| Previous changeset 6:1920244e2895 (2023-10-31) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709 |
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modified:
amrfinderplus.xml macro.xml 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.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.pto test-data/test-db/AMR_CDS test-data/test-db/AMR_DNA-Enterococcus_faecium.nin test-data/test-db/AMR_DNA-Enterococcus_faecium.njs 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 tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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added:
test-data/README.md test-data/amr_targets_to_keep_for_test-db test-data/amrfinderplus_versioned.loc test-data/test-db/AMR_CDS.ndb test-data/test-db/AMR_CDS.nhr test-data/test-db/AMR_CDS.nin test-data/test-db/AMR_CDS.njs test-data/test-db/AMR_CDS.not test-data/test-db/AMR_CDS.nsq test-data/test-db/AMR_CDS.ntf test-data/test-db/AMR_CDS.nto test-data/test-db/AMR_DNA-Enterococcus_faecalis test-data/test-db/AMR_DNA-Enterococcus_faecalis.ndb test-data/test-db/AMR_DNA-Enterococcus_faecalis.nhr test-data/test-db/AMR_DNA-Enterococcus_faecalis.nin test-data/test-db/AMR_DNA-Enterococcus_faecalis.njs test-data/test-db/AMR_DNA-Enterococcus_faecalis.not test-data/test-db/AMR_DNA-Enterococcus_faecalis.nsq test-data/test-db/AMR_DNA-Enterococcus_faecalis.ntf test-data/test-db/AMR_DNA-Enterococcus_faecalis.nto test-data/test-db/AMR_DNA-Enterococcus_faecalis.tab test-data/test-db/ReferenceGeneCatalog.txt test-data/test-db/ReferenceGeneHierarchy.txt test-data/test-db/amr_targets.fa test-data/test-db/bla.tsv test-data/test-db/mcr.tsv test-data/test-db/output.json test-data/test-db/qnr.tsv test-data/to_keep_for_test-db tool-data/amrfinderplus_versioned.loc.sample |
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removed:
test-data/amrfinderplus_database.loc tool-data/amrfinderplus_database.loc.sample |
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| diff -r 1920244e2895 -r 7844dbe4f8e2 amrfinderplus.xml --- a/amrfinderplus.xml Tue Oct 31 14:47:37 2023 +0000 +++ b/amrfinderplus.xml Thu May 30 13:07:03 2024 +0000 |
| [ |
| b'@@ -8,7 +8,6 @@\n <expand macro="biotools"/>\n <expand macro="requirements"/>\n <expand macro="version_command"/>\n-\n <command detect_errors="aggressive"><![CDATA[\n amrfinder\n #*======================================\n@@ -83,8 +82,9 @@\n <!-- DB and file INPUT -->\n <section name="input_option" title="Input/Output options" expanded="true">\n <param name="amrfinder_db_select" type="select" label="The amrfinderplus database">\n- <options from_data_table="amrfinderplus_database">\n- <validator message="No amrfinderplus database is available" type="no_options"/>\n+ <options from_data_table="amrfinderplus_versioned_database">\n+ <filter type="static_value" value="3.12" column="db_version"/>\n+ <validator message="No amrfinderplus database is available" type="no_options"/>\n </options>\n </param>\n <conditional name="input_mode">\n@@ -209,18 +209,32 @@\n <tests> \n <test expect_num_outputs="2"> <!-- TEST_1 simple nucleotide input -->\n <section name="input_option">\n- <param name="amrfinder_db_select" value="V3.11.1-2023-04-17.1"/>\n+ <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/>\n <conditional name="input_mode">\n <param name="input_select" value="nucleotide"/>\n <param name="nucleotide_input" value="enterococcus_faecalis.fna"/>\n </conditional>\n </section>\n- <output name="amrfinderplus_report" value="test_1/amrfinderplus_results.tsv" ftype="tabular" lines_diff="1"/>\n- <output name="nucleotide_output" value="test_1/amrfinderplus_nucleotide_output.fasta" ftype="fasta" lines_diff="1"/>\n+ <output name="amrfinderplus_report" ftype="tabular">\n+ <assert_contents>\n+ <has_n_columns n="22"/>\n+ <has_n_lines n="8"/>\n+ <has_text text="optrA"/>\n+ <has_text text="WP_063854496"/>\n+ <has_text text="WP_063843211"/>\n+ </assert_contents>\n+ </output>\n+ <output name="nucleotide_output" ftype="fasta">\n+ <assert_contents>\n+ <has_n_lines n="142"/>\n+ <has_text text=">contig_26:6581-8545 strand:+ optrA ABC-F type ribosomal protection protein OptrA"/>\n+ <has_text text="TTGTCCAAAGCC"/>\n+ </assert_contents>\n+ </output>\n </test> \n <test expect_num_outputs="3"> <!-- TEST_2 nucleotide input and full options -->\n <section name="input_option">\n- <param name="amrfinder_db_select" value="V3.11.1-2023-04-17.1"/>\n+ <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/>\n <conditional name="input_mode">\n <param name="input_select" value="nucleotide"/>\n <param name="nucleotide_input" value="enterococcus_faecalis.fna"/>\n@@ -235,22 +249,41 @@\n </conditional>\n </section>\n <section name="options">\n- <param name="ident_min" value="1"/>\n+ <param name="ident_min" value="0.1"/>\n <param name="coverage_min" value="0.1"/>\n <param name="translation_table" value="11"/>\n <param name="plus" value="true"/>\n <param name="report_all_equal" value="true"/>\n <param name="print_node" value="true"/>\n <param name="name" value="test_2"/>\n- <param name="log" value="true"/>\n+ <param name="log" value="true"/>\n </section>\n- <output name="amrfinderplus_report" value="test_2/amrfinderplus_results.tsv" ftype="tabular" lines_diff="1"/>\n- <output name="nucleotide_output'..b' </section>\n- <output name="amrfinderplus_report" value="test_8/amrfinderplus_results.tsv" ftype="tabular" lines_diff="1"/>\n- <output name="protein_output" value="test_8/amrfinderplus_protein_output.fasta" ftype="fasta" lines_diff="1"/>\n- <output name="nucleotide_output" value="test_8/amrfinderplus_nucleotide_output.fasta" ftype="fasta" lines_diff="1"/>\n+ <output name="amrfinderplus_report" ftype="tabular">\n+ <assert_contents>\n+ <has_n_columns n="22"/>\n+ <has_n_lines n="8"/>\n+ <has_text text="IDOBJL_14770"/>\n+ <has_text text="WP_063856080"/>\n+ </assert_contents>\n+ </output>\n+ <output name="nucleotide_output" ftype="fasta">\n+ <assert_contents>\n+ <has_n_lines n="143"/>\n+ <has_text text=">contig_26:6581-8545 strand:+ optrA ABC-F type ribosomal protection protein OptrA"/>\n+ <has_text text="CTTATCTGTATAG"/>\n+ </assert_contents>\n+ </output>\n+ <output name="protein_output" ftype="fasta">\n+ <assert_contents>\n+ <has_n_lines n="37"/>\n+ <has_text text=">IDOBJL_14770 aph(3\')-IIIa aminoglycoside O-phosphotransferase APH(3\')-IIIa"/>\n+ <has_text text="QEAGAGMSLLNFT"/>\n+ </assert_contents>\n+ </output>\n </test> \n <test expect_num_outputs="4"> <!-- TEST_9 rast annotation and mutation all results -->\n <section name="input_option">\n- <param name="amrfinder_db_select" value="V3.11.1-2023-04-17.1"/>\n+ <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/>\n <conditional name="input_mode">\n <param name="input_select" value="nucl_prot"/>\n <param name="protein_input" value="e_faecalis_rast.faa"/>\n@@ -380,10 +500,34 @@\n <param name="print_node" value="true"/> \n <param name="name" value="test_5"/> \n </section>\n- <output name="amrfinderplus_report" value="test_9/amrfinderplus_results.tsv" ftype="tabular" lines_diff="1"/>\n- <output name="protein_output" value="test_9/amrfinderplus_protein_output.fasta" ftype="fasta" lines_diff="1"/>\n- <output name="nucleotide_output" value="test_9/amrfinderplus_nucleotide_output.fasta" ftype="fasta" lines_diff="1"/>\n- <output name="mutation_all_report" value="test_9/amrfinderplus_mutation_all.tsv" ftype="tabular" lines_diff="1"/>\n+ <output name="amrfinderplus_report" ftype="tabular">\n+ <assert_contents>\n+ <has_n_columns n="24"/>\n+ <has_n_lines n="2"/>\n+ <has_text text="MUPIROCIN"/>\n+ <has_text text="WP_063854488"/>\n+ </assert_contents>\n+ </output>\n+ <output name="nucleotide_output" ftype="fasta">\n+ <assert_contents>\n+ <has_n_lines n="40"/>\n+ <has_text text=">contig00019:27227-29524 strand:+ mupB mupirocin-resistant isoleucine--tRNA ligase MupB"/>\n+ <has_text text="ATCAGTCGTGAAATAGAA"/>\n+ </assert_contents>\n+ </output>\n+ <output name="protein_output" ftype="fasta">\n+ <assert_contents>\n+ <has_n_lines n="0"/>\n+ </assert_contents>\n+ </output>\n+ <output name="mutation_all_report" ftype="tabular">\n+ <assert_contents>\n+ <has_n_columns n="24"/>\n+ <has_n_lines n="5"/>\n+ <has_text text="23S_GA375AG"/>\n+ <has_text text="NZ_CP04"/>\n+ </assert_contents>\n+ </output>\n </test> \n </tests>\n <help><![CDATA[\n' |
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| diff -r 1920244e2895 -r 7844dbe4f8e2 macro.xml --- a/macro.xml Tue Oct 31 14:47:37 2023 +0000 +++ b/macro.xml Thu May 30 13:07:03 2024 +0000 |
| [ |
