCTGTATATGGAAAGCTATCTGATCAATTAGGCATCAAAAGG\n+TTACTCCTATTTGGAATTATAATAAATTGTTTCGGGTCGGTAATTGGGTTTGTTGGCCAT\n+TCTTTCTTTTCCTTACTTATTATGGCTCGTTTTATTCAAGGGGCTGGTGCAGCTGCATTT\n+CCAGCACTCGTAATGGTTGTAGTTGCGCGCTATATTCCAAAGGAAAATAGGGGTAAAGCA\n+TTTGGTCTTATTGGATCGATAGTAGCCATGGGAGAAGGAGTCGGTCCAGCGATTGGTGGA\n+ATGATAGCCCATTATATTCATTGGTCCTATCTTCTACTCATTCCTATGATAACAATTATC\n+ACTGTTCCGTTTCTTATGAAATTATTAAAGAAAGAAGTAAGGATAAAAGGTCATTTTGAT\n+ATCAAAGGAATTATACTAATGTCTGTAGGCATTGTATTTTTTATGTTGTTTACAACATCA\n+TATAGCATTTCTTTTCTTATCGTTAGCGTGCTGTCATTCCTGATATTTGTAAAACATATC\n+AGGAAAGTAACAGATCCTTTTGTTGATCCCGGATTAGGGAAAAATATACCTTTTATGATT\n+GGAGTTCTTTGTGGGGGAATTATATTTGGAACAGTAGCAGGGTTTGTCTCTATGGTTCCT\n+TATATGATGAAAGATGTTCACCAGCTAAGTACTGCCGAAATCGGAAGTGTAATTATTTTC\n+CCTGGAACAATGAGTGTCATTATTTTCGGCTACATTGGTGGGATACTTGTTGATAGAAGA\n+GGTCCTTTATACGTGTTAAACATCGGAGTTACATTTCTTTCTGTTAGCTTTTTAACTGCT\n+TCCTTTCTTTTAGAAACAACATCATGGTTCATGACAATTATAATCGTATTTGTTTTAGGT\n+GGGCTTTCGTTCACCAAAACAGTTATATCAACAATTGTTTCAAGTAGCTTGAAACAGCAG\n+GAAGCTGGTGCTGGAATGAGTTTGCTTAACTTTACCAGCTTTTTATCAGAGGGAACAGGT\n+ATTGCAATTGTAGGTGGTTTATTATCCATACCCTTACTTGATCAAAGGTTGTTACCTATG\n+GAAGTTGATCAGTCAACTTATCTGTATAGTAATTTGTTATTACTTTTTTCAGGAATCATT\n+GTCATTAGTTGGCTGGTTACCTTGAATGTATATAAACATTCTCAAAGGGATTTC\n' |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test_3/amrfinderplus_results.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_3/amrfinderplus_results.tsv Fri May 26 09:19:12 2023 +0000 |
| b |
| @@ -0,0 +1,9 @@ +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 +NA contig_26 6581 8545 + optrA ABC-F type ribosomal protection protein OptrA core AMR AMR PHENICOL/OXAZOLIDINONE FLORFENICOL/OXAZOLIDINONE EXACTX 655 655 100.00 100.00 655 WP_063854496.1 ABC-F type ribosomal protection protein OptrA NA NA +NA contig_46 2438 3229 - aph(3')-IIIa aminoglycoside O-phosphotransferase APH(3')-IIIa core AMR AMR AMINOGLYCOSIDE AMIKACIN/KANAMYCIN BLASTX 264 264 100.00 99.62 264 WP_063841495.1 aminoglycoside O-phosphotransferase APH(3')-IIIa NA NA +NA contig_46 2438 3229 - aph(3')-IIIa aminoglycoside O-phosphotransferase APH(3')-IIIa core AMR AMR AMINOGLYCOSIDE AMIKACIN/KANAMYCIN BLASTX 264 264 100.00 99.62 264 WP_063841507.1 aminoglycoside O-phosphotransferase APH(3')-IIIa NA NA +NA contig_46 3325 3864 - sat4 streptothricin N-acetyltransferase Sat4 core AMR AMR STREPTOTHRICIN STREPTOTHRICIN BLASTX 180 180 100.00 99.44 180 WP_063854934.1 streptothricin N-acetyltransferase Sat4 NA NA +NA contig_47 3996 5912 - tet(M) tetracycline resistance ribosomal protection protein Tet(M) core AMR AMR TETRACYCLINE TETRACYCLINE BLASTX 639 639 100.00 99.84 639 WP_063856395.1 tetracycline resistance ribosomal protection protein Tet(M) NA NA +NA contig_48 202 936 - erm(B) 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B) core AMR AMR MACROLIDE MACROLIDE BLASTX 245 245 100.00 99.59 245 WP_063844601.1 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B) NA NA +NA contig_48 4344 4988 + catA type A-7 chloramphenicol O-acetyltransferase core AMR AMR PHENICOL CHLORAMPHENICOL BLASTX 215 215 100.00 96.28 215 WP_063843211.1 type A-7 chloramphenicol O-acetyltransferase NA NA +NA contig_50 282 1655 + tet(L) tetracycline efflux MFS transporter Tet(L) core AMR AMR TETRACYCLINE TETRACYCLINE BLASTX 458 458 100.00 99.78 458 WP_063856080.1 tetracycline efflux MFS transporter Tet(L) NA NA |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test_4/amrfinderplus_protein_output.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_4/amrfinderplus_protein_output.fasta Fri May 26 09:19:12 2023 +0000 |
| b |
| @@ -0,0 +1,49 @@ +>IDOBJL_14770 aph(3')-IIIa aminoglycoside O-phosphotransferase APH(3')-IIIa +MAKMRISPELKKLIEKYRCVKDTEGMSPAKVYKLVGENENLYLKMTDSRYKGTTYDVERE +KDMMLWLEGKLPVPKVLHFERHDGWSNLLMSEADGVLCSEEYEDEQSPEKIIELYAECIR +LFHSIDISDCPYTNSLDSRLAELDYLLNNDLADVDCENWEEDTPFKDPRELYDFLKTEKP +EEELVFSHGDLGDSNIFVKDGKVSGFIDLGRSGRADKWYDIAFCVRSIREDIGEEQYVEL +FFDLLGIKPDWEKIKYYILLDELF +>IDOBJL_14775 sat4 streptothricin N-acetyltransferase Sat4 +MITEMKAGHLKDIDKPSEPFEVIGKIIPRYENENWTFTELLYEAPYLKSYQDEEDEEDEE +ADCLEYIDNTDKIIYLYYQDDKCVGKVKLRKNWNRYAYIEDIAVCKDFRGQGIGSALINI +SIEWAKHKNLHGLMLETQDNNLIACKFYHNCGFKIGSVDTMLYANFENNFEKAVFWYLRF +>IDOBJL_14820 tet(M) tetracycline resistance ribosomal protection protein Tet(M) +MKIINIGVLAHVDAGKTTLTESLLYNSGAITELGSVDKGTTRTDNTLLERQRGITIQTGI +TSFQWENTKVNIIDTPGHMDFLAEVYRSLSVLDGAILLISAKDGVQAQTRILFHALRKMG +IPTIFFINKIDQNGIDLSTVYQDIKEKLSAEIVIKQKVELYPNMCVTNFTESEQWDTVIE +GNDDLLEKYMSGKSLEALELEQEESIRFQNCSLFPVYHGSAKNNIGIDNLIEVITNKFYS +STHRGQSELCGNVFKIEYTKKRQRLAYIRLYSGVLHLRDSVRISEKEKIKITEMYTSING +ELCKIDKAYSGEIVILQNEFLKLNSVLGDTKLLPQRERIENPLPLLQTTVEPSKPQQREM +LLDALLEISDSDPLLRYYVDSTTHEIILSFLGKVQMEVISALLQEKYHVEIELKEPTVIY +MERPLKNAEYTIHIEVPPNPFWASIGLSVSPLPLGSGVQYESSVSLGYLNQSFQNAVMEG +IRYGCEQGLYGWNVTDCKICFKYGLYYSPVSTPADFRMLAPIVLEQVLKKAGTELLEPYL +SFKIYAPQEYLSRAYNDAPKYCANIVDTQLKNNEVILSGEIPARCIQEYRSDLTFFTNGR +SVCLTELKGYHVTTGEPVCQPRRPNSRIDKVRYMFNKIT +>IDOBJL_14830 erm(B) 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B) +MNKNIKYSQNFLTSEKVLNQIIKQLNLKETDTVYEIGTGKGHLTTKLAKISKQVTSIELD +SHLFNLSSEKLKLNTRVTLIHQDILQFQFPNKQRYKIVGSIPYHLSTQIIKKVVFESHAS +DIYLIVEEGFYKRTLDIHRTLGLLLHTQVSIQQLLKLPAECFHPKPKVNSVLIKLTRHTT +DVPDKYWKLYTYFVSKWVNREYRQLFTKNQFHQAMKHAKVNNLSTVTYEQVLSIFNSYLL +FNGRK +>IDOBJL_14880 tet(L) tetracycline efflux MFS transporter Tet(L) +MNTSYSQSNLRHNQILIWLCILSFFSVLNEMVLNVSLPDIANDFNKPPASTNWVNTAFML +TFSIGTAVYGKLSDQLGIKRLLLFGIIINCFGSVIGFVGHSFFSLLIMARFIQGAGAAAF +PALVMVVVARYIPKENRGKAFGLIGSIVAMGEGVGPAIGGMIAHYIHWSYLLLIPMITII +TVPFLMKLLKKEVRIKGHFDIKGIILMSVGIVFFMLFTTSYSISFLIVSVLSFLIFVKHI +RKVTDPFVDPGLGKNIPFMIGVLCGGIIFGTVAGFVSMVPYMMKDVHQLSTAEIGSVIIF +PGTMSVIIFGYIGGILVDRRGPLYVLNIGVTFLSVSFLTASFLLETTSWFMTIIIVFVLG +GLSFTKTVISTIVSSSLKQQEAGAGMSLLNFTSFLSEGTGIAIVGGLLSIPLLDQRLLPM +EVDQSTYLYSNLLLLFSGIIVISWLVTLNVYKHSQRDF +>IDOBJL_13105 optrA ABC-F type ribosomal protection protein OptrA +MQYKIINGAVYYDGNMVLENIGIEINDNEKIAIVGRNGCGKTTLLKAIIGEIELEEGTGE +SEFQVIKTGNPYISYLRQMPFEDESISMVDEVRTVFKTLIDMENKMKQLIDKMENQYDDK +IINEYSDISERYMALGGLTYQKEYETMIRSMGFTEADYKKPISEFSGGQRTKIAFIKILL +TKPDILLLDEPTNHLDIETIQWLESYLRSYKSTLVIISHDRMFLNRIVDKVYEIEWGETK +CYKGNYSAFEEQKRENHIKQQKDYDLQQIEIERITRLIERFRYKPTKAKMVQSKIKLLQR +MQILNAPDQYDTKTYMSKFQPRISSSRQVLSASELVIGYDTPLAKVNFNLERGQKLGIVG +SNGIGKSTLLKTLMGGVAALSGDFKFGYNVEISYFDQQLAQISGDDTLFEIFQSEYPELN +DTEVRTALGSFQFSGDDVFRPVSSLSGGEKVRLTLCKLLYKRTNVLILDEPTNHMDIIGK +ENLENILCSYQGTIIFVSHDRYFTNKIADRLLVFDKDGVEFVQSTYGEYEKKRMNSEKPF +NNIKVEQKVEKNNTVKGDRNSIEKEKVKKEKRIEKLEVLINQYDEELERLNKIISEPNNS +SDYIVLTEIQKSIDDVKRCQGNYFNEWEQLMRELEVM |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test_4/amrfinderplus_results.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_4/amrfinderplus_results.tsv Fri May 26 09:19:12 2023 +0000 |
| b |
| @@ -0,0 +1,7 @@ +Protein identifier 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 +IDOBJL_13105 optrA ABC-F type ribosomal protection protein OptrA core AMR AMR PHENICOL/OXAZOLIDINONE FLORFENICOL/OXAZOLIDINONE BLASTP 637 655 97.25 100.00 637 WP_063854496.1 ABC-F type ribosomal protection protein OptrA NA NA +IDOBJL_14770 aph(3')-IIIa aminoglycoside O-phosphotransferase APH(3')-IIIa core AMR AMR AMINOGLYCOSIDE AMIKACIN/KANAMYCIN BLASTP 264 264 100.00 99.62 264 WP_063841495.1 aminoglycoside O-phosphotransferase APH(3')-IIIa NA NA +IDOBJL_14775 sat4 streptothricin N-acetyltransferase Sat4 core AMR AMR STREPTOTHRICIN STREPTOTHRICIN BLASTP 180 180 100.00 99.44 180 WP_063854934.1 streptothricin N-acetyltransferase Sat4 NA NA +IDOBJL_14820 tet(M) tetracycline resistance ribosomal protection protein Tet(M) core AMR AMR TETRACYCLINE TETRACYCLINE BLASTP 639 639 100.00 99.84 639 WP_063856395.1 tetracycline resistance ribosomal protection protein Tet(M) NA NA +IDOBJL_14830 erm(B) 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B) core AMR AMR MACROLIDE MACROLIDE BLASTP 245 245 100.00 99.59 245 WP_063844601.1 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B) NA NA +IDOBJL_14880 tet(L) tetracycline efflux MFS transporter Tet(L) core AMR AMR TETRACYCLINE TETRACYCLINE BLASTP 458 458 100.00 99.78 458 WP_063856080.1 tetracycline efflux MFS transporter Tet(L) NA NA |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test_5/amrfinderplus_mutation_all.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_5/amrfinderplus_mutation_all.tsv Fri May 26 09:19:12 2023 +0000 |
| b |
| @@ -0,0 +1,1 @@ +Name 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 |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test_5/amrfinderplus_nucleotide_output.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_5/amrfinderplus_nucleotide_output.fasta Fri May 26 09:19:12 2023 +0000 |
| b |
