LICENSE
MANIFEST.in
NOTICE
README.md
setup.cfg
setup.py
bin/staramr
staramr/SubCommand.py
staramr/Utils.py
staramr/__init__.py
staramr.egg-info/PKG-INFO
staramr.egg-info/SOURCES.txt
staramr.egg-info/dependency_links.txt
staramr.egg-info/requires.txt
staramr.egg-info/top_level.txt
staramr/blast/AbstractBlastDatabase.py
staramr/blast/BlastHandler.py
staramr/blast/__init__.py
staramr/blast/plasmidfinder/PlasmidfinderBlastDatabase.py
staramr/blast/plasmidfinder/__init__.py
staramr/blast/pointfinder/PointfinderBlastDatabase.py
staramr/blast/pointfinder/PointfinderDatabaseInfo.py
staramr/blast/pointfinder/__init__.py
staramr/blast/resfinder/ResfinderBlastDatabase.py
staramr/blast/resfinder/__init__.py
staramr/blast/results/AMRHitHSP.py
staramr/blast/results/BlastHitPartitions.py
staramr/blast/results/BlastResultsParser.py
staramr/blast/results/__init__.py
staramr/blast/results/plasmidfinder/BlastResultsParserPlasmidfinder.py
staramr/blast/results/plasmidfinder/BlastResultsParserPlasmidfinderResistance.py
staramr/blast/results/plasmidfinder/PlasmidfinderHitHSP.py
staramr/blast/results/plasmidfinder/__init__.py
staramr/blast/results/pointfinder/BlastResultsParserPointfinder.py
staramr/blast/results/pointfinder/BlastResultsParserPointfinderResistance.py
staramr/blast/results/pointfinder/MutationPosition.py
staramr/blast/results/pointfinder/PointfinderHitHSP.py
staramr/blast/results/pointfinder/__init__.py
staramr/blast/results/pointfinder/codon/CodonMutationPosition.py
staramr/blast/results/pointfinder/codon/__init__.py
staramr/blast/results/pointfinder/nucleotide/NucleotideMutationPosition.py
staramr/blast/results/pointfinder/nucleotide/PointfinderHitHSPRNA.py
staramr/blast/results/pointfinder/nucleotide/__init__.py
staramr/blast/results/resfinder/BlastResultsParserResfinder.py
staramr/blast/results/resfinder/BlastResultsParserResfinderResistance.py
staramr/blast/results/resfinder/ResfinderHitHSP.py
staramr/blast/results/resfinder/__init__.py
staramr/databases/AMRDatabasesManager.py
staramr/databases/BlastDatabaseRepositories.py
staramr/databases/BlastDatabaseRepository.py
staramr/databases/__init__.py
staramr/databases/data/dist/plasmidfinder-info.ini
staramr/databases/data/dist/pointfinder-info.ini
staramr/databases/data/dist/resfinder-info.ini
staramr/databases/data/dist/plasmidfinder/.gitignore
staramr/databases/data/dist/plasmidfinder/INSTALL.py
staramr/databases/data/dist/plasmidfinder/config
staramr/databases/data/dist/plasmidfinder/enterobacteriaceae.fsa
staramr/databases/data/dist/plasmidfinder/gram_positive.fsa
staramr/databases/data/dist/pointfinder/.gitignore
staramr/databases/data/dist/pointfinder/config
staramr/databases/data/dist/pointfinder/campylobacter/23S.fsa
staramr/databases/data/dist/pointfinder/campylobacter/L22.fsa
staramr/databases/data/dist/pointfinder/campylobacter/RNA_genes.txt
staramr/databases/data/dist/pointfinder/campylobacter/cmeR.fsa
staramr/databases/data/dist/pointfinder/campylobacter/genes.txt
staramr/databases/data/dist/pointfinder/campylobacter/gyrA.fsa
staramr/databases/data/dist/pointfinder/campylobacter/resistens-overview.txt
staramr/databases/data/dist/pointfinder/campylobacter/rpsL.fsa
staramr/databases/data/dist/pointfinder/e.coli/16S_rrsB.fsa
staramr/databases/data/dist/pointfinder/e.coli/16S_rrsC.fsa