| @@ -1,6 +1,6 @@ <macros> - <token name="@TOOL_VERSION@">3.11.26</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@TOOL_VERSION@">3.12.8</token> + <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">21.05</token> <xml name="version_command"> <version_command><![CDATA[amrfinder --version]]></version_command> @@ -38,6 +38,7 @@ <option value="pseudomonasdb">Pseudomonasdb</option> <option value="rast">Rast</option> <option value="standard">Standard</option> + <option value="prodigal">Prodigal</option> </param> </xml> </macros> |
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| diff -r 1920244e2895 -r 7844dbe4f8e2 test-data/README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/README.md Thu May 30 13:07:03 2024 +0000 |
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| @@ -0,0 +1,20 @@ +# Test data for AMRFinderPlus + +## Create `test-db` + +1. Download ARMFinderPlus database from NCBI using the data-manager Python script after modifying the `main` function to keep only `amrfinderplus_download.download_amrfinderplus_db()` +2. Remove `AMR_DNA` files that are not `Enterococcus` +3. Remove lines not related to `Enterococcus` in `taxgroup.tab` +4. Keep in `AMR_CDS`, `AMRProt`, and `ReferenceGeneCatalog.txt` only sequences listed in `to_keep_from_test-db` +5. Keep in `amr_targets.fa` only sequences listed in `amr_targets_to_keep_from_test-db` +6. Copy the `AMR.LIB` from a previous version +7. Run the data-manager Python script after modifying `main` function like this: + + ``` + amrfinderplus_download.download_amrfinderplus_db() + amrfinderplus_download.amrfinderplus_db_path = f'{amrfinderplus_download._output_dir}/{amrfinderplus_download._db_name}' + amrfinderplus_download.make_hmm_profile() + amrfinderplus_download.make_blastdb() + ``` + +6. Move the `amrfinderplus-db` folder content to `test-db` \ No newline at end of file |
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| diff -r 1920244e2895 -r 7844dbe4f8e2 test-data/amr_targets_to_keep_for_test-db --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amr_targets_to_keep_for_test-db Thu May 30 13:07:03 2024 +0000 |
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| @@ -0,0 +1,11 @@ +optrA +aph3p-IIIa +sat4 +tetM +ermB +catA +tetL +vanG +sul2 +tetA46 +mupB \ No newline at end of file |
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| diff -r 1920244e2895 -r 7844dbe4f8e2 test-data/amrfinderplus_database.loc --- a/test-data/amrfinderplus_database.loc Tue Oct 31 14:47:37 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,7 +0,0 @@ -# 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 |
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| diff -r 1920244e2895 -r 7844dbe4f8e2 test-data/amrfinderplus_versioned.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amrfinderplus_versioned.loc Thu May 30 13:07:03 2024 +0000 |
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| @@ -0,0 +1,7 @@ +# this is a tab separated file describing the location of amrfinderplus database +# +# the columns are: +# value, name, db_version, path +# +# for example +amrfinderplus_V3.12_2024-05-02.2 V3.12-2024-05-02.2 3.12 ${__HERE__}/test-db |
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| diff -r 1920244e2895 -r 7844dbe4f8e2 test-data/test-db/AMR.LIB.h3i |
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| Binary file test-data/test-db/AMR.LIB.h3i has changed |
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| diff -r 1920244e2895 -r 7844dbe4f8e2 test-data/test-db/AMR.LIB.h3m |
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| Binary file test-data/test-db/AMR.LIB.h3m has changed |
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| diff -r 1920244e2895 -r 7844dbe4f8e2 test-data/test-db/AMR.LIB.h3p |
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| Binary file test-data/test-db/AMR.LIB.h3p has changed |
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| diff -r 1920244e2895 -r 7844dbe4f8e2 test-data/test-db/AMRProt --- a/test-data/test-db/AMRProt Tue Oct 31 14:47:37 2023 +0000 +++ b/test-data/test-db/AMRProt Thu May 30 13:07:03 2024 +0000 |
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| b'@@ -1,1981 +1,22 @@\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'CDLSMADFRNAS\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+MPTSDGLGLRQAITKEVLKQEKIIP*\n' |
| b |
| diff -r 1920244e2895 -r 7844dbe4f8e2 test-data/test-db/AMRProt-mutation.tab --- a/test-data/test-db/AMRProt-mutation.tab Tue Oct 31 14:47:37 2023 +0000 +++ b/test-data/test-db/AMRProt-mutation.tab Thu May 30 13:07:03 2024 +0000 |
| b |
| b'@@ -1,6 +1,8 @@\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+Streptococcus_pneumoniae\tWP_000024543.1\t65\trplD_WR65del\tMACROLIDE/OXAZOLIDINONE/PHENICOL\tAZITHROMYCIN/CHLORAMPHENICOL/CLARITHROMYCIN/ERYTHROMYCIN/LINEZOLID\tStreptococcus_pneumoniae_azithromycin/chloramphenicol/clarithromycin/erythromycin/linezolid_resistant_RplD\n+Streptococcus_pneumoniae\tWP_000024543.1\t68\trplD_KG68del\tMACROLIDE/OXAZOLIDINONE/PHENICOL\tAZITHROMYCIN/CHLORAMPHENICOL/CLARITHROMYCIN/ERYTHROMYCIN/LINEZOLID\tStreptococcus_pneumoniae_azithromycin/chloramphenicol/clarithromycin/erythromycin/linezolid_resistant_RplD\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@@ -26,9 +28,9 @@\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\t464\tgyrB_S464F\tQUINOLONE\tQUINOLONE\tSalmonella_quinolone_resistant_GyrB\n+Salmonella\tWP_000072047.1\t464\tgyrB_S464T\tQUINOLONE\tQUINOLONE\tSalmonella_quinolone_resistant_GyrB\n+Salmonella\tWP_000072047.1\t464\tgyrB_S464Y\tQUINOLONE\tQUINOLONE\tSalmonella_quinolone_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@@ -118,13 +120,23 @@\n Staphylococcus_aureus\tWP_000160212.1\t152\trplC_G152D\tOXAZOLIDINONE\tLINEZOLID\tStaphylococcus_aureus_linezolid_resistant_RplC\n Staphylococcus_aureus\tWP_000160212.1\t155\trplC_G155R\tOXAZOLIDINONE\tLINEZOLID\tStaphylococcus_aureus_linezolid_resistant_RplC\n Staphylococcus_aureus\tWP_000160212.1\t169\trplC_M169L\tOXAZOLIDINONE\tLINEZOLID\tStaphylococcus_aureus_linezolid_resistant_RplC\n+Acinetobacter_baumannii\tWP_000161505.1\t8\tpmrA_E8D\tCOLISTIN\tCOLISTIN\tAcinetobacter_baumannii_colistin_resistant_PmrA\n+Acinetobacter_baumannii\tWP_000161505.1\t12\tpmrA_M12I\tCOLISTIN\tCOLISTIN\tAcinetobacter_baumannii_colistin_resistant_PmrA\n+Staphylococcus_aureus\tWP_000167936.1\t17\tfolP_F17L\tSULFONAMIDE\tSULFONAMIDE\tStaphylococcus_aureus_sulfonamide_resistant_FolP\n+Staphylococcus_aureus\tWP_000167936.1\t18\tfolP_S18L\tSULFONAMIDE\tSULFONAMIDE\tStaphylococcus_aureus_sulfonamide_resistant_FolP\n+Staphylococcus_aureus\tWP_000167936.1\t51\tfolP_T51M\tSULFONAMIDE\tSULFONAMIDE\tStaphylococcus_aureus_sulfonamide_resistant_FolP\n+Staphylococcus_aureus\tWP_000167936.1\t184\tfolP_A184V\tSULFONAMIDE\tSULFONAMIDE\tStaphylococcus_aureus_sulfonamide_resistant_FolP\n+Staphylococcus_aureus\tWP_000167936.1\t208\tfolP_E208K\tSULFONAMIDE\tSULFONAMIDE\tStaphylococcus_aureus_sulfonamide_resistant_FolP\n+Staphylococcus_aureus\tWP_000167936.1\t258\tfolP_E258EKE\tSULFONAMIDE\tSULFONAMIDE\tStaphylococcus_aureus_sulfonamide_resistant_FolP\n St'..b'phylococcus_pseudintermedius_quinolone_resistant_GrlA\n+Enterobacter_asburiae\tWP_023312417.1\t175\tbaeS_T175P\tBETA-LACTAM\tAZTREONAM/TEMOCILLIN/TICARCILLIN\tEnterobacter_asburiae_aztreonam/temocillin/ticarcillin_resistant_BaeS\n Serratia_marcescens\tWP_028127742.1\t83\tgyrA_S83I\tQUINOLONE\tQUINOLONE\tSerratia_marcescens_quinolone_resistant_GyrA\n Serratia_marcescens\tWP_028127742.1\t83\tgyrA_S83R\tQUINOLONE\tQUINOLONE\tSerratia_marcescens_quinolone_resistant_GyrA\n Serratia_marcescens\tWP_028127742.1\t87\tgyrA_D87N\tQUINOLONE\tQUINOLONE\tSerratia_marcescens_quinolone_resistant_GyrA\n@@ -957,6 +1100,8 @@\n Enterococcus_faecalis\tWP_033785346.1\t88\tgyrA_E87K\tQUINOLONE\tQUINOLONE\tEnterococcus_faecalis_quinolone_resistant_GyrA\n Enterococcus_faecalis\tWP_033785346.1\t88\tgyrA_E87L\tQUINOLONE\tQUINOLONE\tEnterococcus_faecalis_quinolone_resistant_GyrA\n Enterococcus_faecalis\tWP_033785346.1\t88\tgyrA_E87Y\tQUINOLONE\tQUINOLONE\tEnterococcus_faecalis_quinolone_resistant_GyrA\n+Vibrio_vulnificus\tWP_039540073.1\t83\tgyrA_S83I\tQUINOLONE\tQUINOLONE\tVibrio_vulnificus_quinolone_resistant_GyrA\n+Vibrio_vulnificus\tWP_039540073.1\t83\tgyrA_S83R\tQUINOLONE\tQUINOLONE\tVibrio_vulnificus_quinolone_resistant_GyrA\n Neisseria_gonorrhoeae\tWP_047924300.1\t39\tmtrR_A39T\tMACROLIDE/BETA-LACTAM/TETRACYCLINE\tAZITHROMYCIN/BETA-LACTAM/TETRACYCLINE\tNeisseria_gonorrhoeae_azithromycin/beta-lactam/tetracycline_resistant_MtrR\n Neisseria_gonorrhoeae\tWP_047924300.1\t45\tmtrR_G45D\tMACROLIDE/BETA-LACTAM/TETRACYCLINE\tAZITHROMYCIN/CEPHALOSPORIN/TETRACYCLINE\tNeisseria_gonorrhoeae_azithromycin/cephalosporin/tetracycline_resistant_MtrR\n Neisseria_gonorrhoeae\tWP_047924300.1\t45\tmtrR_G45S\tMACROLIDE/BETA-LACTAM/TETRACYCLINE\tAZITHROMYCIN/BETA-LACTAM/TETRACYCLINE\tNeisseria_gonorrhoeae_azithromycin/beta-lactam/tetracycline_resistant_MtrR\n@@ -974,12 +1119,19 @@\n Escherichia\tWP_086259262.1\t620\tacrB_R620C\tTETRACYCLINE\tTIGECYCLINE\tEscherichia_tigecycline_resistant_AcrB\n Escherichia\tWP_086259262.1\t717\tacrB_R717L\tMACROLIDE\tAZITHROMYCIN/CLARITHROMYCIN/ERYTHROMYCIN\tEscherichia_azithromycin/clarithromycin/erythromycin_resistant_AcrB\n Escherichia\tWP_086259262.1\t717\tacrB_R717Q\tMACROLIDE\tAZITHROMYCIN/CLARITHROMYCIN/ERYTHROMYCIN\tEscherichia_azithromycin/clarithromycin/erythromycin_resistant_AcrB\n+Escherichia\tWP_089631889.1\t11\tnfsA_H11Y\tNITROFURAN\tNITROFURANTOIN\tEscherichia_nitrofurantoin_resistant_NfsA\n Escherichia\tWP_089631889.1\t15\tnfsA_R15C\tNITROFURAN\tNITROFURANTOIN\tEscherichia_nitrofurantoin_resistant_NfsA\n Escherichia\tWP_089631889.1\t33\tnfsA_S33R\tNITROFURAN\tNITROFURANTOIN\tEscherichia_nitrofurantoin_resistant_NfsA\n Escherichia\tWP_089631889.1\t44\tnfsA_Q44STOP\tNITROFURAN\tNITROFURANTOIN\tEscherichia_nitrofurantoin_resistant_NfsA\n+Escherichia\tWP_089631889.1\t67\tnfsA_Q67STOP\tNITROFURAN\tNITROFURANTOIN\tEscherichia_nitrofurantoin_resistant_NfsA\n+Escherichia\tWP_089631889.1\t75\tnfsA_E75STOP\tNITROFURAN\tNITROFURANTOIN\tEscherichia_nitrofurantoin_resistant_NfsA\n+Escherichia\tWP_089631889.1\t113\tnfsA_Q113STOP\tNITROFURAN\tNITROFURANTOIN\tEscherichia_nitrofurantoin_resistant_NfsA\n+Escherichia\tWP_089631889.1\t126\tnfsA_G126R\tNITROFURAN\tNITROFURANTOIN\tEscherichia_nitrofurantoin_resistant_NfsA\n Escherichia\tWP_089631889.1\t131\tnfsA_G131D\tNITROFURAN\tNITROFURANTOIN\tEscherichia_nitrofurantoin_resistant_NfsA\n Escherichia\tWP_089631889.1\t133\tnfsA_R133S\tNITROFURAN\tNITROFURANTOIN\tEscherichia_nitrofurantoin_resistant_NfsA\n Escherichia\tWP_089631889.1\t141\tnfsA_K141STOP\tNITROFURAN\tNITROFURANTOIN\tEscherichia_nitrofurantoin_resistant_NfsA\n+Escherichia\tWP_089631889.1\t154\tnfsA_G154E\tNITROFURAN\tNITROFURANTOIN\tEscherichia_nitrofurantoin_resistant_NfsA\n+Escherichia\tWP_089631889.1\t159\tnfsA_W159STOP\tNITROFURAN\tNITROFURANTOIN\tEscherichia_nitrofurantoin_resistant_NfsA\n Escherichia\tWP_089631889.1\t203\tnfsA_R203C\tNITROFURAN\tNITROFURANTOIN\tEscherichia_nitrofurantoin_resistant_NfsA\n Escherichia\tWP_089631889.1\t203\tnfsA_R203L\tNITROFURAN\tNITROFURANTOIN\tEscherichia_nitrofurantoin_resistant_NfsA\n Escherichia\tWP_089631889.1\t223\tnfsA_E223STOP\tNITROFURAN\tNITROFURANTOIN\tEscherichia_nitrofurantoin_resistant_NfsA\n' |
| b |
| diff -r 1920244e2895 -r 7844dbe4f8e2 test-data/test-db/AMRProt.pdb |
| b |
| Binary file test-data/test-db/AMRProt.pdb has changed |
| b |
| diff -r 1920244e2895 -r 7844dbe4f8e2 test-data/test-db/AMRProt.phr |
| b |
| Binary file test-data/test-db/AMRProt.phr has changed |
| b |
| diff -r 1920244e2895 -r 7844dbe4f8e2 test-data/test-db/AMRProt.pin |
| b |
| Binary file test-data/test-db/AMRProt.pin has changed |
| b |
| diff -r 1920244e2895 -r 7844dbe4f8e2 test-data/test-db/AMRProt.pjs --- a/test-data/test-db/AMRProt.pjs Tue Oct 31 14:47:37 2023 +0000 +++ b/test-data/test-db/AMRProt.pjs Thu May 30 13:07:03 2024 +0000 |
| [ |
| @@ -3,13 +3,13 @@ "dbname": "AMRProt", "dbtype": "Protein", "db-version": 5, - "description": "AMRProt", - "number-of-letters": 585748, - "number-of-sequences": 1848, - "last-updated": "2023-05-12T11:10:00", + "description": "/Users/bebatut/Documents/projects/galaxyproject/tools-iuc/data_managers/data_manager_build_amrfinderplus/amrfinderplus-db/AMRProt", + "number-of-letters": 4850, + "number-of-sequences": 12, + "last-updated": "2024-05-27T16:19:00", "number-of-volumes": 1, - "bytes-total": 1038796, - "bytes-to-cache": 602469, + "bytes-total": 44751, + "bytes-to-cache": 5175, "files": [ "AMRProt.pdb", "AMRProt.phr", |
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| diff -r 1920244e2895 -r 7844dbe4f8e2 test-data/test-db/AMRProt.psq |
| b |
| Binary file test-data/test-db/AMRProt.psq has changed |
| b |
| diff -r 1920244e2895 -r 7844dbe4f8e2 test-data/test-db/AMRProt.pto |
| b |
| Binary file test-data/test-db/AMRProt.pto has changed |
| b |
| diff -r 1920244e2895 -r 7844dbe4f8e2 test-data/test-db/AMR_CDS --- a/test-data/test-db/AMR_CDS Tue Oct 31 14:47:37 2023 +0000 +++ b/test-data/test-db/AMR_CDS Thu May 30 13:07:03 2024 +0000 |
| b |
| b'@@ -1,1000 +1,199 @@\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-agaagcaggtcattctggt'..b"aatacaacatgttagttggaggctgtttagtgaagtctgcgtccgcgaaagatttaggaaatattactgatgctt\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+ctcgatttgggcgtggttaaggatgaacaccaagtctttaagtgggatggacagacgcgtgatatcgccgcttggaatcg\n+tgaccatgacttaattaccgcgatgaagtactcagttgtgcctgtttatcaagaatttgcccgccaaattggtgaggcac\n+gtatgagtaaaatgctgcacgccttcgattatggcaatgaggatatctcgggcaatgtagacagtttttggctcgatggt\n+ggtattcgcatttcggctacccagcaaatcgcttttttacgcaagctgtatcacaacaagctgcacgtttctgagcgtag\n+tcagcgcatcgtgaaacaagccatgctgaccgaagccaatggcgactatattattcgggctaaaacgggatactcgactg\n+gaatcgaacctaagattggctggtgggttggttgggttgaacttgatgataatgtgtggttttttgcgatgaatatggat\n+atgcccacatcggatggtttagggctgcgccaagccatcacaaaagaagtgctcaaacaggagaaaattattccctag\n" |
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| diff -r 1920244e2895 -r 7844dbe4f8e2 test-data/test-db/AMR_CDS.njs --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/AMR_CDS.njs Thu May 30 13:07:03 2024 +0000 |
| [ |
| @@ -0,0 +1,22 @@ +{ + "version": "1.2", + "dbname": "AMR_CDS", + "dbtype": "Nucleotide", + "db-version": 5, + "description": "/Users/bebatut/Documents/projects/galaxyproject/tools-iuc/data_managers/data_manager_build_amrfinderplus/amrfinderplus-db/AMR_CDS", + "number-of-letters": 14550, + "number-of-sequences": 12, + "last-updated": "2024-05-27T16:19:00", + "number-of-volumes": 1, + "bytes-total": 43342, + "bytes-to-cache": 4010, + "files": [ + "AMR_CDS.ndb", + "AMR_CDS.nhr", + "AMR_CDS.nin", + "AMR_CDS.not", + "AMR_CDS.nsq", + "AMR_CDS.ntf", + "AMR_CDS.nto" + ] +} |
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| Binary file test-data/test-db/AMR_CDS.not has changed |
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| diff -r 1920244e2895 -r 7844dbe4f8e2 test-data/test-db/AMR_DNA-Enterococcus_faecalis --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/AMR_DNA-Enterococcus_faecalis Thu May 30 13:07:03 2024 +0000 |
| b |
| @@ -0,0 +1,38 @@ +>NZ_CP041738.1@23S_ribosomal_RNA@23S:216195-219090 +agggcgcacggtggatgccttggcactaggagccgatgaaggacgggactaacaccgatatgctttggggagctgtaagt +aagctatgatccagagatttccgaatgggggaacccaatatcttttataggatattacttttcagtgaatacatagctga +ttagaggtagacgcagagaactgaaacatcttagtacctgcaggaagagaaagaaaattcgattccctgagtagcggcga +gcgaaacgggaagagcccaaaccaacaagcttgcttgttggggttgtaggactccaatatggtagtctgttagtatagtt +gaaggatttggaaaattccgctaaagagggtgaaagccccgtagacgaaatgctgacaacacctaggaggatcctgagta +cggcggaacacgagaaattccgtcggaatccgcggggaccatcccgcaaggctaaatactccctagtgaccgatagtgaa +ccagtaccgtgagggaaaggtgaaaagcaccccggaaggggagtgaaatagatcctgaaaccgtgtgcctacaacaagtc +aaagctcgttaatgagtgatggcgtgccttttgtagaatgaaccggcgagttacgattgcatgcgaggttaagtcgaaga +gacggagccgcagcgaaagcgagtctgaatagggcgaatgagtatgtagtcgtagacccgaaaccatgtgatctacccat +gtccaggttgaaggtgcggtaaaacgcactggaggaccgaacccacgtacgttgaaaagtgcggggatgaggtgtgggta +gcggagaaattccaaacgaacttggagatagctggttctctccgaaatagctttagggctagcctcggaattgagaatga +tggaggtagagcactgtttggactaggggcccatctcgggttaccgaattcagataaactccgaatgccattcatttata +tccgggagtcagactgcgagtgataagatccgtagtcgaaagggaaacagcccagaccaccagctaaggtcccaaaatat +atgttaagtggaaaaggatgtggggttgcacagacaactaggatgttggcttagaagcagccaccatttaaagagtgcgt +aatagctcactagtcgagtgaccctgcgccgaaaatgtaccggggctaaacatattaccgaagctgtggactacaccatt +aggtgtagtggtaggagagcgttctaagggcgttgaaggtcgatcgtgaggacggctggagcgcttagaagtgagaatgc +cggtatgagtagcgaaagacaggtgagaatcctgtccaccgtatgactaaggtttcctggggaaggctcgtccgcccagg +gttagtcgggacctaagccgaggccgataggcgtaggcgatggacaacaggttgatattcctgtaccagttgtttttgtt +tgagcaatggagggacgcagtaggctaaggaatgcatgcgattggaagtgcatgtccaagcaatgagtcttgagtagagt +taaatgctttactctttaaggacaagttgtgacggggagcgaaataatagtagcgaagttcctgatgtcacactgccaag +aaaagcttctagtgagaaaacaactgcccgtaccgtaaaccgacacaggtagtcgaggagagtatcctaaggtgagcgag +cgaactctcgttaaggaactcggcaaaatgaccccgtaacttcgggagaaggggtgctgacttcggtcagccgcagtgaa +taggcccaagcgactgtttatcaaaaacacaggtctctgcaaaatcgtaagatgaagtataggggctgacgcctgcccgg +tgctggaaggttaagaggatgggttagcttcggcgaagctcagaattgaagccccagtaaacggcggccgtaactataac +ggtcctaaggtagcgaaattccttgtcgggtaagttccgacccgcacgaaaggcgtaacgatttgggcactgtctcaacg +agagactcggtgaaattttagtacctgtgaagatgcaggttacccgcgacaggacggaaagaccccatggagctttactg +tagtttgatattgagtgtttgtaccacatgtacaggataggtaggagccgatgagaccggaacgctagtttcggaggagg +cgctggtgggatactacccttgtgttatgaaccctctaacccgcaccactaatcgtggtgggagacagtgtcagatgggc +agtttgactggggcggtcgcctcctaaaaggtaacggaggcgcccaaaggttccctcagaatggttggaaatcattcgaa +gagtgtaaaggcagaagggagcttgactgcgagacctacaagtcgagcagggacgaaagtcgggcttagtgatccggtgg +ttccgcatggaagggccatcgctcaacggataaaagctaccctggggataacaggcttatctcccccaagagtccacatc +gacggggaggtttggcacctcgatgtcggctcgtcgcatcctggggctgtagtcggtcccaagggttgggctgttcgccc +attaaagcggcacgcgagctgggttcagaacgtcgtgagacagttcggtccctatccgtcgcgggcgttggaaatttgag +aggagctgtccttagtacgagaggaccgggatggacttaccgctggtgtaccagttgttctgccaagggcattgctgggt +agctatgtagggaagggataaacgctgaaagcatctaagtgtgaagcccacctcaagatgagatttcccatttctttaag +aaagtaagacccctgagagatgattaggtagataggttggaagtggaaggctagtgatagttggagcggaccaatactaa +tcggtcgaggacttaa |