| @@ -0,0 +1,49 @@ +>IDOBJL_14770 aph(3')-IIIa aminoglycoside O-phosphotransferase APH(3')-IIIa +MAKMRISPELKKLIEKYRCVKDTEGMSPAKVYKLVGENENLYLKMTDSRYKGTTYDVERE +KDMMLWLEGKLPVPKVLHFERHDGWSNLLMSEADGVLCSEEYEDEQSPEKIIELYAECIR +LFHSIDISDCPYTNSLDSRLAELDYLLNNDLADVDCENWEEDTPFKDPRELYDFLKTEKP +EEELVFSHGDLGDSNIFVKDGKVSGFIDLGRSGRADKWYDIAFCVRSIREDIGEEQYVEL +FFDLLGIKPDWEKIKYYILLDELF +>IDOBJL_14775 sat4 streptothricin N-acetyltransferase Sat4 +MITEMKAGHLKDIDKPSEPFEVIGKIIPRYENENWTFTELLYEAPYLKSYQDEEDEEDEE +ADCLEYIDNTDKIIYLYYQDDKCVGKVKLRKNWNRYAYIEDIAVCKDFRGQGIGSALINI +SIEWAKHKNLHGLMLETQDNNLIACKFYHNCGFKIGSVDTMLYANFENNFEKAVFWYLRF +>IDOBJL_14820 tet(M) tetracycline resistance ribosomal protection protein Tet(M) +MKIINIGVLAHVDAGKTTLTESLLYNSGAITELGSVDKGTTRTDNTLLERQRGITIQTGI +TSFQWENTKVNIIDTPGHMDFLAEVYRSLSVLDGAILLISAKDGVQAQTRILFHALRKMG +IPTIFFINKIDQNGIDLSTVYQDIKEKLSAEIVIKQKVELYPNMCVTNFTESEQWDTVIE +GNDDLLEKYMSGKSLEALELEQEESIRFQNCSLFPVYHGSAKNNIGIDNLIEVITNKFYS +STHRGQSELCGNVFKIEYTKKRQRLAYIRLYSGVLHLRDSVRISEKEKIKITEMYTSING +ELCKIDKAYSGEIVILQNEFLKLNSVLGDTKLLPQRERIENPLPLLQTTVEPSKPQQREM +LLDALLEISDSDPLLRYYVDSTTHEIILSFLGKVQMEVISALLQEKYHVEIELKEPTVIY +MERPLKNAEYTIHIEVPPNPFWASIGLSVSPLPLGSGVQYESSVSLGYLNQSFQNAVMEG +IRYGCEQGLYGWNVTDCKICFKYGLYYSPVSTPADFRMLAPIVLEQVLKKAGTELLEPYL +SFKIYAPQEYLSRAYNDAPKYCANIVDTQLKNNEVILSGEIPARCIQEYRSDLTFFTNGR +SVCLTELKGYHVTTGEPVCQPRRPNSRIDKVRYMFNKIT +>IDOBJL_14830 erm(B) 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B) +MNKNIKYSQNFLTSEKVLNQIIKQLNLKETDTVYEIGTGKGHLTTKLAKISKQVTSIELD +SHLFNLSSEKLKLNTRVTLIHQDILQFQFPNKQRYKIVGSIPYHLSTQIIKKVVFESHAS +DIYLIVEEGFYKRTLDIHRTLGLLLHTQVSIQQLLKLPAECFHPKPKVNSVLIKLTRHTT +DVPDKYWKLYTYFVSKWVNREYRQLFTKNQFHQAMKHAKVNNLSTVTYEQVLSIFNSYLL +FNGRK +>IDOBJL_14880 tet(L) tetracycline efflux MFS transporter Tet(L) +MNTSYSQSNLRHNQILIWLCILSFFSVLNEMVLNVSLPDIANDFNKPPASTNWVNTAFML +TFSIGTAVYGKLSDQLGIKRLLLFGIIINCFGSVIGFVGHSFFSLLIMARFIQGAGAAAF +PALVMVVVARYIPKENRGKAFGLIGSIVAMGEGVGPAIGGMIAHYIHWSYLLLIPMITII +TVPFLMKLLKKEVRIKGHFDIKGIILMSVGIVFFMLFTTSYSISFLIVSVLSFLIFVKHI +RKVTDPFVDPGLGKNIPFMIGVLCGGIIFGTVAGFVSMVPYMMKDVHQLSTAEIGSVIIF +PGTMSVIIFGYIGGILVDRRGPLYVLNIGVTFLSVSFLTASFLLETTSWFMTIIIVFVLG +GLSFTKTVISTIVSSSLKQQEAGAGMSLLNFTSFLSEGTGIAIVGGLLSIPLLDQRLLPM +EVDQSTYLYSNLLLLFSGIIVISWLVTLNVYKHSQRDF +>IDOBJL_13105 optrA ABC-F type ribosomal protection protein OptrA +MQYKIINGAVYYDGNMVLENIGIEINDNEKIAIVGRNGCGKTTLLKAIIGEIELEEGTGE +SEFQVIKTGNPYISYLRQMPFEDESISMVDEVRTVFKTLIDMENKMKQLIDKMENQYDDK +IINEYSDISERYMALGGLTYQKEYETMIRSMGFTEADYKKPISEFSGGQRTKIAFIKILL +TKPDILLLDEPTNHLDIETIQWLESYLRSYKSTLVIISHDRMFLNRIVDKVYEIEWGETK +CYKGNYSAFEEQKRENHIKQQKDYDLQQIEIERITRLIERFRYKPTKAKMVQSKIKLLQR +MQILNAPDQYDTKTYMSKFQPRISSSRQVLSASELVIGYDTPLAKVNFNLERGQKLGIVG +SNGIGKSTLLKTLMGGVAALSGDFKFGYNVEISYFDQQLAQISGDDTLFEIFQSEYPELN +DTEVRTALGSFQFSGDDVFRPVSSLSGGEKVRLTLCKLLYKRTNVLILDEPTNHMDIIGK +ENLENILCSYQGTIIFVSHDRYFTNKIADRLLVFDKDGVEFVQSTYGEYEKKRMNSEKPF +NNIKVEQKVEKNNTVKGDRNSIEKEKVKKEKRIEKLEVLINQYDEELERLNKIISEPNNS +SDYIVLTEIQKSIDDVKRCQGNYFNEWEQLMRELEVM |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test_5/amrfinderplus_results.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_5/amrfinderplus_results.tsv Fri May 26 09:19:12 2023 +0000 |
| b |
| @@ -0,0 +1,8 @@ +Name 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 +test_5 IDOBJL_13105 contig_26 6635 8548 + optrA ABC-F type ribosomal protection protein OptrA core AMR AMR PHENICOL/OXAZOLIDINONE FLORFENICOL/OXAZOLIDINONE BLASTP 637 655 97.25 100.00 637 WP_063854496.1 ABC-F type ribosomal protection protein OptrA NA NA optrA +test_5 IDOBJL_14770 contig_46 2435 3229 - aph(3')-IIIa aminoglycoside O-phosphotransferase APH(3')-IIIa core AMR AMR AMINOGLYCOSIDE AMIKACIN/KANAMYCIN BLASTP 264 264 100.00 99.62 264 WP_063841495.1 aminoglycoside O-phosphotransferase APH(3')-IIIa NA NA aph(3')-IIIa +test_5 IDOBJL_14770 contig_46 2435 3229 - aph(3')-IIIa aminoglycoside O-phosphotransferase APH(3')-IIIa core AMR AMR AMINOGLYCOSIDE AMIKACIN/KANAMYCIN BLASTP 264 264 100.00 99.62 264 WP_063841507.1 aminoglycoside O-phosphotransferase APH(3')-IIIa NA NA aph(3')-IIIa +test_5 IDOBJL_14775 contig_46 3322 3864 - sat4 streptothricin N-acetyltransferase Sat4 core AMR AMR STREPTOTHRICIN STREPTOTHRICIN BLASTP 180 180 100.00 99.44 180 WP_063854934.1 streptothricin N-acetyltransferase Sat4 NA NA sat4 +test_5 IDOBJL_14820 contig_47 3993 5912 - tet(M) tetracycline resistance ribosomal protection protein Tet(M) core AMR AMR TETRACYCLINE TETRACYCLINE BLASTP 639 639 100.00 99.84 639 WP_063856395.1 tetracycline resistance ribosomal protection protein Tet(M) NA NA tet(M) +test_5 IDOBJL_14830 contig_48 199 936 - erm(B) 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B) core AMR AMR MACROLIDE MACROLIDE BLASTP 245 245 100.00 99.59 245 WP_063844601.1 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B) NA NA erm(B) +test_5 IDOBJL_14880 contig_50 282 1658 + tet(L) tetracycline efflux MFS transporter Tet(L) core AMR AMR TETRACYCLINE TETRACYCLINE BLASTP 458 458 100.00 99.78 458 WP_063856080.1 tetracycline efflux MFS transporter Tet(L) NA NA tet(L) |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test_6/amrfinderplus_protein_output.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_6/amrfinderplus_protein_output.fasta Fri May 26 09:19:12 2023 +0000 |