staramr/databases/data/dist/pointfinder/e.coli/16S_rrsH.fsa
staramr/databases/data/dist/pointfinder/e.coli/23S.fsa
staramr/databases/data/dist/pointfinder/e.coli/RNA_genes.txt
staramr/databases/data/dist/pointfinder/e.coli/ampC_promoter_size_53bp.fsa
staramr/databases/data/dist/pointfinder/e.coli/folP.fsa
staramr/databases/data/dist/pointfinder/e.coli/genes.txt
staramr/databases/data/dist/pointfinder/e.coli/gyrA.fsa
staramr/databases/data/dist/pointfinder/e.coli/gyrB.fsa
staramr/databases/data/dist/pointfinder/e.coli/parC.fsa
staramr/databases/data/dist/pointfinder/e.coli/parE.fsa
staramr/databases/data/dist/pointfinder/e.coli/pmrA.fsa
staramr/databases/data/dist/pointfinder/e.coli/pmrB.fsa
staramr/databases/data/dist/pointfinder/e.coli/resistens-overview.txt
staramr/databases/data/dist/pointfinder/e.coli/rpoB.fsa
staramr/databases/data/dist/pointfinder/gonorrhoeae/16S_rRNA.fsa
staramr/databases/data/dist/pointfinder/gonorrhoeae/23S_rRNA.fsa
staramr/databases/data/dist/pointfinder/gonorrhoeae/RNA_genes.txt
staramr/databases/data/dist/pointfinder/gonorrhoeae/genes.txt
staramr/databases/data/dist/pointfinder/gonorrhoeae/gyrA.fsa
staramr/databases/data/dist/pointfinder/gonorrhoeae/macAB_pro.fsa
staramr/databases/data/dist/pointfinder/gonorrhoeae/macAB_promoter_size_225bp.fsa
staramr/databases/data/dist/pointfinder/gonorrhoeae/mtrC_promoter_size_174bp.fsa
staramr/databases/data/dist/pointfinder/gonorrhoeae/mtrR.fsa
staramr/databases/data/dist/pointfinder/gonorrhoeae/mtrR_locus.fsa
staramr/databases/data/dist/pointfinder/gonorrhoeae/mtrR_promoter_size_66bp.fsa
staramr/databases/data/dist/pointfinder/gonorrhoeae/mtr_locus_promoter_size_76bp.fsa
staramr/databases/data/dist/pointfinder/gonorrhoeae/mutation_notes.txt
staramr/databases/data/dist/pointfinder/gonorrhoeae/parC.fsa
staramr/databases/data/dist/pointfinder/gonorrhoeae/penA.fsa
staramr/databases/data/dist/pointfinder/gonorrhoeae/pilQ.fsa
staramr/databases/data/dist/pointfinder/gonorrhoeae/ponA.fsa
staramr/databases/data/dist/pointfinder/gonorrhoeae/porB.fsa
staramr/databases/data/dist/pointfinder/gonorrhoeae/resistens-overview.txt
staramr/databases/data/dist/pointfinder/gonorrhoeae/rpsE.fsa
staramr/databases/data/dist/pointfinder/gonorrhoeae/rpsJ.fsa
staramr/databases/data/dist/pointfinder/salmonella/16S_rrsD.fsa
staramr/databases/data/dist/pointfinder/salmonella/23S.fsa
staramr/databases/data/dist/pointfinder/salmonella/RNA_genes.txt
staramr/databases/data/dist/pointfinder/salmonella/genes.txt
staramr/databases/data/dist/pointfinder/salmonella/gyrA.fsa
staramr/databases/data/dist/pointfinder/salmonella/gyrB.fsa
staramr/databases/data/dist/pointfinder/salmonella/parC.fsa
staramr/databases/data/dist/pointfinder/salmonella/parE.fsa
staramr/databases/data/dist/pointfinder/salmonella/pmrA.fsa
staramr/databases/data/dist/pointfinder/salmonella/pmrB.fsa
staramr/databases/data/dist/pointfinder/salmonella/resistens-overview.txt
staramr/databases/data/dist/pointfinder/tuberculosis/RNA_genes.txt
staramr/databases/data/dist/pointfinder/tuberculosis/Rv0678.fsa
staramr/databases/data/dist/pointfinder/tuberculosis/ahpC_promoter_size_180bp.fsa
staramr/databases/data/dist/pointfinder/tuberculosis/eis_promoter_size_119bp.fsa
staramr/databases/data/dist/pointfinder/tuberculosis/embA_promoter_size_115bp.fsa
staramr/databases/data/dist/pointfinder/tuberculosis/embB.fsa