| b |
| diff -r 1920244e2895 -r 7844dbe4f8e2 test-data/test-db/AMR_DNA-Enterococcus_faecalis.ndb |
| b |
| Binary file test-data/test-db/AMR_DNA-Enterococcus_faecalis.ndb has changed |
| b |
| diff -r 1920244e2895 -r 7844dbe4f8e2 test-data/test-db/AMR_DNA-Enterococcus_faecalis.nhr |
| b |
| Binary file test-data/test-db/AMR_DNA-Enterococcus_faecalis.nhr has changed |
| b |
| diff -r 1920244e2895 -r 7844dbe4f8e2 test-data/test-db/AMR_DNA-Enterococcus_faecalis.nin |
| b |
| Binary file test-data/test-db/AMR_DNA-Enterococcus_faecalis.nin has changed |
| b |
| diff -r 1920244e2895 -r 7844dbe4f8e2 test-data/test-db/AMR_DNA-Enterococcus_faecalis.njs --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/AMR_DNA-Enterococcus_faecalis.njs Thu May 30 13:07:03 2024 +0000 |
| [ |
| @@ -0,0 +1,22 @@ +{ + "version": "1.2", + "dbname": "AMR_DNA-Enterococcus_faecalis", + "dbtype": "Nucleotide", + "db-version": 5, + "description": "/Users/bebatut/Documents/projects/galaxyproject/tools-iuc/data_managers/data_manager_build_amrfinderplus/amrfinderplus-db/AMR_DNA-Enterococcus_faecalis", + "number-of-letters": 2896, + "number-of-sequences": 1, + "last-updated": "2024-05-27T16:19:00", + "number-of-volumes": 1, + "bytes-total": 38002, + "bytes-to-cache": 998, + "files": [ + "AMR_DNA-Enterococcus_faecalis.ndb", + "AMR_DNA-Enterococcus_faecalis.nhr", + "AMR_DNA-Enterococcus_faecalis.nin", + "AMR_DNA-Enterococcus_faecalis.not", + "AMR_DNA-Enterococcus_faecalis.nsq", + "AMR_DNA-Enterococcus_faecalis.ntf", + "AMR_DNA-Enterococcus_faecalis.nto" + ] +} |
| b |
| diff -r 1920244e2895 -r 7844dbe4f8e2 test-data/test-db/AMR_DNA-Enterococcus_faecalis.not |
| b |
| Binary file test-data/test-db/AMR_DNA-Enterococcus_faecalis.not has changed |
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| diff -r 1920244e2895 -r 7844dbe4f8e2 test-data/test-db/AMR_DNA-Enterococcus_faecalis.nsq |
| b |
| Binary file test-data/test-db/AMR_DNA-Enterococcus_faecalis.nsq has changed |
| b |
| diff -r 1920244e2895 -r 7844dbe4f8e2 test-data/test-db/AMR_DNA-Enterococcus_faecalis.ntf |
| b |
| Binary file test-data/test-db/AMR_DNA-Enterococcus_faecalis.ntf has changed |
| b |
| diff -r 1920244e2895 -r 7844dbe4f8e2 test-data/test-db/AMR_DNA-Enterococcus_faecalis.nto |
| b |
| Binary file test-data/test-db/AMR_DNA-Enterococcus_faecalis.nto has changed |
| b |
| diff -r 1920244e2895 -r 7844dbe4f8e2 test-data/test-db/AMR_DNA-Enterococcus_faecalis.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/AMR_DNA-Enterococcus_faecalis.tab Thu May 30 13:07:03 2024 +0000 |
| b |
| @@ -0,0 +1,3 @@ +#accesion_version@gene_name@gene_symbol:start-stop mutation_position mutation_symbol class subclass mutated_gene_name +NZ_CP041738.1@23S_ribosomal_RNA@23S:216195-219090 2505 23S_G2505A OXAZOLIDINONE LINEZOLID Enterococcus_faecalis_linezolid_resistant_23S +NZ_CP041738.1@23S_ribosomal_RNA@23S:216195-219090 2576 23S_G2576T OXAZOLIDINONE LINEZOLID Enterococcus_faecalis_linezolid_resistant_23S |
| b |
| diff -r 1920244e2895 -r 7844dbe4f8e2 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 1920244e2895 -r 7844dbe4f8e2 test-data/test-db/AMR_DNA-Enterococcus_faecium.njs --- a/test-data/test-db/AMR_DNA-Enterococcus_faecium.njs Tue Oct 31 14:47:37 2023 +0000 +++ b/test-data/test-db/AMR_DNA-Enterococcus_faecium.njs Thu May 30 13:07:03 2024 +0000 |
| [ |
| @@ -3,13 +3,13 @@ "dbname": "AMR_DNA-Enterococcus_faecium", "dbtype": "Nucleotide", "db-version": 5, - "description": "AMR_DNA-Enterococcus_faecium", + "description": "/Users/bebatut/Documents/projects/galaxyproject/tools-iuc/data_managers/data_manager_build_amrfinderplus/amrfinderplus-db/AMR_DNA-Enterococcus_faecium", "number-of-letters": 2901, "number-of-sequences": 1, - "last-updated": "2023-05-12T11:11:00", + "last-updated": "2024-05-27T16:19:00", "number-of-volumes": 1, - "bytes-total": 37883, - "bytes-to-cache": 879, + "bytes-total": 38003, + "bytes-to-cache": 999, "files": [ "AMR_DNA-Enterococcus_faecium.ndb", "AMR_DNA-Enterococcus_faecium.nhr", |
| b |
| diff -r 1920244e2895 -r 7844dbe4f8e2 test-data/test-db/ReferenceGeneCatalog.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/ReferenceGeneCatalog.txt Thu May 30 13:07:03 2024 +0000 |
| b |
| @@ -0,0 +1,14 @@ +allele gene_family whitelisted_taxa product_name scope type subtype class subclass refseq_protein_accession refseq_nucleotide_accession curated_refseq_start genbank_protein_accession genbank_nucleotide_accession genbank_strand genbank_start genbank_stop refseq_strand refseq_start refseq_stop pubmed_reference blacklisted_taxa synonyms hierarchy_node db_version + aph(3')-IIIa aminoglycoside O-phosphotransferase APH(3')-IIIa core AMR AMR AMINOGLYCOSIDE AMIKACIN/KANAMYCIN WP_063841495.1 NG_047419.1 No AAK62562.1 AF330699.1 + 1562 2356 + 101 895 11600397 aph(3')-III aph(3')-IIIa 2024-05-02.2 + aph(3')-IIIa aminoglycoside O-phosphotransferase APH(3')-IIIa core AMR AMR AMINOGLYCOSIDE AMIKACIN/KANAMYCIN WP_063841507.1 NG_047420.1 No CAD36021.1 AJ490186.1 + 1993 2787 + 101 895 aph(3')-III aph(3')-IIIa 2024-05-02.2 + catA type A-7 chloramphenicol O-acetyltransferase core AMR AMR PHENICOL CHLORAMPHENICOL WP_063843211.1 NG_047572.1 No AAA26615.1 M64281.1 + 208 855 + 101 748 1713259 catA7 2024-05-02.2 + erm(B) 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B) core AMR AMR LINCOSAMIDE/MACROLIDE/STREPTOGRAMIN CLINDAMYCIN/ERYTHROMYCIN/STREPTOGRAMIN B WP_063844601.1 NG_047793.1 No CAA57314.1 X81655.1 + 300 1037 + 101 838 7486927 erm(AM),erm(TE) erm(B) 2024-05-02.2 + mupB mupirocin-resistant isoleucine--tRNA ligase MupB core AMR AMR MUPIROCIN MUPIROCIN WP_063854488.1 NG_048009.1 No AEY83581.1 JQ231224.1 + 91 3192 + 91 3192 22252810 mupB 2024-05-02.2 + optrA ABC-F type ribosomal protection protein OptrA core AMR AMR PHENICOL/OXAZOLIDINONE FLORFENICOL/OXAZOLIDINONE WP_063854496.1 NG_048023.1 No AKA86814.1 KP399637.1 + 31477 33444 + 101 2068 25977397 optrA 2024-05-02.2 + sat4 streptothricin N-acetyltransferase Sat4 core AMR AMR STREPTOTHRICIN STREPTOTHRICIN WP_063854934.1 NG_048070.1 No AAB53445.1 U01945.1 + 374 916 + 101 643 8056285 sat4A sat4 2024-05-02.2 + sul2 sulfonamide-resistant dihydropteroate synthase Sul2 core AMR AMR SULFONAMIDE SULFONAMIDE WP_063855540.1 NG_048108.1 No CAC81945.1 AJ289135.1 + 3990 4805 + 101 916 sul2 2024-05-02.2 + tet(L) tetracycline efflux MFS transporter Tet(L) core AMR AMR TETRACYCLINE TETRACYCLINE WP_063856080.1 NG_048201.1 No AAA22851.1 M11036.1 + 189 1565 + 101 1477 2996983 tetL tet(L) 2024-05-02.2 + tet(M) tetracycline resistance ribosomal protection protein Tet(M) core AMR AMR TETRACYCLINE TETRACYCLINE WP_063856395.1 NG_048234.1 No ABB70053.1 DQ223247.1 + 1 1920 + 1 1920 16565159 tet(M) 2024-05-02.2 + tetA(46) tetracycline efflux ABC transporter Tet(46) subunit A core AMR AMR TETRACYCLINE TETRACYCLINE WP_063856469.1 NG_048312.1 No AET10444.1 HQ652506.1 + 374 2098 + 101 1825 22941900 tetA(46) 2024-05-02.2 + vanG D-alanine--D-serine ligase VanG core AMR AMR GLYCOPEPTIDE VANCOMYCIN WP_063856695.1 NG_048368.1 No AAF71281.1 AF253562.2 + 3715 4764 + 101 1150 11036060 vanA-G,vanG-G vanG 2024-05-02.2 +blaOXA-484 blaOXA OXA-48 family carbapenem-hydrolyzing class D beta-lactamase OXA-484 core AMR AMR BETA-LACTAM CARBAPENEM WP_063864110.1 NG_049766.1 No ALI16502.1 KR401105.1 + 1 798 + 1 798 blaOXA-484 2024-05-02.2 |
| b |
| diff -r 1920244e2895 -r 7844dbe4f8e2 test-data/test-db/ReferenceGeneHierarchy.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/ReferenceGeneHierarchy.txt Thu May 30 13:07:03 2024 +0000 |
| b |