| b |
| @@ -0,0 +1,49 @@ +>FODBOAIN_02586 optrA ABC-F type ribosomal protection protein OptrA +MQYKIINGAVYYDGNMVLENIGIEINDNEKIAIVGRNGCGKTTLLKAIIGEIELEEGTGE +SEFQVIKTGNPYISYLRQMPFEDESISMVDEVRTVFKTLIDMENKMKQLIDKMENQYDDK +IINEYSDISERYMALGGLTYQKEYETMIRSMGFTEADYKKPISEFSGGQRTKIAFIKILL +TKPDILLLDEPTNHLDIETIQWLESYLRSYKSTLVIISHDRMFLNRIVDKVYEIEWGETK +CYKGNYSAFEEQKRENHIKQQKDYDLQQIEIERITRLIERFRYKPTKAKMVQSKIKLLQR +MQILNAPDQYDTKTYMSKFQPRISSSRQVLSASELVIGYDTPLAKVNFNLERGQKLGIVG +SNGIGKSTLLKTLMGGVAALSGDFKFGYNVEISYFDQQLAQISGDDTLFEIFQSEYPELN +DTEVRTALGSFQFSGDDVFRPVSSLSGGEKVRLTLCKLLYKRTNVLILDEPTNHMDIIGK +ENLENILCSYQGTIIFVSHDRYFTNKIADRLLVFDKDGVEFVQSTYGEYEKKRMNSEKPF +NNIKVEQKVEKNNTVKGDRNSIEKEKVKKEKRIEKLEVLINQYDEELERLNKIISEPNNS +SDYIVLTEIQKSIDDVKRCQGNYFNEWEQLMRELEVM +>FODBOAIN_02916 aph(3')-IIIa aminoglycoside O-phosphotransferase APH(3')-IIIa +MAKMRISPELKKLIEKYRCVKDTEGMSPAKVYKLVGENENLYLKMTDSRYKGTTYDVERE +KDMMLWLEGKLPVPKVLHFERHDGWSNLLMSEADGVLCSEEYEDEQSPEKIIELYAECIR +LFHSIDISDCPYTNSLDSRLAELDYLLNNDLADVDCENWEEDTPFKDPRELYDFLKTEKP +EEELVFSHGDLGDSNIFVKDGKVSGFIDLGRSGRADKWYDIAFCVRSIREDIGEEQYVEL +FFDLLGIKPDWEKIKYYILLDELF +>FODBOAIN_02917 sat4 streptothricin N-acetyltransferase Sat4 +MITEMKAGHLKDIDKPSEPFEVIGKIIPRYENENWTFTELLYEAPYLKSYQDEEDEEDEE +ADCLEYIDNTDKIIYLYYQDDKCVGKVKLRKNWNRYAYIEDIAVCKDFRGQGIGSALINI +SIEWAKHKNLHGLMLETQDNNLIACKFYHNCGFKIGSVDTMLYANFENNFEKAVFWYLRF +>FODBOAIN_02926 tet(M) tetracycline resistance ribosomal protection protein Tet(M) +MKIINIGVLAHVDAGKTTLTESLLYNSGAITELGSVDKGTTRTDNTLLERQRGITIQTGI +TSFQWENTKVNIIDTPGHMDFLAEVYRSLSVLDGAILLISAKDGVQAQTRILFHALRKMG +IPTIFFINKIDQNGIDLSTVYQDIKEKLSAEIVIKQKVELYPNMCVTNFTESEQWDTVIE +GNDDLLEKYMSGKSLEALELEQEESIRFQNCSLFPVYHGSAKNNIGIDNLIEVITNKFYS +STHRGQSELCGNVFKIEYTKKRQRLAYIRLYSGVLHLRDSVRISEKEKIKITEMYTSING +ELCKIDKAYSGEIVILQNEFLKLNSVLGDTKLLPQRERIENPLPLLQTTVEPSKPQQREM +LLDALLEISDSDPLLRYYVDSTTHEIILSFLGKVQMEVISALLQEKYHVEIELKEPTVIY +MERPLKNAEYTIHIEVPPNPFWASIGLSVSPLPLGSGVQYESSVSLGYLNQSFQNAVMEG +IRYGCEQGLYGWNVTDCKICFKYGLYYSPVSTPADFRMLAPIVLEQVLKKAGTELLEPYL +SFKIYAPQEYLSRAYNDAPKYCANIVDTQLKNNEVILSGEIPARCIQEYRSDLTFFTNGR +SVCLTELKGYHVTTGEPVCQPRRPNSRIDKVRYMFNKIT +>FODBOAIN_02928 erm(B) 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B) +MNKNIKYSQNFLTSEKVLNQIIKQLNLKETDTVYEIGTGKGHLTTKLAKISKQVTSIELD +SHLFNLSSEKLKLNTRVTLIHQDILQFQFPNKQRYKIVGSIPYHLSTQIIKKVVFESHAS +DIYLIVEEGFYKRTLDIHRTLGLLLHTQVSIQQLLKLPAECFHPKPKVNSVLIKLTRHTT +DVPDKYWKLYTYFVSKWVNREYRQLFTKNQFHQAMKHAKVNNLSTVTYEQVLSIFNSYLL +FNGRK +>FODBOAIN_02936 tet(L) tetracycline efflux MFS transporter Tet(L) +MNTSYSQSNLRHNQILIWLCILSFFSVLNEMVLNVSLPDIANDFNKPPASTNWVNTAFML +TFSIGTAVYGKLSDQLGIKRLLLFGIIINCFGSVIGFVGHSFFSLLIMARFIQGAGAAAF +PALVMVVVARYIPKENRGKAFGLIGSIVAMGEGVGPAIGGMIAHYIHWSYLLLIPMITII +TVPFLMKLLKKEVRIKGHFDIKGIILMSVGIVFFMLFTTSYSISFLIVSVLSFLIFVKHI +RKVTDPFVDPGLGKNIPFMIGVLCGGIIFGTVAGFVSMVPYMMKDVHQLSTAEIGSVIIF +PGTMSVIIFGYIGGILVDRRGPLYVLNIGVTFLSVSFLTASFLLETTSWFMTIIIVFVLG +GLSFTKTVISTIVSSSLKQQEAGAGMSLLNFTSFLSEGTGIAIVGGLLSIPLLDQRLLPM +EVDQSTYLYSNLLLLFSGIIVISWLVTLNVYKHSQRDF |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test_6/amrfinderplus_results.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_6/amrfinderplus_results.tsv Fri May 26 09:19:12 2023 +0000 |
| b |
| @@ -0,0 +1,7 @@ +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 +FODBOAIN_02586 contig_26 6635 8548 + optrA ABC-F type ribosomal protection protein OptrA core AMR AMR PHENICOL/OXAZOLIDINONE FLORFENICOL/OXAZOLIDINONE BLASTP 637 655 97.25 100.00 637 WP_063854496.1 ABC-F type ribosomal protection protein OptrA NA NA +FODBOAIN_02916 contig_46 2435 3229 - aph(3')-IIIa aminoglycoside O-phosphotransferase APH(3')-IIIa core AMR AMR AMINOGLYCOSIDE AMIKACIN/KANAMYCIN BLASTP 264 264 100.00 99.62 264 WP_063841495.1 aminoglycoside O-phosphotransferase APH(3')-IIIa NA NA +FODBOAIN_02917 contig_46 3322 3864 - sat4 streptothricin N-acetyltransferase Sat4 core AMR AMR STREPTOTHRICIN STREPTOTHRICIN BLASTP 180 180 100.00 99.44 180 WP_063854934.1 streptothricin N-acetyltransferase Sat4 NA NA +FODBOAIN_02926 contig_47 3993 5912 - tet(M) tetracycline resistance ribosomal protection protein Tet(M) core AMR AMR TETRACYCLINE TETRACYCLINE BLASTP 639 639 100.00 99.84 639 WP_063856395.1 tetracycline resistance ribosomal protection protein Tet(M) NA NA +FODBOAIN_02928 contig_48 199 936 - erm(B) 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B) core AMR AMR MACROLIDE MACROLIDE BLASTP 245 245 100.00 99.59 245 WP_063844601.1 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B) NA NA +FODBOAIN_02936 contig_50 282 1658 + tet(L) tetracycline efflux MFS transporter Tet(L) core AMR AMR TETRACYCLINE TETRACYCLINE BLASTP 458 458 100.00 99.78 458 WP_063856080.1 tetracycline efflux MFS transporter Tet(L) NA NA |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test_7/amrfinderplus_protein_output.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_7/amrfinderplus_protein_output.fasta Fri May 26 09:19:12 2023 +0000 |