staramr/databases/data/dist/pointfinder/tuberculosis/embC.fsa
staramr/databases/data/dist/pointfinder/tuberculosis/embR.fsa
staramr/databases/data/dist/pointfinder/tuberculosis/ethA.fsa
staramr/databases/data/dist/pointfinder/tuberculosis/ethR.fsa
staramr/databases/data/dist/pointfinder/tuberculosis/fabG1_promoter_size_223bp.fsa
staramr/databases/data/dist/pointfinder/tuberculosis/folC.fsa
staramr/databases/data/dist/pointfinder/tuberculosis/genes.txt
staramr/databases/data/dist/pointfinder/tuberculosis/gyrA.fsa
staramr/databases/data/dist/pointfinder/tuberculosis/gyrB.fsa
staramr/databases/data/dist/pointfinder/tuberculosis/inhA.fsa
staramr/databases/data/dist/pointfinder/tuberculosis/kasA.fsa
staramr/databases/data/dist/pointfinder/tuberculosis/katG_promoter_size_107bp.fsa
staramr/databases/data/dist/pointfinder/tuberculosis/panD.fsa
staramr/databases/data/dist/pointfinder/tuberculosis/pncA_promoter_size_107bp.fsa
staramr/databases/data/dist/pointfinder/tuberculosis/resistens-overview.txt
staramr/databases/data/dist/pointfinder/tuberculosis/ribD.fsa
staramr/databases/data/dist/pointfinder/tuberculosis/rplC.fsa
staramr/databases/data/dist/pointfinder/tuberculosis/rpoB.fsa
staramr/databases/data/dist/pointfinder/tuberculosis/rpoC.fsa
staramr/databases/data/dist/pointfinder/tuberculosis/rpsA.fsa
staramr/databases/data/dist/pointfinder/tuberculosis/rpsL.fsa
staramr/databases/data/dist/pointfinder/tuberculosis/rrs.fsa
staramr/databases/data/dist/pointfinder/tuberculosis/thyA.fsa
staramr/databases/data/dist/pointfinder/tuberculosis/tlyA.fsa
staramr/databases/data/dist/resfinder/README.md
staramr/databases/data/dist/resfinder/aminoglycoside.fsa
staramr/databases/data/dist/resfinder/beta-lactam.fsa
staramr/databases/data/dist/resfinder/colistin.fsa
staramr/databases/data/dist/resfinder/config
staramr/databases/data/dist/resfinder/fosfomycin.fsa
staramr/databases/data/dist/resfinder/fusidicacid.fsa
staramr/databases/data/dist/resfinder/glycopeptide.fsa
staramr/databases/data/dist/resfinder/macrolide.fsa
staramr/databases/data/dist/resfinder/nitroimidazole.fsa
staramr/databases/data/dist/resfinder/notes.txt
staramr/databases/data/dist/resfinder/oxazolidinone.fsa
staramr/databases/data/dist/resfinder/phenicol.fsa
staramr/databases/data/dist/resfinder/quinolone.fsa
staramr/databases/data/dist/resfinder/rifampicin.fsa
staramr/databases/data/dist/resfinder/sulphonamide.fsa
staramr/databases/data/dist/resfinder/tetracycline.fsa
staramr/databases/data/dist/resfinder/trimethoprim.fsa
staramr/databases/exclude/ExcludeGenesList.py
staramr/databases/exclude/__init__.py
staramr/databases/exclude/data/genes_to_exclude.tsv
staramr/databases/resistance/ARGDrugTable.py
staramr/databases/resistance/__init__.py
staramr/databases/resistance/data/ARG_drug_key_pointfinder.tsv
staramr/databases/resistance/data/ARG_drug_key_resfinder.tsv
staramr/databases/resistance/data/info.ini
staramr/databases/resistance/pointfinder/ARGDrugTablePointfinder.py
staramr/databases/resistance/pointfinder/__init__.py
staramr/databases/resistance/resfinder/ARGDrugTableResfinder.py
staramr/databases/resistance/resfinder/__init__.py
staramr/detection/AMRDetection.py
staramr/detection/AMRDetectionFactory.py
staramr/detection/AMRDetectionResistance.py
staramr/detection/__init__.py
staramr/exceptions/BlastProcessError.py