| b'@@ -0,0 +1,7043 @@\n+node_id\tparent_node_id\tsymbol\tnum_prots\thmm_acc\tprot_acc\tscope\ttype\tsubtype\tclass\tsubclass\tname\tsynonyms\tdisplay_parent\tallele\tdb_version\n+HEAT\tSTRESS\t\t10\t\t\tnon-reported\tSTRESS\tHEAT\t\t\t\t\t0\t0\t2024-05-02.2\n+HTH_5\tMETAL\t\t13\t\t\tnon-reported\tSTRESS\tMETAL\t\t\tArsR/SmtB family metalloregulatory transcriptional repressor\t\t0\t0\t2024-05-02.2\n+IONOPHORE\tAMR\t\t2\t\t\tnon-reported\tAMR\tAMR\t\t\t\t\t0\t0\t2024-05-02.2\n+LHR_hdeD\tHEAT\thdeD-GI\t1\t\t\tplus\tSTRESS\tHEAT\t\t\theat resistance membrane protein HdeD-GI\t\t0\t0\t2024-05-02.2\n+LHR_hsp20A\tHEAT\thsp20\t1\t\t\tplus\tSTRESS\tHEAT\t\t\tsmall heat shock protein sHSP20\t\t0\t0\t2024-05-02.2\n+LHR_hsp20B\tHEAT\tshsP\t1\t\t\tplus\tSTRESS\tHEAT\t\t\tsmall heat shock protein sHSP20-GI\t\t0\t0\t2024-05-02.2\n+LHR_kefB\tHEAT\tkefB-GI\t1\t\t\tplus\tSTRESS\tHEAT\t\t\theat resistance system K+/H+ antiporter KefB-GI\t\t0\t0\t2024-05-02.2\n+LHR_psiE\tHEAT\tpsi-GI\t1\t\t\tplus\tSTRESS\tHEAT\t\t\theat resistance protein PsiE-GI\t\t0\t0\t2024-05-02.2\n+LHR_trx\tHEAT\ttrxLHR\t1\t\t\tplus\tSTRESS\tHEAT\t\t\theat resistance system thioredoxin Trx-GI\t\t0\t0\t2024-05-02.2\n+LHR_yfdX1\tHEAT\tyfdX1\t1\t\t\tplus\tSTRESS\tHEAT\t\t\theat resistance protein YfdX1\t\t0\t0\t2024-05-02.2\n+LHR_yfdX2\tHEAT\tyfdX2\t1\t\t\tplus\tSTRESS\tHEAT\t\t\theat resistance protein YfdX2\t\t0\t0\t2024-05-02.2\n+MATE_efflux\tEFFLUX\t\t8\t\t\tnon-reported\tAMR\tAMR\t\t\tmultidrug efflux MATE transporter\t\t0\t0\t2024-05-02.2\n+METAL\tSTRESS\t\t180\t\t\tnon-reported\tSTRESS\tMETAL\t\t\tMetal Resistance\t\t0\t0\t2024-05-02.2\n+METAL-RND-IM\tMETAL\t\t2\t\t\tnon-reported\tSTRESS\tMETAL\t\t\tcation efflux RND transporter permease subunit\t\t0\t0\t2024-05-02.2\n+MFS_efflux\tEFFLUX\t\t199\t\t\tnon-reported\tAMR\tAMR\t\t\tmultidrug efflux MFS transporter\t\t0\t0\t2024-05-02.2\n+MFS_efflux_CHL\tMFS_efflux\tcml\t48\t\t\tcore\tAMR\tAMR\tPHENICOL\tCHLORAMPHENICOL\tchloramphenicol efflux MFS transporter\t\t0\t0\t2024-05-02.2\n+ACID\tSTRESS\t\t3\t\t\tnon-reported\tSTRESS\tACID\t\t\t\t\t0\t0\t2024-05-02.2\n+ALL\t\t\t8180\t\t\tnon-reported\tROOT\tROOT\t\t\t\t\t0\t0\t2024-05-02.2\n+AME\tAMR\t\t676\t\t\tnon-reported\tAMR\tAMR\t\t\taminoglycoside modifying enzymes\t\t0\t0\t2024-05-02.2\n+AMR\tALL\t\t6990\t\t\tnon-reported\tAMR\tAMR\t\t\t\t\t0\t0\t2024-05-02.2\n+AMR-SUSCEPTIBLE\tAMR\t\t26\t\t\tnon-reported\tAMR\tAMR-SUSCEPTIBLE\t\t\tFamilies implicated in adaptive resistance by mutation\t\t0\t0\t2024-05-02.2\n+BIOCIDE\tSTRESS\t\t64\t\t\tnon-reported\tSTRESS\tBIOCIDE\t\t\t\t\t0\t0\t2024-05-02.2\n+CDF_efflux\tMETAL\t\t2\t\t\tnon-reported\tSTRESS\tMETAL\t\t\tCDF family cation efflux transporter\t\t0\t0\t2024-05-02.2\n+EFFLUX\tAMR\t\t295\t\t\tnon-reported\tAMR\tAMR\t\t\tefflux\t\t0\t0\t2024-05-02.2\n+OM_sidero\tVIRULENCE_Ecoli\t\t27\t\t\tnon-reported\tVIRULENCE\tVIRULENCE\t\t\tTonB-dependent siderophore receptor\t\t0\t0\t2024-05-02.2\n+P-type_ATPase\tMETAL\t\t8\t\t\tnon-reported\tSTRESS\tMETAL\t\t\tmetal-translocating P-type ATPase\t\t0\t0\t2024-05-02.2\n+PERI-SENSOR\tMETAL\t\t1\t\t\tnon-reported\tSTRESS\tMETAL\t\t\tperiplasmic heavy metal sensor\t\t0\t0\t2024-05-02.2\n+RESPONSE_REG\tAMR\t\t30\t\t\tnon-reported\tAMR\tAMR\t\t\tDNA-binding response regulator\t\t0\t0\t2024-05-02.2\n+RND-OM\tEFFLUX\t\t10\t\t\tnon-reported\tAMR\tAMR\t\t\tmultidrug efflux transporter outer membrane subunit\t\t0\t0\t2024-05-02.2\n+RND-peri\tEFFLUX\t\t27\t\t\tnon-reported\tAMR\tAMR\t\t\tmultidrug efflux RND transporter periplasmic adaptor subunit\t\t0\t0\t2024-05-02.2\n+SMR_efflux\tBIOCIDE\tqac\t38\t\t\tcore\tSTRESS\tBIOCIDE\tQUATERNARY AMMONIUM\tQUATERNARY AMMONIUM\tSMR family small multidrug resistance efflux protein\t\t0\t0\t2024-05-02.2\n+STRESS\tALL\t\t257\t\t\tnon-reported\tSTRESS\tSTRESS\t\t\t\t\t0\t0\t2024-05-02.2\n+VIRULENCE\tALL\t\t933\t\t\tnon-reported\tVIRULENCE\tVIRULENCE\t\t\t\t\t0\t0\t2024-05-02.2\n+VIRULENCE_Bcer\tVIRULENCE\t\t62\t\t\tnon-reported\tVIRULENCE\tVIRULENCE\t\t\t\t\t0\t0\t2024-05-02.2\n+VIRULENCE_Burk\tVIRULENCE\t\t2\t\t\tnon-reported\tVIRULENCE\tVIRULENCE\t\t\t\t\t0\t0\t2024-05-02.2\n+VIRULENCE_Cbot\tVIRULENCE\t\t46\t\t\tnon-reported\tVIRULENCE\tVIRULENCE\t\t\t\t\t0\t0\t2024-05-02.2\n+VIRULENCE_Cdiff\tVIRULENCE\t\t7\t\t\tnon-reported\tVIRULENCE\tVIRULENCE\t\t\t\t\t0\t0\t2024-05-02.2\n+VIRULENCE_Cperf\tVIRULENCE\t\t16\t\t\tnon-reported\tVIRULENCE\tVIRULENCE\t\t\t\t\t0\t0\t2024-05-02.2\n+VIRULENCE_Ecoli\tVIRULENCE\t\t629\t\t\tnon-reported\tVIRULENCE\tVIRULENCE\t\t\t\t\t0\t0\t2024-05-02.2\n+VIRULENCE_Lmon\tVIRULENCE\t\t18\t\t\tnon-reported\tVIRULENCE\tVIRULENCE\t\t\t\t\t0\t0\t2024-05-02.2\n+VIRULENCE_Salmo\tVIRULENCE\t\t8\t\t\tnon-re'..b'repeat protein QnrVC3\t\t0\t1\t2024-05-02.2\n+qnrVC4\tqnrVC\tqnrVC4\t1\t\tWP_000361704.1\tcore\tAMR\tAMR\tQUINOLONE\tQUINOLONE\tquinolone resistance pentapeptide repeat protein QnrVC4\t\t0\t1\t2024-05-02.2\n+qnrVC5\tqnrVC\tqnrVC5\t1\t\tWP_000361705.1\tcore\tAMR\tAMR\tQUINOLONE\tQUINOLONE\tquinolone resistance pentapeptide repeat protein QnrVC5\t\t0\t1\t2024-05-02.2\n+qnrVC6\tqnrVC\tqnrVC6\t1\t\tWP_032495607.1\tcore\tAMR\tAMR\tQUINOLONE\tQUINOLONE\tquinolone resistance pentapeptide repeat protein QnrVC6\t\t0\t1\t2024-05-02.2\n+qnrVC7\tqnrVC\tqnrVC7\t1\t\tWP_063866460.1\tcore\tAMR\tAMR\tQUINOLONE\tQUINOLONE\tquinolone resistance pentapeptide repeat protein QnrVC7\t\t0\t1\t2024-05-02.2\n+qnrVC8\tqnrVC\tqnrVC8\t1\t\tWP_206627591.1\tcore\tAMR\tAMR\tQUINOLONE\tQUINOLONE\tquinolone resistance pentapeptide repeat protein QnrVC8\t\t0\t1\t2024-05-02.2\n+qnrVC9\tqnrVC\tqnrVC9\t1\t\tWP_148560450.1\tcore\tAMR\tAMR\tQUINOLONE\tQUINOLONE\tquinolone resistance pentapeptide repeat protein QnrVC9\t\t0\t1\t2024-05-02.2\n+rmtB1\trmtB\trmtB1\t1\t\tWP_012372818.1\tcore\tAMR\tAMR\tAMINOGLYCOSIDE\tAMINOGLYCOSIDE\t16S rRNA (guanine(1405)-N(7))-methyltransferase RmtB1\t\t0\t1\t2024-05-02.2\n+rmtB2\trmtB\trmtB2\t1\t\tWP_063854854.1\tcore\tAMR\tAMR\tAMINOGLYCOSIDE\tAMINOGLYCOSIDE\t16S rRNA (guanine(1405)-N(7))-methyltransferase RmtB2\t\t0\t1\t2024-05-02.2\n+rmtB3\trmtB\trmtB3\t1\t\tWP_048266647.1\tcore\tAMR\tAMR\tAMINOGLYCOSIDE\tAMINOGLYCOSIDE\t16S rRNA (guanine(1405)-N(7))-methyltransferase RmtB3\t\t0\t1\t2024-05-02.2\n+rmtB4\trmtB\trmtB4\t1\t\tWP_032634099.1\tcore\tAMR\tAMR\tAMINOGLYCOSIDE\tAMINOGLYCOSIDE\t16S rRNA (guanine(1405)-N(7))-methyltransferase RmtB4\t\t0\t1\t2024-05-02.2\n+rmtD1\trmtD\trmtD1\t1\t\tWP_019726361.1\tcore\tAMR\tAMR\tAMINOGLYCOSIDE\tAMINOGLYCOSIDE\t16S rRNA (guanine(1405)-N(7))-methyltransferase RmtD1\t\t0\t1\t2024-05-02.2\n+rmtD2\trmtD\trmtD2\t1\t\tWP_063866469.1\tcore\tAMR\tAMR\tAMINOGLYCOSIDE\tAMINOGLYCOSIDE\t16S rRNA (guanine(1405)-N(7))-methyltransferase RmtD2\t\t0\t1\t2024-05-02.2\n+rmtE1\trmtE\trmtE1\t1\t\tWP_063866478.1\tcore\tAMR\tAMR\tAMINOGLYCOSIDE\tAMINOGLYCOSIDE\t16S rRNA (guanine(1405)-N(7))-methyltransferase RmtE1\t\t0\t1\t2024-05-02.2\n+rmtE2\trmtE\trmtE2\t1\t\tWP_063866490.1\tcore\tAMR\tAMR\tAMINOGLYCOSIDE\tAMINOGLYCOSIDE\t16S rRNA (guanine(1405)-N(7))-methyltransferase RmtE2\t\t0\t1\t2024-05-02.2\n+rmtF1\trmtF\trmtF1\t1\t\tWP_015632396.1\tcore\tAMR\tAMR\tAMINOGLYCOSIDE\tAMINOGLYCOSIDE\t16S rRNA (guanine(1405)-N(7))-methyltransferase RmtF1\t\t0\t1\t2024-05-02.2\n+rmtF2\trmtF\trmtF2\t1\t\tWP_023434793.1\tcore\tAMR\tAMR\tAMINOGLYCOSIDE\tAMINOGLYCOSIDE\t16S rRNA (guanine(1405)-N(7))-methyltransferase RmtF2\t\t0\t1\t2024-05-02.2\n+tmexC1\ttmexC\ttmexC1\t1\t\tWP_118842626.1\tcore\tAMR\tAMR\tTETRACYCLINE\tTIGECYCLINE\tmultidrug efflux RND transporter periplasmic adaptor subunit TMexC1\t\t0\t1\t2024-05-02.2\n+tmexC2\ttmexC\ttmexC2\t1\t\tWP_088903431.1\tcore\tAMR\tAMR\tTETRACYCLINE\tTIGECYCLINE\tmultidrug efflux RND transporter periplasmic adaptor subunit TMexC2\t\t0\t1\t2024-05-02.2\n+tmexC3\ttmexC\ttmexC3\t1\t\tWP_034039546.1\tcore\tAMR\tAMR\tTETRACYCLINE\tTIGECYCLINE\tmultidrug efflux RND transporter periplasmic adaptor subunit TMexC3\t\t0\t1\t2024-05-02.2\n+tmexD1\ttmexD\ttmexD1\t1\t\tWP_118842627.1\tcore\tAMR\tAMR\tTETRACYCLINE\tTIGECYCLINE\tmultidrug efflux RND transporter permease subunit TMexD1\t\t0\t1\t2024-05-02.2\n+tmexD2\ttmexD\ttmexD2\t1\t\tWP_027591160.1\tcore\tAMR\tAMR\tTETRACYCLINE\tTIGECYCLINE\tmultidrug efflux RND transporter permease subunit TMexD2\t\t0\t1\t2024-05-02.2\n+tmexD3\ttmexD\ttmexD3\t1\t\tWP_034065037.1\tcore\tAMR\tAMR\tTETRACYCLINE\tTIGECYCLINE\tmultidrug efflux RND transporter permease subunit TMexD3\t\t0\t1\t2024-05-02.2\n+toprJ1\ttoprJ\ttoprJ1\t1\t\tWP_003152694.1\tcore\tAMR\tAMR\tTETRACYCLINE\tTIGECYCLINE\tmultidrug efflux transporter outer membrane subunit TOprJ1\t\t0\t1\t2024-05-02.2\n+toprJ2\ttoprJ\ttoprJ2\t1\t\tWP_088903432.1\tcore\tAMR\tAMR\tTETRACYCLINE\tTIGECYCLINE\tmultidrug efflux transporter outer membrane subunit TOprJ2\t\t0\t1\t2024-05-02.2\n+vanS-B-Delta\tvanS-B\tvanS-B-Delta\t1\t\tWP_063856737.1\tcore\tAMR\tAMR\tGLYCOPEPTIDE\tVANCOMYCIN\tVanB-type vancomycin resistance histidine kinase VanS-B-Delta\t\t0\t1\t2024-05-02.2\n+vga(A)-LC\tvga(A)\tvga(A)-LC\t1\t\tWP_002449123.1\tcore\tAMR\tAMR\tLINCOSAMIDE\tLINCOSAMIDE\tABC-F type ribosomal protection protein Vga(A)-LC\t\t0\t1\t2024-05-02.2\n' |
| b |
| diff -r 1920244e2895 -r 7844dbe4f8e2 test-data/test-db/amr_targets.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/amr_targets.fa Thu May 30 13:07:03 2024 +0000 |