| b |
| @@ -0,0 +1,35 @@ +>blaTEM-156 blaTEM-156 class A beta-lactamase TEM-156 +MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRP +EERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVREL +CSAAITMSDNTAANLLLTTIGGPKELTAFLHNIGDHVTRLDRWEPELNEAIPNDERDTTM +PAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGS +RGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW +>blaPDC-114_blast blaPDC PDC family class C beta-lactamase +MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISL +KGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWP +ALVGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNP +SIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAG +PGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEA +YDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRD +LGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR +>blaOXA-436_partial blaOXA OXA-48 family class D beta-lactamase +MRALALSAVLMVTTMIGMPAVAKEWQENKSWNAHFSEHKTQGVVVLWNENTQQGFTNDLK +RANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIAAWNRDHDLITAMKYSVV +PVYQEFARQIGEARMSKMLHAFDYGNEDISGNLDSFWLDGGIRISATQQIAFLRKLYHNK +LHVSERSQRIVKQAMLTEANADYIIRAKTGYSVRIEPKIGWWVGWIELDDNVW +>vanG vanG D-alanine--D-serine ligase VanG +MQNKKIAVIFGGNSTEYEVSLQSASAVFENINTNKFDIIPIGITRSGEWYHYTGEKEKIL +NNTWFEDSKNLCPVVVSQNRSVKGFLEIASDKYRIIKVDLVFPVLHGKNGENGTLQGIFE +LAGIPVVGCDTLSSALCMDKDRAHKLVSLAGISVPKSVTFKRFNEEAAMKEIEANLTYPL +FIKPVRAGSSFGITKVIEKQELDAAIELAFEHDTEVIVEETINGFEVGCAVLGIDELIVG +RVDEIELSSGFFDYTEKYTLKSSKIYMPARIDAEAEKRIQEAAVTIYKALGCSGFSRVDM +FYTPSGEIVFNEVNTIPGFTSHSRYPNMMKGIGLSFSQMLDKLIGLYVE +>sul2_partial_3p_neg sul2 sulfonamide-resistant dihydropteroate synthase Sul2 +SSNPDAAPVSSDTEIERIAPVLDALKADGIPVSLDSYQPATQAYALSRGVAYLNDIRGFP +DAAFYPQLAKSSAKLVVMHSVQDGQADRREAPAGDIMDHIAAFFDARIAALTGAGIKRNR +LVLDPGMGFFLGAAPETSLSVLARFDELRLRFDLPVLLSVSRKSFLRALTGRGPGDVGAA +TLAAELAAAAGGADFIRTHEPRPLRDGLAVLAALKETARIR +>blaTEM-internal_stop blaTEM TEM family class A beta-lactamase +HFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVNYIELDLNSGKILESFRPEERF +PMMSTFKVLLCGAVLSCVDAGQEQLGRSIHYSQNDLVEYSPVTEKHLTDGMTLRELCSAA +ITMSDNTAANLLLTTIGGPKELTA |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test_7/amrfinderplus_results.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_7/amrfinderplus_results.tsv Fri May 26 09:19:12 2023 +0000 |
| b |
| @@ -0,0 +1,7 @@ +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 +blaTEM-156 contig01 101 961 + blaTEM-156 class A beta-lactamase TEM-156 core AMR AMR BETA-LACTAM BETA-LACTAM ALLELEP 286 286 100.00 100.00 286 WP_061158039.1 class A beta-lactamase TEM-156 NA NA +blaPDC-114_blast contig02 1 1191 + blaPDC PDC family class C beta-lactamase core AMR AMR BETA-LACTAM CEPHALOSPORIN BLASTP 397 397 100.00 99.75 397 WP_061189306.1 class C beta-lactamase PDC-114 NA NA +blaOXA-436_partial contig03 101 802 + blaOXA OXA-48 family class D beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM PARTIALP 233 265 87.92 93.56 233 WP_063864110.1 OXA-48 family carbapenem-hydrolyzing class D beta-lactamase OXA-484 NA NA +vanG contig04 101 1147 + vanG D-alanine--D-serine ligase VanG core AMR AMR GLYCOPEPTIDE VANCOMYCIN EXACTP 349 349 100.00 100.00 349 WP_063856695.1 D-alanine--D-serine ligase VanG NA NA +sul2_partial_3p_neg contig09 715 1377 - sul2 sulfonamide-resistant dihydropteroate synthase Sul2 core AMR AMR SULFONAMIDE SULFONAMIDE PARTIALP 221 271 81.55 99.10 221 WP_063855540.1 sulfonamide-resistant dihydropteroate synthase Sul2 NA NA +blaTEM-internal_stop contig11 113 547 + blaTEM TEM family class A beta-lactamase core AMR AMR BETA-LACTAM BETA-LACTAM PARTIALP 144 286 50.35 97.22 144 WP_061158039.1 class A beta-lactamase TEM-156 NA NA |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test_8/amrfinderplus_mutation_all.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_8/amrfinderplus_mutation_all.tsv Fri May 26 09:19:12 2023 +0000 |
| b |
| @@ -0,0 +1,1 @@ +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 |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test_8/amrfinderplus_nucleotide_output.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_8/amrfinderplus_nucleotide_output.fasta Fri May 26 09:19:12 2023 +0000 |
