LICENSE
README.md
pyproject.toml
kleborate/__init__.py
kleborate/__main__.py
kleborate/version.py
kleborate.egg-info/PKG-INFO
kleborate.egg-info/SOURCES.txt
kleborate.egg-info/dependency_links.txt
kleborate.egg-info/entry_points.txt
kleborate.egg-info/requires.txt
kleborate.egg-info/top_level.txt
kleborate/modules/__init__.py
kleborate/modules/enterobacterales__species/__init__.py
kleborate/modules/enterobacterales__species/enterobacterales__species.py
kleborate/modules/enterobacterales__species/test_enterobacterales__species.py
kleborate/modules/enterobacterales__species/data/species_mash_sketches.msh
kleborate/modules/escherichia__amr/__init__.py
kleborate/modules/escherichia__amr/escherichia__amr.py
kleborate/modules/escherichia__ectyper/__init__.py
kleborate/modules/escherichia__ectyper/ectyper.py
kleborate/modules/escherichia__ectyper/escherichia__ectyper.py
kleborate/modules/escherichia__ectyper/data/ectyper_alleles_db.fasta
kleborate/modules/escherichia__ectyper/data/ectyper_alleles_db.json
kleborate/modules/escherichia__ezclermont/__init__.py
kleborate/modules/escherichia__ezclermont/escherichia__ezclermont.py
kleborate/modules/escherichia__mlst_achtman/__init__.py
kleborate/modules/escherichia__mlst_achtman/escherichia__mlst_achtman.py
kleborate/modules/escherichia__mlst_achtman/test_escherichia__mlst_achtman.py
kleborate/modules/escherichia__mlst_achtman/data/adk.fasta
kleborate/modules/escherichia__mlst_achtman/data/download.sh
kleborate/modules/escherichia__mlst_achtman/data/fumC.fasta
kleborate/modules/escherichia__mlst_achtman/data/gyrB.fasta
kleborate/modules/escherichia__mlst_achtman/data/icd.fasta
kleborate/modules/escherichia__mlst_achtman/data/mdh.fasta
kleborate/modules/escherichia__mlst_achtman/data/profiles.tsv
kleborate/modules/escherichia__mlst_achtman/data/purA.fasta
kleborate/modules/escherichia__mlst_achtman/data/recA.fasta
kleborate/modules/escherichia__mlst_lee/__init__.py
kleborate/modules/escherichia__mlst_lee/escherichia__mlst_lee.py
kleborate/modules/escherichia__mlst_lee/data/eae.fasta
kleborate/modules/escherichia__mlst_lee/data/espA.fasta
kleborate/modules/escherichia__mlst_lee/data/espB.fasta
kleborate/modules/escherichia__mlst_lee/data/espD.fasta
kleborate/modules/escherichia__mlst_lee/data/espH.fasta
kleborate/modules/escherichia__mlst_lee/data/espZ.fasta
kleborate/modules/escherichia__mlst_lee/data/profiles.tsv
kleborate/modules/escherichia__mlst_lee/data/tir.fasta
kleborate/modules/escherichia__mlst_pasteur/__init__.py
kleborate/modules/escherichia__mlst_pasteur/escherichia__mlst_pasteur.py
kleborate/modules/escherichia__mlst_pasteur/test_escherichia__mlst_pasteur.py
kleborate/modules/escherichia__mlst_pasteur/data/dinB.fasta
kleborate/modules/escherichia__mlst_pasteur/data/download.sh
kleborate/modules/escherichia__mlst_pasteur/data/icdA.fasta
kleborate/modules/escherichia__mlst_pasteur/data/pabB.fasta
kleborate/modules/escherichia__mlst_pasteur/data/polB.fasta
kleborate/modules/escherichia__mlst_pasteur/data/profiles.tsv
kleborate/modules/escherichia__mlst_pasteur/data/putP.fasta
kleborate/modules/escherichia__mlst_pasteur/data/trpA.fasta