| b |
| b'@@ -0,0 +1,394 @@\n+>NG_048023.1__optrA\n+ttgtccaaagccacctttgcaattgctagtactaacgcaaaggaggatatgaaaatgcaatacaaaataattaatggtgc\n+cgtttactatgatggtaatatggtgttggaaaacatcggtattgaaatcaatgataatgaaaagattgctattgttggta\n+gaaatggatgtggaaaaacaaccttgctaaaagctattataggcgaaattgaattagaagaaggaactggtgaaagtgag\n+tttcaagtaataaagaccggtaacccttatattagctatttaagacagatgccttttgaagatgaaagtatatcaatggt\n+ggatgaagtccgtacggtatttaagacgcttattgatatggaaaacaagatgaaacagctgatagataaaatggagaatc\n+aatatgatgataaaatcatcaatgaatactctgatatcagtgaaaggtatatggctcttggaggtctaacctaccaaaaa\n+gaatatgaaacgatgattcgtagtatgggttttactgaagcagattataaaaaacccatttctgaattttcaggtggtca\n+gcgaactaagatagcttttataaaaatacttttaacaaagccagacattctattacttgatgaacctactaaccaccttg\n+atatagaaacaatacaatggttggagagttatttgagaagttataaatctacattggttattatttcccatgatagaatg\n+tttcttaatcgaattgtggataaggtttatgaaatcgaatggggagagaccaaatgttataaaggtaattattcagcctt\n+tgaggagcaaaaacgagaaaatcatatcaaacagcaaaaagattacgacttgcaacagatagaaattgaaaggattacac\n+gcttgattgaacgttttcgttataaacctacgaaagctaaaatggtgcaatctaaaattaaattattacagcgtatgcaa\n+atattaaatgcaccagaccaatacgatacaaaaacttatatgtctaaatttcaaccgagaatcagtagttcaaggcaagt\n+attaagtgcttcagaacttgtgataggctatgatactcctcttgcaaaggttaatttcaaccttgaaaggggacagaagc\n+ttggaattgttgggagtaatggtattggtaaatccacgttgcttaaaacacttatgggtggtgtggcagcattgtctgga\n+gattttaaattcggatacaatgttgaaattagctattttgaccaacagcttgctcaaatcagtggagatgatacactatt\n+cgaaatttttcaaagcgaataccctgagctaaatgacacagaggtcagaactgctcttggctcatttcagtttagtggag\n+atgatgtttttagaccggtgtcctctttgtcaggtggagaaaaggttagattgacattatgtaaattattatataaacgt\n+actaatgttttaatcttagatgaaccgacaaaccacatggatattattggaaaagagaatttagagaatatcttatgcag\n+ttatcaaggtacaattatttttgtgtcacatgatagatattttactaataagattgctgacagattacttgtttttgata\n+aggatggtgtagagtttgtacaatctacttatggtgagtacgagaaaaaaaggatgaattctgaaaagccatttaataac\n+attaaagttgagcagaaagtagagaaaaataacacagtaaaaggcgatcgtaactccattgagaaggagaaggttaagaa\n+ggagaaacgaattgaaaagcttgaagtgttaataaatcaatatgatgaagaattagaaagattgaataaaatcatttctg\n+aaccaaacaattcttctgattatatagtactgacggaaatacaaaaatcaattgatgatgttaaaaggtgtcagggtaat\n+tattttaatgaatgggaacagttgatgagagaattggaagttatgtaa\n+>NG_047419.1__aph3p-IIIa\n+atggctaaaatgagaatatcaccggaattgaaaaaactgatcgaaaaataccgctgcgtaaaagatacggaaggaatgtc\n+tcctgctaaggtatataagctggtgggagaaaatgaaaacctatatttaaaaatgacggacagccggtataaagggacca\n+cctatgatgtggaacgggaaaaggacatgatgctatggctggaaggaaagctgcctgttccaaaggtcctgcactttgaa\n+cggcatgatggctggagcaatctgctcatgagtgaggccgatggcgtcctttgctcggaagagtatgaagatgaacaaag\n+ccctgaaaagattatcgagctgtatgcggagtgcatcaggctctttcactccatcgacatatcggattgtccctatacga\n+atagcttagacagccgcttagccgaattggattacttactgaataacgatctggccgatgtggattgcgaaaactgggaa\n+gaagacactccatttaaagatccgcgcgagctgtatgattttttaaagacggaaaagcccgaagaggaacttgtcttttc\n+ccacggcgacctgggagacagcaacatctttgtgaaagatggcaaagtaagtggctttattgatcttgggagaagcggca\n+gggcggacaagtggtatgacattgccttctgcatccggtcgatcagggaggatatcggggaagaacagtatgtcgagcta\n+ttttttgacttactggggatcaagcctgattgggagaaaataaaatattatattttactggatgaattgttttag\n+>NG_048070.1__sat4\n+gtgattacagaaatgaaagcagagcacctgaaagatatcgataaacccagcgaaccatttgaggtgataggtaagattat\n+accgaggtatgaaaacgagaattggacctttacagaattactctatgaagcgccatatttaaaaagctaccaagacgaag\n+aggatgaagaggatgaggaggcagattgccttgaatatattgacaatactgataagataatatatctttactaccaagac\n+gataaatgcgtcggaaaagttaaactgcgaaaaaattggaaccggtacgcttatatagaagatatcgccgtatgtaagga\n+tttcagggggcaaggcataggcagcgcgcttatcaatatatctatagaatgggcaaagcataaaaacttgcatggactaa\n+tgcttgaaacccaggacaataaccttatagcttgtaaattctatcataattgtggtttcaaaatcggctccgtcgatact\n+atgttatacgccaactttgaaaacaactttgaaaaagctgttttctggtatttaaggttttag\n+>NG_048214.1__tetM\n+atgaaaattattaatattggagttttagctcatgttgatgcaggaaaaactaccttaacagaaagcttattatataacag\n+tggagcgattacagaattaggaagcgtggacaaaggtacaacgaggacggataatacgcttttagaacgtcagagaggaa\n+ttacaattcagacaggaataacctcttttcagtgggaaaatacgaaggtgaacatcatagacacgccaggacatatggat\n+ttcttagcagaagtatatcgttcattatcagttttagatggggcaattctactgatttctgcaaaagatttcgtacaagc\n+acaaactcgtatattatttcatgcacttaggaaaatggggattcccacaatcttttttatcaataagattgaccaaaatg\n+gaattgatttatcaacggtttatcaggatattaaagagaaactttctgccgaaattgtaatcaaacagaaggtagaactg\n+tatcctaatat'..b'atttagagcagatcgattcggtagagtttaaggattattccttcagttatcctggtgctgagcgaaa\n+gagcctatcaggcattgattggactatccagcgaggacagacggttggaattgttggtcgtaccggtgcaggaaagacta\n+ccctggttcgacaattcttgcggcaatacccagttggtgagggagaattcttggtcaaccagcaaccgatcgtggactac\n+aaccgacactcgattgaagaaaaaattggttatgtttcccaagaacatattttattttctaagtctatccgtgagaatat\n+agcgcttggtaaaaaaggagccagccaagaagacttgatggaagcagtagcccaagctgcttttgcggatgatctcgagc\n+ggatgtctcatggaatggacaccctgatcggtgagaaaggggtctctgtatcaggaggtcaaaaacagcggatctctttg\n+gcgcgtgccttcttaagagatgcagatctcttgttgttagatgattccctttcggcagtggatgcgaagaccgaacaggc\n+cattattgacaccattcaaaaagaacgaaaagacaagacgaccatcattgtttctcatcgcttgtcggctgtccatcagg\n+ctgattggatcatcgtcttggatcaaggacagattgttgaagaaggcagggctagtgatttattagctcaagagggctgg\n+tattatgaacaataccaacggcaacaaaaacaggaaggagaataa\n+>NG_048009.1__mupB\n+ttggaaaacgagaatataatagaagaacaaaaaatcttaaatttttggaaagaagaaaacattttcaaaaagagtattga\n+taatagaaaaaatgataatccatttgttttttacgatggtcctccaactgccaatggcttaccacatacaggtcacgtgt\n+taggaagagtaataaaagatttatttgctcgatataagacaatgcaaggattttatgttgaaagaaaagctgggtgggat\n+acccatggactacctgtagaacttggtgttgaaaaaaaacttggaattaaggataaaaatgaaatagaaaaatatggaat\n+agaaaaatttataaatgaatgtaaaaatagtgtgtttatgtatgaaaaacagtggagagaatttagtgaactaatcggat\n+attgggtagatatggaaaaaccgtacaaaacaatggataatacgtatatagaatcaatctggtatatattgtctgacttt\n+cataaaaaaggtcttttatacaaagggcataaagttaccccgtattgtccaagctgtgaaacttctttaagttctcatga\n+agtagctcagggatataaggaagtaaaagatatctctgtaatcttaaaatttccgattttagacagtgatgagaatttct\n+tagtttggacgacaactccatggagcttaccaggtaatatagctttagccataaatgctgaagaaatatatgttaaagtt\n+aattatgataatgaaatttttattatcatggaaagtttgttgcaaagtgtttttaaagatgaagacaatatagatatagt\n+aagtaaacataaaggaaaagaatttgtaggaaaagaatacctcgctcctttccctaacaagtctcttatgaacaatgaaa\n+actcatataaagttttacctgctgattttgttacaaataaagatggtacgggtatcgtccatattgctccggcttatggg\n+gaagatgattacaaattagttcaagaaaataatataccctttattaatgttattgattctagaggaaaatataatcaaga\n+ttctcctatttttaaaggagagctagctaaagaatcagatattaacattattaaagaacttacacatttaaatctacttt\n+tcaaaaaagaaaaatatgaacatagctatcctttttgttggagatgtgataatccattaatctattatgcaatggaaggt\n+tggtttataaaaacaacggcttataaaaatgaaataaaggaaaacaatcaaaaaatagaatggtatccagaccatattaa\n+aaatggaaggtttggaaatttcttagataatatgattgattggaatattggtagaaaaagatattggggcactccactaa\n+atatatggaaatgctccacgtgttcccatgagttttcacctaaaagcataaatgatctaatacaacattccattgaagat\n+attccttctgatatagaattacatcgaccttatatagataatgtgaaatgtaaatgtcaaaattgtggtggtgacatgtg\n+tagagaagaagaagtcattgatgtatggtttgatagtggatcgatgccttttgcacaaaatcactatccatttagtggtc\n+ccattcaaaactcatacccagctgactttatagctgaaggagttgatcaaactagagggtggttttatagcttattggtg\n+atttcaacaattttcaaaggggaagcaccttataaaaacgcattgtcattaggacatatattagattccaatggacaaaa\n+aatgtcgaaaagtaaagggaatgttatagatcctatatcaatgataaaaacttatggcgctgattctttaagatggacat\n+tagtttctgacagcgttccttggactaacaaaaggttttcagaaaatatggtggcacaatcaaaatcgagagtaattgat\n+actttaaaaaatatatttaacttctataatatgtatcaaaaaattgataattatgactatactagggatactcctaaaca\n+gctgaatttacttgataattgggctatatctcgaatgaattcagttataaaagaggtagagctgcatttagaaaaatata\n+accctacaaatgcatcaagagctattggggagtttatcaatgaaataagtaattggtatattagaagatctagaagtcga\n+ttttggagtagtgaaatgaatgaggataaaaagagtgcgtattttactcttagacttattttgattaatacttgtaaaat\n+aatagctcctttcaccccatttactagcgaggaaatacatctaaatctcaccaaaaaaagtgtacacttagaagatttcc\n+ctcaagccaaggaagaatatataaatttaaaactagaagaagatatgaataaagttttagatattgtcgaaaaatctaga\n+agcataagaaataacataaacatcaaaacaaaacaaccactttcaaacatgtatatatatgacaataataatcttgataa\n+tgaatttctaagaaaatacaaagacatcattaaagatgaaataaatgttaaaaagataaatattgtttctgatttagaca\n+attttttagaatatgatgtaaaaccgaacttttcaactttaggccctaaattaggaaaagatatgaaacaattccaaatt\n+ttatttaaaaatattaaaaaagaagaaatgaataaactaatcaatgatttcgataaacttcaaaaagtttttgactcttt\n+aggtgtaacaattgaggaaaaggattttattattagtaaaatacctaaaaagggattctctctttcaagcaatgactctg\n+atcgtcttatcattttagacactaatttgactcaagaattaattcgcgaagggtttgtcagagaattaattcgtgttatt\n+caacaactaagaaaacaacagaactttaatattgaagaacgtataaatgtagtaatagacatagattccgatggtttact\n+atcaattaaaaataatatcaatatattgaaagaaaatgtactaattaataatctaaaatttgagaaaagagaaactatga\n+aatattttaaaattaatcagaaagaaattggtattcagttaatgtctagctttacaaattaa\n\\ No newline at end of file\n' |
| b |
| diff -r 1920244e2895 -r 7844dbe4f8e2 test-data/test-db/bla.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/bla.tsv Thu May 30 13:07:03 2024 +0000 |
| b |