| b |
| b"@@ -0,0 +1,143 @@\n+>contig_26:6581-8545 strand:+ optrA ABC-F type ribosomal protection protein OptrA\n+TTGTCCAAAGCCACCTTTGCAATTGCTAGTACTAACGCAAAGGAGGATATGAAAATGCAA\n+TACAAAATAATTAATGGTGCCGTTTACTATGATGGTAATATGGTGTTGGAAAACATCGGT\n+ATTGAAATCAATGATAATGAAAAGATTGCTATTGTTGGTAGAAATGGATGTGGAAAAACA\n+ACCTTGCTAAAAGCTATTATAGGCGAAATTGAATTAGAAGAAGGAACTGGTGAAAGTGAG\n+TTTCAAGTAATAAAGACCGGTAACCCTTATATTAGCTATTTAAGACAGATGCCTTTTGAA\n+GATGAAAGTATATCAATGGTGGATGAAGTCCGTACGGTATTTAAGACGCTTATTGATATG\n+GAAAACAAGATGAAACAGCTGATAGATAAAATGGAGAATCAATATGATGATAAAATCATC\n+AATGAATACTCTGATATCAGTGAAAGGTATATGGCTCTTGGAGGTCTAACCTACCAAAAA\n+GAATATGAAACGATGATTCGTAGTATGGGTTTTACTGAAGCAGATTATAAAAAACCCATT\n+TCTGAATTTTCAGGTGGTCAGCGAACTAAGATAGCTTTTATAAAAATACTTTTAACAAAG\n+CCAGACATTCTATTACTTGATGAACCTACTAACCACCTTGATATAGAAACAATACAATGG\n+TTGGAGAGTTATTTGAGAAGTTATAAATCTACATTGGTTATTATTTCCCATGATAGAATG\n+TTTCTTAATCGAATTGTGGATAAGGTTTATGAAATCGAATGGGGAGAGACCAAATGTTAT\n+AAAGGTAATTATTCAGCCTTTGAGGAGCAAAAACGAGAAAATCATATCAAACAGCAAAAA\n+GATTACGACTTGCAACAGATAGAAATTGAAAGGATTACACGCTTGATTGAACGTTTTCGT\n+TATAAACCTACGAAAGCTAAAATGGTGCAATCTAAAATTAAATTATTACAGCGTATGCAA\n+ATATTAAATGCACCAGACCAATACGATACAAAAACTTATATGTCTAAATTTCAACCGAGA\n+ATCAGTAGTTCAAGGCAAGTATTAAGTGCTTCAGAACTTGTGATAGGCTATGATACTCCT\n+CTTGCAAAGGTTAATTTCAACCTTGAAAGGGGACAGAAGCTTGGAATTGTTGGGAGTAAT\n+GGTATTGGTAAATCCACGTTGCTTAAAACACTTATGGGTGGTGTGGCAGCATTGTCTGGA\n+GATTTTAAATTCGGATACAATGTTGAAATTAGCTATTTTGACCAACAGCTTGCTCAAATC\n+AGTGGAGATGATACACTATTCGAAATTTTTCAAAGCGAATACCCTGAGCTAAATGACACA\n+GAGGTCAGAACTGCTCTTGGCTCATTTCAGTTTAGTGGAGATGATGTTTTTAGACCGGTG\n+TCCTCTTTGTCAGGTGGAGAAAAGGTTAGATTGACATTATGTAAATTATTATATAAACGT\n+ACTAATGTTTTAATCTTAGATGAACCGACAAACCACATGGATATTATTGGAAAAGAGAAT\n+TTAGAGAATATCTTATGCAGTTATCAAGGTACAATTATTTTTGTGTCACATGATAGATAT\n+TTTACTAATAAGATTGCTGACAGATTACTTGTTTTTGATAAGGATGGTGTAGAGTTTGTA\n+CAATCTACTTATGGTGAGTACGAGAAAAAAAGGATGAATTCTGAAAAGCCATTTAATAAC\n+ATTAAAGTTGAGCAGAAAGTAGAGAAAAATAACACAGTAAAAGGCGATCGTAACTCCATT\n+GAGAAGGAGAAGGTTAAGAAGGAGAAACGAATTGAAAAGCTTGAAGTGTTAATAAATCAA\n+TATGATGAAGAATTAGAAAGATTGAATAAAATCATTTCTGAACCAAACAATTCTTCTGAT\n+TATATAGTACTGACGGAAATACAAAAATCAATTGATGATGTTAAAAGGTGTCAGGGTAAT\n+TATTTTAATGAATGGGAACAGTTGATGAGAGAATTGGAAGTTATG\n+>contig_46:2435-3229 strand:- aph(3')-IIIa aminoglycoside O-phosphotransferase APH(3')-IIIa\n+ATGGCTAAAATGAGAATATCACCGGAATTGAAAAAACTGATCGAAAAATACCGCTGCGTA\n+AAAGATACGGAAGGAATGTCTCCTGCTAAGGTATATAAGCTGGTGGGAGAAAATGAAAAC\n+CTATATTTAAAAATGACGGACAGCCGGTATAAAGGGACCACCTATGATGTGGAACGGGAA\n+AAGGACATGATGCTATGGCTGGAAGGAAAGCTGCCTGTTCCAAAGGTCCTGCACTTTGAA\n+CGGCATGATGGCTGGAGCAATCTGCTCATGAGTGAGGCCGATGGCGTCCTTTGCTCGGAA\n+GAGTATGAAGATGAACAAAGCCCTGAAAAGATTATCGAGCTGTATGCGGAGTGCATCAGG\n+CTCTTTCACTCCATCGACATATCGGATTGTCCCTATACGAATAGCTTAGACAGCCGCTTA\n+GCCGAATTGGATTACTTACTGAATAACGATCTGGCCGATGTGGATTGCGAAAACTGGGAA\n+GAAGACACTCCATTTAAAGATCCGCGCGAGCTGTATGATTTTTTAAAGACGGAAAAGCCC\n+GAAGAGGAACTTGTCTTTTCCCACGGCGACCTGGGAGACAGCAACATCTTTGTGAAAGAT\n+GGCAAAGTAAGTGGCTTTATTGATCTTGGGAGAAGCGGCAGGGCGGACAAGTGGTATGAC\n+ATTGCCTTCTGCGTCCGGTCGATCAGGGAGGATATCGGGGAAGAACAGTATGTCGAGCTA\n+TTTTTTGACTTACTGGGGATCAAGCCTGATTGGGAGAAAATAAAATATTATATTTTACTG\n+GATGAATTGTTTTAG\n+>contig_46:3322-3864 strand:- sat4 streptothricin N-acetyltransferase Sat4\n+GTGATTACAGAAATGAAAGCAGGGCACCTGAAAGATATCGATAAACCCAGCGAACCATTT\n+GAGGTGATAGGTAAGATTATACCGAGGTATGAAAACGAGAATTGGACCTTTACAGAATTA\n+CTCTATGAAGCGCCATATTTAAAAAGCTACCAAGACGAAGAGGATGAAGAGGATGAGGAG\n+GCAGATTGCCTTGAATATATTGACAATACTGATAAGATAATATATCTTTACTACCAAGAC\n+GATAAATGCGTCGGAAAAGTTAAACTGCGAAAAAATTGGAACCGGTACGCTTATATAGAA\n+GATATCGCCGTATGTAAGGATTTCAGGGGGCAAGGCATAGGCAGCGCGCTTATCAATATA\n+TCTATAGAATGGGCAAAGCATAAAAACTTGCATGGACTAATGCTTGAAACCCAGGACAAT\n+AACCTTATAGCTTGTAAATTCTATCATAATTGTGGTTTCAAAATCGGCTCCGTCGATACT\n+ATGTTATACGCCAACTTTGAAAACAACTTTGAAAAAGCTGTTTTCTGGTATTTAAGGTTT\n+TAG\n+>contig_47:3993-5912 strand:- tet(M) tetracycline resistance ribosomal protection protein Tet(M)\n+ATGAAAATTATTAATATTGGAGTTTTAGCTCATGTTGATGCGGGAAAAACTACCTTAACA\n+GAAAGCTTATTATATAACAGTGGAGCGATTACAGAATTAGGAAGCGTGGACAAAGGTACA\n+ACGAGGACGGATAATACGCTTTTAGAACGTCAGAGAGGAATTACAATTCAGACAGGAATA\n+ACCTCTTTTCAGTGGGAAAATACGAAG"..b'AGCAAACCTCAACAAAGGGAAATG\n+TTGCTTGATGCCCTTTTGGAAATCTCAGATAGTGATCCGCTTCTACGATATTACGTGGAT\n+TCTACGACACATGAAATTATACTTTCTTTCTTAGGGAAAGTACAAATGGAAGTGATTAGT\n+GCACTGTTGCAAGAAAAGTATCATGTGGAGATAGAACTAAAAGAGCCTACAGTCATTTAT\n+ATGGAGAGACCGTTAAAAAATGCAGAATATACCATTCACATCGAAGTGCCGCCAAATCCT\n+TTCTGGGCTTCCATTGGTTTATCTGTATCACCGCTTCCATTAGGGAGCGGAGTGCAGTAT\n+GAGAGCTCGGTTTCTCTTGGATACTTAAATCAATCGTTTCAAAATGCAGTTATGGAGGGG\n+ATACGCTATGGCTGTGAACAAGGATTGTATGGTTGGAATGTGACGGACTGTAAAATCTGT\n+TTTAAGTATGGCTTATACTATAGCCCTGTTAGTACCCCAGCAGATTTTCGGATGCTTGCT\n+CCTATTGTATTGGAACAAGTCTTAAAAAAAGCTGGAACAGAATTGTTAGAGCCATATCTT\n+AGTTTTAAAATTTATGCGCCACAGGAATATCTTTCACGAGCATACAACGATGCTCCTAAA\n+TATTGTGCGAACATCGTAGACACTCAATTGAAAAATAATGAGGTCATTCTTAGTGGAGAA\n+ATCCCTGCTCGGTGTATTCAAGAATATCGTAGTGATTTAACTTTCTTTACAAATGGACGT\n+AGTGTTTGTTTAACAGAGTTAAAAGGGTACCATGTTACTACCGGTGAACCTGTTTGCCAG\n+CCCCGTCGTCCAAATAGTCGGATAGATAAAGTACGATATATGTTCAATAAAATAACTTAG\n+>contig_48:199-936 