kleborate/modules/escherichia__mlst_pasteur/data/trpB.fasta
kleborate/modules/escherichia__mlst_pasteur/data/uidA.fasta
kleborate/modules/escherichia__pathovar/__init__.py
kleborate/modules/escherichia__pathovar/escherichia__pathovar.py
kleborate/modules/escherichia__pathovar/pathovar.py
kleborate/modules/escherichia__pathovar/shigella__typing.py
kleborate/modules/escherichia__pathovar/shigella_classify.py
kleborate/modules/escherichia__pathovar/data/ShigellaRef5.fasta
kleborate/modules/escherichia__pathovar/data/shigella_serotype_markers.txt
kleborate/modules/escherichia__pathovar/data/virulence_ecoli.fsa
kleborate/modules/escherichia__stxtyper/__init__.py
kleborate/modules/escherichia__stxtyper/escherichia__stxtyper.py
kleborate/modules/general__contig_stats/__init__.py
kleborate/modules/general__contig_stats/general__contig_stats.py
kleborate/modules/general__contig_stats/test_general__contig_stats.py
kleborate/modules/general__contig_stats/data/species_specification.txt
kleborate/modules/klebsiella__abst/__init__.py
kleborate/modules/klebsiella__abst/klebsiella__abst.py
kleborate/modules/klebsiella__abst/test_klebsiella__abst.py
kleborate/modules/klebsiella__abst/data/download.sh
kleborate/modules/klebsiella__abst/data/iucA.fasta
kleborate/modules/klebsiella__abst/data/iucB.fasta
kleborate/modules/klebsiella__abst/data/iucC.fasta
kleborate/modules/klebsiella__abst/data/iucD.fasta
kleborate/modules/klebsiella__abst/data/iutA.fasta
kleborate/modules/klebsiella__abst/data/profiles.tsv
kleborate/modules/klebsiella__cbst/__init__.py
kleborate/modules/klebsiella__cbst/klebsiella__cbst.py
kleborate/modules/klebsiella__cbst/test_klebsiella__cbst.py
kleborate/modules/klebsiella__cbst/data/clbA.fasta
kleborate/modules/klebsiella__cbst/data/clbB.fasta
kleborate/modules/klebsiella__cbst/data/clbC.fasta
kleborate/modules/klebsiella__cbst/data/clbD.fasta
kleborate/modules/klebsiella__cbst/data/clbE.fasta
kleborate/modules/klebsiella__cbst/data/clbF.fasta
kleborate/modules/klebsiella__cbst/data/clbG.fasta
kleborate/modules/klebsiella__cbst/data/clbH.fasta
kleborate/modules/klebsiella__cbst/data/clbI.fasta
kleborate/modules/klebsiella__cbst/data/clbL.fasta
kleborate/modules/klebsiella__cbst/data/clbM.fasta
kleborate/modules/klebsiella__cbst/data/clbN.fasta
kleborate/modules/klebsiella__cbst/data/clbO.fasta
kleborate/modules/klebsiella__cbst/data/clbP.fasta
kleborate/modules/klebsiella__cbst/data/clbQ.fasta
kleborate/modules/klebsiella__cbst/data/download.sh
kleborate/modules/klebsiella__cbst/data/profiles.tsv
kleborate/modules/klebsiella__rmpa2/__init__.py
kleborate/modules/klebsiella__rmpa2/klebsiella__rmpa2.py
kleborate/modules/klebsiella__rmpa2/rmpa2.py
kleborate/modules/klebsiella__rmpa2/data/rmpA2.fasta
kleborate/modules/klebsiella__rmst/__init__.py
kleborate/modules/klebsiella__rmst/klebsiella__rmst.py
kleborate/modules/klebsiella__rmst/test_klebsiella__rmst.py
kleborate/modules/klebsiella__rmst/data/download.sh
kleborate/modules/klebsiella__rmst/data/profiles.tsv
kleborate/modules/klebsiella__rmst/data/rmpA.fasta
kleborate/modules/klebsiella__rmst/data/rmpC.fasta
kleborate/modules/klebsiella__rmst/data/rmpD.fasta