| b'@@ -0,0 +1,257 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HW\tCARBAPENEM\tbla-B\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\n+blaSIM\tCARBAPENEM\tbla-B\t1\t1\t1\t1\t1\t2\t2\t2\t2\t2\t2\t2\t2\t2\t2\n+blaSMB\tCARBAPENEM\tbla-B\t0\t1\t1\t1'..b'RIN\tbla-D\t0\t0\t0\t0\t0\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\n+blaOXY-2\tCEPHALOSPORIN\tbla-A\t11\t11\t14\t15\t16\t18\t21\t22\t22\t22\t27\t28\t29\t29\t29\n+blaOXA-2_fam\tCEPHALOSPORIN\tbla-D\t6\t6\t6\t6\t6\t6\t7\t9\t10\t10\t10\t10\t10\t10\t10\n+blaTLA2\tCEPHALOSPORIN\tbla-A\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\n+blaPEDO-3_fam\tCARBAPENEM\tbla-B\t0\t0\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\n+blaCRD3\tCARBAPENEM\tbla-B\t0\t0\t0\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\n+blaOXY-3\tCEPHALOSPORIN\tbla-A\t1\t1\t1\t1\t1\t1\t1\t1\t1\t3\t3\t3\t3\t3\t3\n+blaOXY-4\tCEPHALOSPORIN\tbla-A\t1\t1\t1\t1\t1\t1\t1\t1\t1\t4\t4\t5\t5\t5\t5\n+blaOXA-5_fam\tBETA-LACTAM\tbla-D\t2\t2\t2\t2\t2\t2\t2\t2\t2\t2\t2\t2\t2\t2\t2\n+blaOXY-5\tCEPHALOSPORIN\tbla-A\t2\t2\t2\t3\t3\t4\t4\t4\t5\t5\t10\t10\t11\t11\t11\n+blaALG6\tCARBAPENEM\tbla-B\t0\t0\t0\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\n+blaOXY-6\tCEPHALOSPORIN\tbla-A\t4\t4\t4\t4\t4\t5\t5\t5\t5\t7\t9\t10\t11\t11\t11\n+blaADC-8_fam\tCEPHALOSPORIN\tbla-C\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\n+blaOXA-10_fam\tBETA-LACTAM\tbla-D\t4\t7\t8\t8\t8\t9\t11\t12\t14\t20\t22\t24\t38\t40\t43\n+blaOXA-10_fam\tCARBAPENEM\tbla-D\t0\t0\t0\t0\t1\t1\t1\t1\t2\t2\t2\t2\t2\t2\t2\n+blaOXA-10_fam\tCEPHALOSPORIN\tbla-D\t11\t11\t11\t11\t12\t12\t12\t12\t14\t15\t15\t15\t15\t15\t15\n+blaALG11\tCARBAPENEM\tbla-B\t0\t0\t0\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\n+blaOXA-12_fam\tBETA-LACTAM\tbla-D\t3\t3\t3\t3\t3\t3\t3\t4\t4\t4\t5\t9\t11\t11\t11\n+blaOXA-22_fam\tBETA-LACTAM\tbla-D\t1\t1\t1\t1\t1\t2\t2\t2\t5\t5\t6\t6\t7\t7\t7\n+blaOXA-23_fam\tCARBAPENEM\tbla-D\t14\t15\t16\t17\t20\t25\t25\t26\t27\t40\t41\t45\t47\t49\t51\n+blaGRD23\tCARBAPENEM\tbla-B\t0\t0\t0\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\n+blaOXA-24_fam\tCARBAPENEM\tbla-D\t6\t6\t7\t7\t7\t8\t8\t8\t9\t9\t10\t11\t12\t12\t13\n+blaGRD33\tCARBAPENEM\tbla-B\t0\t0\t0\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\n+blaOXA-46_fam\tBETA-LACTAM\tbla-D\t3\t4\t4\t4\t4\t4\t4\t4\t5\t6\t6\t6\t6\t6\t6\n+blaOXA-48_fam\tBETA-LACTAM\tbla-D\t0\t0\t0\t0\t0\t0\t0\t0\t1\t1\t1\t1\t2\t7\t9\n+blaOXA-48_fam\tCARBAPENEM\tbla-D\t4\t5\t7\t10\t12\t17\t24\t25\t25\t27\t27\t27\t27\t27\t27\n+blaOXA-48_fam\tCEPHALOSPORIN\tbla-D\t0\t0\t0\t1\t2\t2\t2\t5\t5\t7\t15\t18\t23\t25\t25\n+blaOXA-50_fam\tBETA-LACTAM\tbla-D\t4\t4\t4\t6\t7\t7\t7\t7\t7\t13\t24\t44\t58\t60\t60\n+blaOXA-51_fam\tBETA-LACTAM\tbla-D\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t4\t6\n+blaOXA-51_fam\tCARBAPENEM\tbla-D\t66\t80\t87\t100\t141\t156\t172\t185\t273\t322\t326\t339\t374\t375\t375\n+blaOXA-55_fam\tBETA-LACTAM\tbla-D\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t7\t7\t7\t7\n+blaOXA-55_fam\tCARBAPENEM\tbla-D\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\n+blaOXA-58_fam\tCARBAPENEM\tbla-D\t4\t4\t4\t4\t6\t6\t7\t7\t7\t7\t7\t7\t8\t8\t8\n+blaOXA-60_fam\tBETA-LACTAM\tbla-D\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t1\t1\n+blaOXA-60_fam\tCARBAPENEM\tbla-D\t1\t1\t1\t1\t1\t2\t2\t2\t5\t5\t6\t6\t6\t6\t6\n+blaOXA-61_fam\tBETA-LACTAM\tbla-D\t2\t2\t3\t3\t3\t9\t9\t9\t49\t49\t49\t49\t49\t49\t49\n+blaOXA-62_fam\tCARBAPENEM\tbla-D\t1\t1\t1\t1\t2\t10\t10\t10\t10\t10\t10\t10\t12\t12\t14\n+blaOXA-63_fam\tBETA-LACTAM\tbla-D\t4\t5\t5\t5\t5\t14\t14\t14\t14\t14\t14\t14\t23\t23\t23\n+blaSPN79\tCARBAPENEM\tbla-B\t0\t0\t0\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\n+blaOXA-85_fam\tBETA-LACTAM\tbla-D\t0\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\t1\n+blaOXA-114_fam\tBETA-LACTAM\tbla-D\t7\t7\t14\t21\t21\t21\t23\t23\t23\t26\t26\t26\t26\t26\t26\n+blaOXA-134_fam\tCARBAPENEM\tbla-D\t1\t1\t5\t16\t16\t17\t18\t18\t21\t21\t22\t24\t28\t28\t28\n+blaOXA-143_fam\tBETA-LACTAM\tbla-D\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t3\t3\t3\n+blaOXA-143_fam\tCARBAPENEM\tbla-D\t2\t2\t3\t5\t5\t6\t6\t6\t7\t8\t8\t8\t8\t8\t8\n+blaOXA-184_fam\tBETA-LACTAM\tbla-D\t0\t0\t2\t2\t2\t8\t8\t8\t39\t39\t39\t39\t39\t39\t39\n+blaOXA-211_fam\tBETA-LACTAM\tbla-D\t0\t0\t0\t0\t0\t0\t1\t1\t5\t5\t5\t6\t6\t7\t7\n+blaOXA-211_fam\tCARBAPENEM\tbla-D\t0\t2\t2\t7\t8\t9\t10\t10\t11\t11\t11\t11\t11\t11\t11\n+blaOXA-213_fam\tCARBAPENEM\tbla-D\t0\t1\t2\t32\t34\t38\t42\t47\t51\t67\t67\t86\t97\t99\t102\n+blaOXA-214_fam\tBETA-LACTAM\tbla-D\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t2\t2\t2\t2\t2\n+blaOXA-214_fam\tCARBAPENEM\tbla-D\t0\t2\t2\t4\t4\t4\t4\t4\t5\t5\t5\t5\t5\t5\t5\n+blaOXA-229_fam\tCARBAPENEM\tbla-D\t0\t0\t3\t8\t9\t9\t9\t9\t10\t15\t17\t23\t25\t26\t26\n+blaOXA-266_fam\tBETA-LACTAM\tbla-D\t0\t0\t0\t1\t1\t1\t1\t1\t2\t2\t2\t2\t2\t2\t2\n+blaOXA-274_fam\tCARBAPENEM\tbla-D\t0\t0\t0\t2\t4\t5\t5\t5\t5\t5\t5\t6\t6\t6\t6\n+blaOXA-286_fam\tCARBAPENEM\tbla-D\t0\t0\t0\t10\t13\t13\t13\t15\t15\t15\t15\t15\t16\t17\t17\n+blaOXA-364_fam\tBETA-LACTAM\tbla-D\t0\t0\t1\t1\t1\t2\t3\t3\t3\t5\t5\t5\t5\t5\t5\n+blaOXA-372_fam\tCARBAPENEM\tbla-D\t0\t0\t0\t0\t1\t1\t1\t1\t2\t2\t2\t3\t3\t3\t3\n+blaOXA-493_fam\tBETA-LACTAM\tbla-D\t0\t0\t0\t0\t0\t1\t2\t2\t2\t2\t2\t2\t2\t2\t2\n+blaOXA-542_fam\tCARBAPENEM\tbla-D\t0\t0\t0\t0\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\n+blaOXA-548_fam\tBETA-LACTAM\tbla-D\t0\t0\t0\t0\t0\t0\t0\t6\t6\t6\t6\t6\t6\t6\t6\n+blaOXA-576_fam\tBETA-LACTAM\tbla-D\t0\t0\t0\t0\t0\t0\t0\t1\t1\t1\t1\t1\t1\t1\t1\n+blaOXA-727_fam\tBETA-LACTAM\tbla-D\t0\t0\t0\t0\t0\t0\t0\t0\t2\t2\t2\t2\t2\t2\t2\n+\n' |
| b |
| diff -r 1920244e2895 -r 7844dbe4f8e2 test-data/test-db/database_format_version.txt --- a/test-data/test-db/database_format_version.txt Tue Oct 31 14:47:37 2023 +0000 +++ b/test-data/test-db/database_format_version.txt Thu May 30 13:07:03 2024 +0000 |
| b |
| @@ -1,1 +1,1 @@ -3.11.1 +3.12.1 |
| b |
| diff -r 1920244e2895 -r 7844dbe4f8e2 test-data/test-db/fam.tab --- a/test-data/test-db/fam.tab Tue Oct 31 14:47:37 2023 +0000 +++ b/test-data/test-db/fam.tab Thu May 30 13:07:03 2024 +0000 |
| b |
| b"@@ -11,6 +11,7 @@\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+IONOPHORE\tAMR\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\t\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@@ -35,28 +36,36 @@\n RND-peri\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 periplasmic adaptor subunit\n SMR_efflux_bcrB\tSMR_efflux\tbcrB\tNF033469.1\t205.00\t205.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tSTRESS\tBIOCIDE\tBACITRACIN\tBACITRACIN\tquaternary ammonium compound efflux SMR transporter BcrB\n SMR_efflux_bcrC\tSMR_efflux\tbcrC\tNF033470.1\t225.00\t225.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tSTRESS\tBIOCIDE\tBACITRACIN\tBACITRACIN\tquaternary ammonium compound efflux SMR transporter BcrC\n-SMR_efflux_emrE\tSMR_efflux\temrE\tNF000336.1\t195.00\t195.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t1\tSTRESS\tBIOCIDE\tEFFLUX\tEFFLUX\tmultidrug efflux SMR transporter EmrE\n+SMR_efflux_emrE\tSMR_efflux\temrE\tNF042984.1\t226.00\t226.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t1\tSTRESS\tBIOCIDE\tEFFLUX\tEFFLUX\tmultidrug efflux SMR transporter EmrE\n SMR_efflux_smr\tSMR_efflux\tsmr\tNF000280.1\t200.00\t200.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tSTRESS\tBIOCIDE\tQUATERNARY AMMONIUM\tQUATERNARY AMMONIUM\tmultidrug efflux SMR transporter Smr\n SMR_efflux\tBIOCIDE\tqac\t-\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tSTRESS\tBIOCIDE\tQUATERNARY AMMONIUM\tQUATERNARY AMMONIUM\tSMR family small multidrug resistance efflux protein\n SMR_qac_int\tSMR_efflux\tqac\tNF033137.0\t188.00\t188.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tSTRESS\tBIOCIDE\tQUATERNARY AMMONIUM\tQUATERNARY AMMONIUM\tQac family quaternary ammonium compound efflux SMR transporter\n SMR_qac_pB8\tSMR_efflux\tqac\tNF000148.1\t200.00\t200.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tSTRESS\tBIOCIDE\tQUATERNARY AMMONIUM\tQUATERNARY AMMONIUM\tQac-pB8 family quaternary ammonium compound efflux SMR transporter\n STRESS\tALL\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tSTRESS\t\t\t\n VIRULENCE_Bcer\tVIRULENCE\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tVIRULENCE\tVIRULENCE\t\t\t\n+VIRULENCE_Burk\tVIRULENCE\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tVIRULENCE\tVIRULENCE\t\t\t\n+VIRULENCE_Cbot\tVIRULENCE\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tVIRULENCE\tVIRULENCE\t\t\t\n VIRULENCE_Cdiff\tVIRULENCE\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tVIRULENCE\tVIRULENCE\t\t\t\n VIRULENCE_Cperf\tVIRULENCE\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tVIRULENCE\tVIRULENCE\t\t\t\n VIRULENCE_Ecoli\tVIRULENCE\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tVIRULENCE\tVIRULENCE\t\t\t\n+VIRULENCE_Lmon\tVIRULENCE\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tVIRULENCE\tVIRULENCE\t\t\t\n+VIRULENCE_Salmo\tVIRULENCE\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tVIRULENCE\tVIRULENCE\t\t\t\n VIRULENCE_Saur\tVIRULENCE\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tVIRULENCE\tVIRULENCE\t\t\t\n VIRULENCE_Vchol\tVIRULENCE\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tVIRULENCE\tVIRULENCE\t\t\t\n VIRULENCE_Yersi\tVIRULENCE\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tVIRULENCE\tVIRULENCE\t\t\t\n VIRULENCE\tALL\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tVIRULENCE\tVIRULENCE\t\t\t\n-aac(2')-IIa\taac(2')\taac(2')-IIa\tNF000100.2\t510.00\t510.