strand:- erm(B) 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B)\n+ATGAACAAAAATATAAAATATTCTCAAAACTTTTTAACGAGTGAAAAAGTACTCAACCAA\n+ATAATAAAACAATTGAATTTAAAAGAAACCGATACCGTTTACGAAATTGGAACAGGTAAA\n+GGGCATTTAACGACGAAACTGGCTAAAATAAGTAAACAGGTAACGTCTATTGAATTAGAC\n+AGTCATCTATTCAACTTATCGTCAGAAAAATTAAAACTGAATACTCGTGTCACTTTAATT\n+CACCAAGATATTCTACAGTTTCAATTCCCTAACAAACAGAGGTATAAAATTGTTGGGAGT\n+ATTCCTTACCATTTAAGCACACAAATTATTAAAAAAGTGGTTTTTGAAAGCCATGCGTCT\n+GACATCTATCTGATTGTTGAAGAAGGATTCTACAAGCGTACCTTGGATATTCACCGAACA\n+CTAGGGTTGCTCTTGCACACTCAAGTCTCGATTCAGCAATTGCTTAAGCTGCCAGCGGAA\n+TGCTTTCATCCTAAACCAAAAGTAAACAGTGTCTTAATAAAACTTACCCGCCATACCACA\n+GATGTTCCAGATAAATATTGGAAGCTATATACGTACTTTGTTTCAAAATGGGTCAATCGA\n+GAATATCGTCAACTGTTTACTAAAAATCAGTTTCATCAAGCAATGAAACACGCCAAAGTA\n+AACAATTTAAGTACCGTTACTTATGAGCAAGTATTGTCTATTTTTAATAGTTATCTATTA\n+TTTAACGGGAGGAAATAA\n+>contig_48:4344-4988 strand:+ catA type A-7 chloramphenicol O-acetyltransferase\n+ATGACTTTTAATATTATTGAATTAGAAAATTGGGATAGAAAAGAATATTTTGAACACTAT\n+TTTAATCAGCAAACTACTTATAGCATTACTAAAGAAATTGATATTACTTTGTTTAAAGAT\n+ATGATAAAAAAGAAAGGATATGAAATTTATCCCTCTTTAATTTATGCAATTATGGAAGTT\n+GTAAATAAAAATAAAGTGTTTAGAACAGGAATTAATAGTGAGAATAAATTAGGTTATTGG\n+GATAAGTTAAATCCTTTGTATACAGTTTTTAATAAGCAAACTGAAAAATTTACTAACATT\n+TGGACTGAATCTGATAAAAACTTCATTTCTTTTTATAATAATTATAAAAATGACTTGCTT\n+GAATATAAAGATAAAGAAGAAATGTTTCCTAAAAAACCGATACCTGAAAACACCATACCG\n+ATTTCAATGATTCCTTGGATTGATTTTAGTTCATTTAATTTAAATATTGGTAACAATAGC\n+AGCTTTTTATTGCCTATTATTACGATAGGTAAATTTTATAGTGAGAATAATAAAATTTAT\n+ATACCAGTTGCTCTGCAACTTCATCATTCTGTATGTGATGGTTACCATGCTTCACTATTT\n+ATGAATGAATTTCAAGATATAATTCATAGGGTAGATGATTGGATT\n+>contig_50:282-1658 strand:+ tet(L) tetracycline efflux MFS transporter Tet(L)\n+GTGAATACATCCTATTCACAATCGAATTTACGACACAACCAAATTTTAATTTGGCTTTGC\n+ATTTTATCTTTTTTTAGCGTATTAAATGAAATGGTTTTGAACGTCTCATTACCTGATATT\n+GCAAATGATTTTAATAAACCACCTGCGAGTACAAACTGGGTGAACACAGCCTTTATGTTA\n+ACCTTTTCCATTGGAACAGCTGTATATGGAAAGCTATCTGATCAATTAGGCATCAAAAGG\n+TTACTCCTATTTGGAATTATAATAAATTGTTTCGGGTCGGTAATTGGGTTTGTTGGCCAT\n+TCTTTCTTTTCCTTACTTATTATGGCTCGTTTTATTCAAGGGGCTGGTGCAGCTGCATTT\n+CCAGCACTCGTAATGGTTGTAGTTGCGCGCTATATTCCAAAGGAAAATAGGGGTAAAGCA\n+TTTGGTCTTATTGGATCGATAGTAGCCATGGGAGAAGGAGTCGGTCCAGCGATTGGTGGA\n+ATGATAGCCCATTATATTCATTGGTCCTATCTTCTACTCATTCCTATGATAACAATTATC\n+ACTGTTCCGTTTCTTATGAAATTATTAAAGAAAGAAGTAAGGATAAAAGGTCATTTTGAT\n+ATCAAAGGAATTATACTAATGTCTGTAGGCATTGTATTTTTTATGTTGTTTACAACATCA\n+TATAGCATTTCTTTTCTTATCGTTAGCGTGCTGTCATTCCTGATATTTGTAAAACATATC\n+AGGAAAGTAACAGATCCTTTTGTTGATCCCGGATTAGGGAAAAATATACCTTTTATGATT\n+GGAGTTCTTTGTGGGGGAATTATATTTGGAACAGTAGCAGGGTTTGTCTCTATGGTTCCT\n+TATATGATGAAAGATGTTCACCAGCTAAGTACTGCCGAAATCGGAAGTGTAATTATTTTC\n+CCTGGAACAATGAGTGTCATTATTTTCGGCTACATTGGTGGGATACTTGTTGATAGAAGA\n+GGTCCTTTATACGTGTTAAACATCGGAGTTACATTTCTTTCTGTTAGCTTTTTAACTGCT\n+TCCTTTCTTTTAGAAACAACATCATGGTTCATGACAATTATAATCGTATTTGTTTTAGGT\n+GGGCTTTCGTTCACCAAAACAGTTATATCAACAATTGTTTCAAGTAGCTTGAAACAGCAG\n+GAAGCTGGTGCTGGAATGAGTTTGCTTAACTTTACCAGCTTTTTATCAGAGGGAACAGGT\n+ATTGCAATTGTAGGTGGTTTATTATCCATACCCTTACTTGATCAAAGGTTGTTACCTATG\n+GAAGTTGATCAGTCAACTTATCTGTATAGTAATTTGTTATTACTTTTTTCAGGAATCATT\n+GTCATTAGTTGGCTGGTTACCTTGAATGTATATAAACATTCTCAAAGGGATTTCTAA\n' |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test_8/amrfinderplus_protein_output.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_8/amrfinderplus_protein_output.fasta Fri May 26 09:19:12 2023 +0000 |
| b |
| @@ -0,0 +1,37 @@ +>IDOBJL_14770 aph(3')-IIIa aminoglycoside O-phosphotransferase APH(3')-IIIa +MAKMRISPELKKLIEKYRCVKDTEGMSPAKVYKLVGENENLYLKMTDSRYKGTTYDVERE +KDMMLWLEGKLPVPKVLHFERHDGWSNLLMSEADGVLCSEEYEDEQSPEKIIELYAECIR +LFHSIDISDCPYTNSLDSRLAELDYLLNNDLADVDCENWEEDTPFKDPRELYDFLKTEKP +EEELVFSHGDLGDSNIFVKDGKVSGFIDLGRSGRADKWYDIAFCVRSIREDIGEEQYVEL +FFDLLGIKPDWEKIKYYILLDELF +>IDOBJL_14775 sat4 streptothricin N-acetyltransferase Sat4 +MITEMKAGHLKDIDKPSEPFEVIGKIIPRYENENWTFTELLYEAPYLKSYQDEEDEEDEE +ADCLEYIDNTDKIIYLYYQDDKCVGKVKLRKNWNRYAYIEDIAVCKDFRGQGIGSALINI +SIEWAKHKNLHGLMLETQDNNLIACKFYHNCGFKIGSVDTMLYANFENNFEKAVFWYLRF +>IDOBJL_14820 tet(M) tetracycline resistance ribosomal protection protein Tet(M) +MKIINIGVLAHVDAGKTTLTESLLYNSGAITELGSVDKGTTRTDNTLLERQRGITIQTGI +TSFQWENTKVNIIDTPGHMDFLAEVYRSLSVLDGAILLISAKDGVQAQTRILFHALRKMG +IPTIFFINKIDQNGIDLSTVYQDIKEKLSAEIVIKQKVELYPNMCVTNFTESEQWDTVIE +GNDDLLEKYMSGKSLEALELEQEESIRFQNCSLFPVYHGSAKNNIGIDNLIEVITNKFYS +STHRGQSELCGNVFKIEYTKKRQRLAYIRLYSGVLHLRDSVRISEKEKIKITEMYTSING +ELCKIDKAYSGEIVILQNEFLKLNSVLGDTKLLPQRERIENPLPLLQTTVEPSKPQQREM +LLDALLEISDSDPLLRYYVDSTTHEIILSFLGKVQMEVISALLQEKYHVEIELKEPTVIY +MERPLKNAEYTIHIEVPPNPFWASIGLSVSPLPLGSGVQYESSVSLGYLNQSFQNAVMEG +IRYGCEQGLYGWNVTDCKICFKYGLYYSPVSTPADFRMLAPIVLEQVLKKAGTELLEPYL +SFKIYAPQEYLSRAYNDAPKYCANIVDTQLKNNEVILSGEIPARCIQEYRSDLTFFTNGR +SVCLTELKGYHVTTGEPVCQPRRPNSRIDKVRYMFNKIT +>IDOBJL_14830 erm(B) 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B) +MNKNIKYSQNFLTSEKVLNQIIKQLNLKETDTVYEIGTGKGHLTTKLAKISKQVTSIELD +SHLFNLSSEKLKLNTRVTLIHQDILQFQFPNKQRYKIVGSIPYHLSTQIIKKVVFESHAS +DIYLIVEEGFYKRTLDIHRTLGLLLHTQVSIQQLLKLPAECFHPKPKVNSVLIKLTRHTT +DVPDKYWKLYTYFVSKWVNREYRQLFTKNQFHQAMKHAKVNNLSTVTYEQVLSIFNSYLL +FNGRK +>IDOBJL_14880 tet(L) tetracycline efflux MFS transporter Tet(L) +MNTSYSQSNLRHNQILIWLCILSFFSVLNEMVLNVSLPDIANDFNKPPASTNWVNTAFML +TFSIGTAVYGKLSDQLGIKRLLLFGIIINCFGSVIGFVGHSFFSLLIMARFIQGAGAAAF +PALVMVVVARYIPKENRGKAFGLIGSIVAMGEGVGPAIGGMIAHYIHWSYLLLIPMITII +TVPFLMKLLKKEVRIKGHFDIKGIILMSVGIVFFMLFTTSYSISFLIVSVLSFLIFVKHI +RKVTDPFVDPGLGKNIPFMIGVLCGGIIFGTVAGFVSMVPYMMKDVHQLSTAEIGSVIIF +PGTMSVIIFGYIGGILVDRRGPLYVLNIGVTFLSVSFLTASFLLETTSWFMTIIIVFVLG +GLSFTKTVISTIVSSSLKQQEAGAGMSLLNFTSFLSEGTGIAIVGGLLSIPLLDQRLLPM +EVDQSTYLYSNLLLLFSGIIVISWLVTLNVYKHSQRDF |
| b |
| diff -r 000000000000 -r a968af0a91f9 test-data/test_8/amrfinderplus_results.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_8/amrfinderplus_results.tsv Fri May 26 09:19:12 2023 +0000 |
| b |
| @@ -0,0 +1,8 @@ +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 +NA contig_26 6581 8545 + optrA ABC-F type ribosomal protection protein OptrA core AMR AMR PHENICOL/OXAZOLIDINONE FLORFENICOL/OXAZOLIDINONE EXACTX 655 655 100.00 100.00 655 WP_063854496.1 ABC-F type ribosomal protection protein OptrA NA NA +IDOBJL_14770 contig_46 2435 3229 - aph(3')-IIIa aminoglycoside O-phosphotransferase APH(3')-IIIa core AMR AMR AMINOGLYCOSIDE AMIKACIN/KANAMYCIN BLASTP 264 264 100.00 99.62 264 WP_063841495.1 aminoglycoside O-phosphotransferase APH(3')-IIIa NA NA +IDOBJL_14775 contig_46 3322 3864 - sat4 streptothricin N-acetyltransferase Sat4 core AMR AMR STREPTOTHRICIN STREPTOTHRICIN BLASTP 180 180 100.00 99.44 180 WP_063854934.1 streptothricin N-acetyltransferase Sat4 NA NA +IDOBJL_14820 contig_47 3993 5912 - tet(M) tetracycline resistance ribosomal protection protein Tet(M) core AMR AMR TETRACYCLINE TETRACYCLINE BLASTP 639 639 100.00 99.84 639 WP_063856395.1 tetracycline resistance ribosomal protection protein Tet(M) NA NA +IDOBJL_14830 contig_48 199 936 - erm(B) 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B) core AMR AMR MACROLIDE MACROLIDE BLASTP 245 245 100.00 99.59 245 WP_063844601.1 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B) NA NA +NA contig_48 4344 4988 + catA type A-7 chloramphenicol O-acetyltransferase core AMR AMR PHENICOL CHLORAMPHENICOL BLASTX 215 215 100.00 96.28 215 WP_063843211.1 type A-7 chloramphenicol O-acetyltransferase NA NA +IDOBJL_14880 contig_50 282 1658 + tet(L) tetracycline efflux MFS transporter Tet(L) core AMR AMR TETRACYCLINE TETRACYCLINE BLASTP 458 458 100.00 99.78 458 WP_063856080.1 tetracycline efflux MFS transporter Tet(L) NA NA |
| b |
| diff -r 000000000000 -r a968af0a91f9 tool-data/amrfinderplus_database.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/amrfinderplus_database.loc.sample Fri May 26 09:19:12 2023 +0000 |
| b |
| @@ -0,0 +1,7 @@ +# this is a tab separated file describing the location of amrfinderplus database +# +# the columns are: +# value, name, path +# +# for example +amrfinderplus_V3.11.1_2023-04-17.1 V3.11.1-2023-04-17.1 ${__HERE__}/test-db \ No newline at end of file |
| b |
| diff -r 000000000000 -r a968af0a91f9 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Fri May 26 09:19:12 2023 +0000 |
| b |
| @@ -0,0 +1,7 @@ +<?xml version="1.0"?> +<tables> + <table name="amrfinderplus_database" comment_char="#"> + <columns>value, dbkey, bakta_version, path</columns> + <file path="tool-data/amrfinderplus_database.loc.sample" /> + </table> +</tables> |
| b |
| diff -r 000000000000 -r a968af0a91f9 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Fri May 26 09:19:12 2023 +0000 |
| b |
| @@ -0,0 +1,7 @@ +<?xml version="1.0"?> +<tables> + <table name="amrfinderplus_database" comment_char="#"> + <columns>value, name, path</columns> + <file path="${__HERE__}/test-data/amrfinderplus_database.loc" /> + </table> +</tables> |