kleborate/modules/klebsiella__smst/__init__.py
kleborate/modules/klebsiella__smst/klebsiella__smst.py
kleborate/modules/klebsiella__smst/test_klebsiella__smst.py
kleborate/modules/klebsiella__smst/data/download.sh
kleborate/modules/klebsiella__smst/data/iroB.fasta
kleborate/modules/klebsiella__smst/data/iroC.fasta
kleborate/modules/klebsiella__smst/data/iroD.fasta
kleborate/modules/klebsiella__smst/data/iroN.fasta
kleborate/modules/klebsiella__smst/data/profiles.tsv
kleborate/modules/klebsiella__ybst/__init__.py
kleborate/modules/klebsiella__ybst/klebsiella__ybst.py
kleborate/modules/klebsiella__ybst/test_klebsiella__ybst.py
kleborate/modules/klebsiella__ybst/data/download.sh
kleborate/modules/klebsiella__ybst/data/fyuA.fasta
kleborate/modules/klebsiella__ybst/data/irp1.fasta
kleborate/modules/klebsiella__ybst/data/irp2.fasta
kleborate/modules/klebsiella__ybst/data/profiles.tsv
kleborate/modules/klebsiella__ybst/data/ybtA.fasta
kleborate/modules/klebsiella__ybst/data/ybtE.fasta
kleborate/modules/klebsiella__ybst/data/ybtP.fasta
kleborate/modules/klebsiella__ybst/data/ybtQ.fasta
kleborate/modules/klebsiella__ybst/data/ybtS.fasta
kleborate/modules/klebsiella__ybst/data/ybtT.fasta
kleborate/modules/klebsiella__ybst/data/ybtU.fasta
kleborate/modules/klebsiella__ybst/data/ybtX.fasta
kleborate/modules/klebsiella_oxytoca_complex__mlst/__init__.py
kleborate/modules/klebsiella_oxytoca_complex__mlst/klebsiella_oxytoca_complex__mlst.py
kleborate/modules/klebsiella_oxytoca_complex__mlst/test_klebsiella_oxytoca_complex__mlst.py
kleborate/modules/klebsiella_oxytoca_complex__mlst/data/download.sh
kleborate/modules/klebsiella_oxytoca_complex__mlst/data/gapA.fasta
kleborate/modules/klebsiella_oxytoca_complex__mlst/data/infB.fasta
kleborate/modules/klebsiella_oxytoca_complex__mlst/data/mdh.fasta
kleborate/modules/klebsiella_oxytoca_complex__mlst/data/pgi.fasta
kleborate/modules/klebsiella_oxytoca_complex__mlst/data/phoE.fasta
kleborate/modules/klebsiella_oxytoca_complex__mlst/data/profiles.tsv
kleborate/modules/klebsiella_oxytoca_complex__mlst/data/rpoB.fasta
kleborate/modules/klebsiella_oxytoca_complex__mlst/data/tonB.fasta
kleborate/modules/klebsiella_pneumo_complex__amr/__init__.py
kleborate/modules/klebsiella_pneumo_complex__amr/col_mutations.py
kleborate/modules/klebsiella_pneumo_complex__amr/klebsiella_pneumo_complex__amr.py
kleborate/modules/klebsiella_pneumo_complex__amr/omp_mutations.py
kleborate/modules/klebsiella_pneumo_complex__amr/qrdr_mutations.py
kleborate/modules/klebsiella_pneumo_complex__amr/shv_mutations.py
kleborate/modules/klebsiella_pneumo_complex__amr/data/CARD_AMR_clustered.csv
kleborate/modules/klebsiella_pneumo_complex__amr/data/CARD_v3.2.9.fasta
kleborate/modules/klebsiella_pneumo_complex__amr/data/Kleborate_classes.csv
kleborate/modules/klebsiella_pneumo_complex__amr/data/MgrB_and_PmrB.fasta
kleborate/modules/klebsiella_pneumo_complex__amr/data/OmpK.fasta
kleborate/modules/klebsiella_pneumo_complex__amr/data/QRDR_120.fasta
kleborate/modules/klebsiella_pneumo_complex__amr/test/test_mgrb_pmrb_klebsiella_pneumo_complex__amr.py
kleborate/modules/klebsiella_pneumo_complex__amr/test/test_omp_klebsiella_pneumo_complex__amr.py