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tAMINOGLYCOSIDE\tKASUGAMYCIN\tkasugamycin N-acetyltransferase AAC(2')-IIa\n-aac(2')-IIb\taac(2')\taac(2')-IIb\tNF033472.1\t390.00\t390.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tAMINOGLYCOSIDE\tKASUGAMYCIN\tkasugamycin N-acetyltransferase AAC(2')-IIb\n-aac(2')-Ia\taac(2')\taac(2')-Ia\tNF000108.1\t350.00\t350.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tAMINOGLYCOSIDE\tGENTAMICIN/TOBRAMCYIN\taminoglycoside N-acetyltransfe"..b'7 @@\n vanY-F\tvanY_AFMPt\tvanY-F\t-\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tGLYCOPEPTIDE\tVANCOMYCIN\tD-Ala-D-Ala carboxypeptidase VanY-F\n vanY-G1\tvanY_BG\tvanY-G1\t-\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tGLYCOPEPTIDE\tVANCOMYCIN\tD-Ala-D-Ala carboxypeptidase VanY-G1\n vanY-G\tvanY_BG\tvanY-G\t-\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tGLYCOPEPTIDE\tVANCOMYCIN\tD-Ala-D-Ala carboxypeptidase VanY-G\n+vanY-M\tvanY_AFMPt\tvanY-M\t-\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tGLYCOPEPTIDE\tVANCOMYCIN\tD-Ala-D-Ala carboxypeptidase VanY-M\n vanY-N\tvanY\tvanY-N\tNF000086.1\t250.00\t250.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tGLYCOPEPTIDE\tVANCOMYCIN\tD,D-peptidase/D,D-carboxypeptidase VanY-N\n vanY-Pt\tvanY_AFMPt\tvanY-Pt\t-\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tGLYCOPEPTIDE\tVANCOMYCIN\tD-Ala-D-Ala carboxypeptidase VanY-Pt\n vanY_AFMPt\tvanY\tvanY\tNF000472.1\t425.00\t425.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tGLYCOPEPTIDE\tVANCOMYCIN\tVanY-A/VanY-F/VanY-M family D-Ala-D-Ala carboxypeptidase\n@@ -1873,16 +2056,17 @@\n vga(C)\tvga\tvga(C)\t-\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tLINCOSAMIDE\tLINCOSAMIDE\tABC-F type ribosomal protection protein Vga(C)\n vga(D)\tvga\tvga(D)\t-\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tLINCOSAMIDE\tLINCOSAMIDE\tABC-F type ribosomal protection protein Vga(D)\n vga(E)\tvga\tvga(E)\t-\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tLINCOSAMIDE\tLINCOSAMIDE\tABC-F type ribosomal protection protein Vga(E)\n-vga(F)\tvga\tvga(F)\t-\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tLINCOSAMIDE\tLINCOSAMIDE\tABC-F type ribosomal protection protein Vga(F)\n+vga(F)\tvga\tvga(F)\tNF045691.1\t975.00\t975.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tLINCOSAMIDE\tLINCOSAMIDE\tABC-F type ribosomal protection protein Vga(F)\n vga(G)\tvga\tvga(G)\t-\t0.00\t0.00\t94.00\t90.00\t90.00\t96.00\t90.00\t25.00\t2\tAMR\tAMR\tLINCOSAMIDE\tLINCOSAMIDE\tABC-F type ribosomal protection protein Vga(G)\n-vga\tabc-f\tvga\tNF000170.1\t800.00\t800.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tLINCOSAMIDE\tLINCOSAMIDE\tVga family ABC-F type ribosomal protection protein\n+vga\tabc-f\tvga\tNF000170.2\t725.00\t725.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tLINCOSAMIDE\tLINCOSAMIDE\tVga family 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+vip\tVIRULENCE_Lmon\tvip\tNF033201.1\t600.00\t400.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t1\tVIRULENCE\tVIRULENCE\t\t\tcell invasion LPXTG protein Vip\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+vmlR\tabc-f\tvmlR\t-\t0.00\t0.00\t90.00\t90.00\t90.00\t96.00\t90.00\t25.00\t2\tAMR\tAMR\tLINCOSAMIDE/PLEUROMUTILIN/STREPTOGRAMIN\tLINCOMYCIN/TIAMULIN/VIRGINIAMYCIN M\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' |
| b |
| diff -r 1920244e2895 -r 7844dbe4f8e2 test-data/test-db/mcr.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/mcr.tsv Thu May 30 13:07:03 2024 +0000 |
| b |
| @@ -0,0 +1,11 @@ +Family Subclass Ambler_class 2010 2011 2012 2013 2014 2015 2016 2017 2018 2019 2020 2021 2022 2023 2024 +mcr-1 COLISTIN 0 0 0 0 0 1 5 14 18 23 31 34 35 37 37 +mcr-2 COLISTIN 0 0 0 0 0 0 1 3 3 3 7 8 8 8 8 +mcr-3 COLISTIN 0 0 0 0 0 0 2 16 28 29 40 40 41 41 41 +mcr-4 COLISTIN 0 0 0 0 0 0 0 2 6 6 6 7 7 8 9 +mcr-5 COLISTIN 0 0 0 0 0 1 1 1 3 4 4 4 4 5 5 +mcr-6 COLISTIN 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 +mcr-7 COLISTIN 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 +mcr-8 COLISTIN 0 0 0 0 0 0 1 1 4 4 4 4 4 4 4 +mcr-10 COLISTIN 0 0 0 0 0 0 0 0 0 1 1 4 5 5 5 + |
| b |
| diff -r 1920244e2895 -r 7844dbe4f8e2 test-data/test-db/output.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/output.json Thu May 30 13:07:03 2024 +0000 |
| [ |
| @@ -0,0 +1,1 @@ +{"data_tables": {"amrfinderplus_new_database": [{"db_version": "3.12", "name": "V3.12-2024-05-02.2", "path": "amrfinderplus-db", "value": "amrfinderplus_V3.12_2024-05-02.2"}]}} \ No newline at end of file |
| b |
| diff -r 1920244e2895 -r 7844dbe4f8e2 test-data/test-db/qnr.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/qnr.tsv Thu May 30 13:07:03 2024 +0000 |
| b |
| @@ -0,0 +1,8 @@ +Family Subclass Ambler_class 2010 2011 2012 2013 2014 2015 2016 2017 2018 2019 2020 2021 2022 2023 2024 +qnrA QUINOLONE 7 7 7 7 7 7 7 8 9 9 11 12 12 12 12 +qnrB QUINOLONE 16 27 30 45 49 54 78 79 81 82 84 85 85 87 87 +qnrD QUINOLONE 1 1 1 1 2 2 3 3 3 3 3 3 3 3 3 +qnrE QUINOLONE 0 0 0 1 1 1 2 3 4 4 4 4 4 4 4 +qnrS QUINOLONE 3 6 7 9 10 10 12 13 14 14 14 14 14 14 14 +qnrVC QUINOLONE 3 4 4 6 7 7 7 7 7 8 8 9 9 9 9 + |
| b |
| diff -r 1920244e2895 -r 7844dbe4f8e2 test-data/test-db/taxgroup.tab --- a/test-data/test-db/taxgroup.tab Tue Oct 31 14:47:37 2023 +0000 +++ b/test-data/test-db/taxgroup.tab Thu May 30 13:07:03 2024 +0000 |
| b |
| @@ -1,25 +1,3 @@ #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 1920244e2895 -r 7844dbe4f8e2 test-data/test-db/version.txt --- a/test-data/test-db/version.txt Tue Oct 31 14:47:37 2023 +0000 +++ b/test-data/test-db/version.txt Thu May 30 13:07:03 2024 +0000 |
| b |
| @@ -1,1 +1,1 @@ -2023-04-17.1 +2024-05-02.2 |
| b |
| diff -r 1920244e2895 -r 7844dbe4f8e2 test-data/to_keep_for_test-db --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/to_keep_for_test-db Thu May 30 13:07:03 2024 +0000 |
| b |
| @@ -0,0 +1,15 @@ +WP_061158039 +WP_061189306 +WP_063841495 +WP_063841507 +WP_063843211 +WP_063844601 +WP_063854488 +WP_063854496 +WP_063854934 +WP_063855540 +WP_063856080 +WP_063856395 +WP_063856469 +WP_063856695 +WP_063864110 \ No newline at end of file |
| b |
| diff -r 1920244e2895 -r 7844dbe4f8e2 tool-data/amrfinderplus_database.loc.sample --- a/tool-data/amrfinderplus_database.loc.sample Tue Oct 31 14:47:37 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,7 +0,0 @@ -# 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 1920244e2895 -r 7844dbe4f8e2 tool-data/amrfinderplus_versioned.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/amrfinderplus_versioned.loc.sample Thu May 30 13:07:03 2024 +0000 |
| b |
| @@ -0,0 +1,7 @@ +# this is a tab separated file describing the location of amrfinderplus database +# +# the columns are: +# value, name, db_version, path +# +# for example +amrfinderplus_V3.12_2024-05-02.2 V3.12-2024-05-02.2 3.12 ${__HERE__}/test-db \ No newline at end of file |
| b |
| diff -r 1920244e2895 -r 7844dbe4f8e2 tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Tue Oct 31 14:47:37 2023 +0000 +++ b/tool_data_table_conf.xml.sample Thu May 30 13:07:03 2024 +0000 |
| b |
| @@ -1,7 +1,7 @@ <?xml version="1.0"?> <tables> - <table name="amrfinderplus_database" comment_char="#"> - <columns>value, dbkey, bakta_version, path</columns> - <file path="tool-data/amrfinderplus_database.loc.sample" /> + <table name="amrfinderplus_versioned_database" comment_char="#"> + <columns>value, name, db_version, path</columns> + <file path="tool-data/amrfinderplus_versioned.loc.sample" /> </table> </tables> |
| b |
| diff -r 1920244e2895 -r 7844dbe4f8e2 tool_data_table_conf.xml.test --- a/tool_data_table_conf.xml.test Tue Oct 31 14:47:37 2023 +0000 +++ b/tool_data_table_conf.xml.test Thu May 30 13:07:03 2024 +0000 |
| b |
| @@ -1,7 +1,7 @@ <?xml version="1.0"?> <tables> - <table name="amrfinderplus_database" comment_char="#"> - <columns>value, name, path</columns> - <file path="${__HERE__}/test-data/amrfinderplus_database.loc" /> + <table name="amrfinderplus_versioned_database" comment_char="#"> + <columns>value, name, db_version, path</columns> + <file path="${__HERE__}/test-data/amrfinderplus_versioned.loc" /> </table> </tables> |