staramr/exceptions/CommandParseException.py
staramr/exceptions/DatabaseErrorException.py
staramr/exceptions/DatabaseNotFoundException.py
staramr/exceptions/InvalidPositionException.py
staramr/exceptions/__init__.py
staramr/results/AMRDetectionSummary.py
staramr/results/AMRDetectionSummaryResistance.py
staramr/results/__init__.py
staramr/subcommand/Database.py
staramr/subcommand/Search.py
staramr/subcommand/__init__.py
staramr/tests/__init__.py
staramr/tests/integration/__init__.py
staramr/tests/integration/data/16S-rc_gyrA-rc_beta-lactam.fsa
staramr/tests/integration/data/16S_gyrA_beta-lactam.fsa
staramr/tests/integration/data/16S_rrsD-1T1065.fsa
staramr/tests/integration/data/23S-A2075G.fsa
staramr/tests/integration/data/beta-lactam-blaIMP-42-del-middle-rc.fsa
staramr/tests/integration/data/beta-lactam-blaIMP-42-del-middle.fsa
staramr/tests/integration/data/beta-lactam-blaIMP-42-del-start.fsa
staramr/tests/integration/data/beta-lactam-blaIMP-42-ins-middle.fsa
staramr/tests/integration/data/beta-lactam-blaIMP-42-ins-start.fsa
staramr/tests/integration/data/beta-lactam-blaIMP-42-mut-2-two-copies-one-rev-complement.fsa
staramr/tests/integration/data/beta-lactam-blaIMP-42-mut-2-two-copies.fsa
staramr/tests/integration/data/beta-lactam-blaIMP-42-mut-2.fsa
staramr/tests/integration/data/gyrA-A67P-del-end.fsa
staramr/tests/integration/data/gyrA-A67P-rc.fsa
staramr/tests/integration/data/gyrA-A67P.fsa
staramr/tests/integration/data/gyrA-A67T.fsa
staramr/tests/integration/data/gyrA-A70T.fsa
staramr/tests/integration/data/gyrA-S97N.fsa
staramr/tests/integration/data/non-match.fsa
staramr/tests/integration/data/resfinder_beta-lactam-blaIMP-42-del-middle.fsa
staramr/tests/integration/data/test-aminoglycoside.fsa
staramr/tests/integration/data/test-detailed-summary.fsa
staramr/tests/integration/data/test-index-range-plasmid.fsa
staramr/tests/integration/data/test-plasmids-seq.fsa
staramr/tests/integration/data/test-resistance-plasmid.fsa
staramr/tests/integration/data/test-seq-id.fsa
staramr/tests/integration/databases/__init__.py
staramr/tests/integration/databases/test_AMRDatabasesManager.py
staramr/tests/integration/databases/test_BlastDatabaseRepositories.py
staramr/tests/integration/detection/__init__.py
staramr/tests/integration/detection/test_AMRDetection.py
staramr/tests/integration/detection/test_AMRDetectionPlasmid.py
staramr/tests/unit/__init__.py
staramr/tests/unit/blast/__init__.py
staramr/tests/unit/blast/pointfinder/__init__.py
staramr/tests/unit/blast/pointfinder/test_PointfinderDatabaseInfo.py
staramr/tests/unit/blast/results/__init__.py
staramr/tests/unit/blast/results/test_BlastHitPartitions.py
staramr/tests/unit/blast/results/pointfinder/__init__.py
staramr/tests/unit/blast/results/pointfinder/test_PlasmidfinderHitHSP.py
staramr/tests/unit/blast/results/pointfinder/test_PointfinderHitHSP.py
staramr/tests/unit/blast/results/pointfinder/codon/__init__.py
staramr/tests/unit/blast/results/pointfinder/codon/test_CodonMutationPosition.py
staramr/tests/unit/blast/results/pointfinder/nucleotide/__init__.py
staramr/tests/unit/blast/results/pointfinder/nucleotide/test_NucleotideMutationPosition.py
staramr/tests/unit/results/__init__.py
staramr/tests/unit/results/test_AMRDetectionSummary.py
staramr/tests/unit/results/test_AMRDetectionSummaryResistance.py