kleborate/modules/klebsiella_pneumo_complex__amr/test/test_qrdr_klebsiella_pneumo_complex__amr.py
kleborate/modules/klebsiella_pneumo_complex__amr/test/test_res_aac_klebsiella_pneumo_complex__amr.py
kleborate/modules/klebsiella_pneumo_complex__amr/test/test_shv_klebsiella_pneumo_complex__amr.py
kleborate/modules/klebsiella_pneumo_complex__amr/test/test_tem_klebsiella_pneumo_complex__amr.py
kleborate/modules/klebsiella_pneumo_complex__cipro_prediction/__init__.py
kleborate/modules/klebsiella_pneumo_complex__cipro_prediction/klebsiella_pneumo_complex__cipro_prediction.py
kleborate/modules/klebsiella_pneumo_complex__kaptive/__init__.py
kleborate/modules/klebsiella_pneumo_complex__kaptive/klebsiella_pneumo_complex__kaptive.py
kleborate/modules/klebsiella_pneumo_complex__mlst/__init__.py
kleborate/modules/klebsiella_pneumo_complex__mlst/klebsiella_pneumo_complex__mlst.py
kleborate/modules/klebsiella_pneumo_complex__mlst/test_klebsiella_pneumo_complex__mlst.py
kleborate/modules/klebsiella_pneumo_complex__mlst/data/download.sh
kleborate/modules/klebsiella_pneumo_complex__mlst/data/gapA.fasta
kleborate/modules/klebsiella_pneumo_complex__mlst/data/infB.fasta
kleborate/modules/klebsiella_pneumo_complex__mlst/data/mdh.fasta
kleborate/modules/klebsiella_pneumo_complex__mlst/data/pgi.fasta
kleborate/modules/klebsiella_pneumo_complex__mlst/data/phoE.fasta
kleborate/modules/klebsiella_pneumo_complex__mlst/data/profiles.tsv
kleborate/modules/klebsiella_pneumo_complex__mlst/data/rpoB.fasta
kleborate/modules/klebsiella_pneumo_complex__mlst/data/tonB.fasta
kleborate/modules/klebsiella_pneumo_complex__resistance_class_count/__init__.py
kleborate/modules/klebsiella_pneumo_complex__resistance_class_count/klebsiella_pneumo_complex__resistance_class_count.py
kleborate/modules/klebsiella_pneumo_complex__resistance_gene_count/__init__.py
kleborate/modules/klebsiella_pneumo_complex__resistance_gene_count/klebsiella_pneumo_complex__resistance_gene_count.py
kleborate/modules/klebsiella_pneumo_complex__resistance_score/__init__.py
kleborate/modules/klebsiella_pneumo_complex__resistance_score/klebsiella_pneumo_complex__resistance_score.py
kleborate/modules/klebsiella_pneumo_complex__virulence_score/__init__.py
kleborate/modules/klebsiella_pneumo_complex__virulence_score/klebsiella_pneumo_complex__virulence_score.py
kleborate/modules/klebsiella_pneumo_complex__virulence_score/test_klebsiella_pneumo_complex__virulence_score.py
kleborate/modules/klebsiella_pneumo_complex__wzi/__init__.py
kleborate/modules/klebsiella_pneumo_complex__wzi/klebsiella_pneumo_complex__wzi.py
kleborate/modules/klebsiella_pneumo_complex__wzi/wzi.py
kleborate/modules/klebsiella_pneumo_complex__wzi/data/wzi.fasta
kleborate/modules/klebsiella_pneumo_complex__wzi/data/wzi.txt
kleborate/shared/__init__.py
kleborate/shared/alignment.py
kleborate/shared/help_formatter.py
kleborate/shared/misc.py
kleborate/shared/mlst.py
kleborate/shared/multi_mlst.py
kleborate/shared/resMinimap.py
kleborate/shared/species_defs.py
kleborate/shared/trim_headers.py
test/test_alignment.py
test/test_main.py
test/test_misc.py
test/test_mlst.py
test/test_modules.py
test/test_multi_mlst.py