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/escherichia__amr/__init__.py
kleborate/modules/escherichia__amr/escherichia__amr.py
kleborate/modules/escherichia__cgmlst/__init__.py
kleborate/modules/escherichia__cgmlst/escherichia__cgmlst.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__kaptive/__init__.py
kleborate/modules/escherichia__kaptive/escherichia__kaptive.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/data/ShigaPass.sh
kleborate/modules/escherichia__pathovar/data/shigella_serotype_markers.txt
kleborate/modules/escherichia__pathovar/data/virulence_ecoli.fsa
kleborate/modules/escherichia__pathovar/data/ShigaPass_DataBases/RFB_hits_count.csv
kleborate/modules/escherichia__pathovar/data/ShigaPass_DataBases/ST_profiles.txt
kleborate/modules/escherichia__pathovar/data/ShigaPass_DataBases/ShigaPass_meta_profiles_v5.csv
kleborate/modules/escherichia__pathovar/data/ShigaPass_DataBases/CRISPR/CRISPR_spacers.fasta
kleborate/modules/escherichia__pathovar/data/ShigaPass_DataBases/CRISPR/CRISPR_spacers.fasta.njs
kleborate/modules/escherichia__pathovar/data/ShigaPass_DataBases/FLIC/fliC_Shigella_v1.fasta
kleborate/modules/escherichia__pathovar/data/ShigaPass_DataBases/FLIC/fliC_Shigella_v1.fasta.njs
kleborate/modules/escherichia__pathovar/data/ShigaPass_DataBases/IPAH/ipaH_150-mers.fasta
kleborate/modules/escherichia__pathovar/data/ShigaPass_DataBases/IPAH/ipaH_150-mers.fasta.njs
kleborate/modules/escherichia__pathovar/data/ShigaPass_DataBases/MLST/ST_profiles.txt
kleborate/modules/escherichia__pathovar/data/ShigaPass_DataBases/MLST/adk_len.fasta
kleborate/modules/escherichia__pathovar/data/ShigaPass_DataBases/MLST/adk_len.fasta.njs
kleborate/modules/escherichia__pathovar/data/ShigaPass_DataBases/MLST/fumC_len.fasta
kleborate/modules/escherichia__pathovar/data/ShigaPass_DataBases/MLST/fumC_len.fasta.njs
kleborate/modules/escherichia__pathovar/data/ShigaPass_DataBases/MLST/gyrB_len.fasta
kleborate/modules/escherichia__pathovar/data/ShigaPass_DataBases/MLST/gyrB_len.fasta.njs
kleborate/modules/escherichia__pathovar/data/ShigaPass_DataBases/MLST/icd_len.fasta
kleborate/modules/escherichia__pathovar/data/ShigaPass_DataBases/MLST/icd_len.fasta.njs
kleborate/modules/escherichia__pathovar/data/ShigaPass_DataBases/MLST/mdh_len.fasta
kleborate/modules/escherichia__pathovar/data/ShigaPass_DataBases/MLST/mdh_len.fasta.njs
kleborate/modules/escherichia__pathovar/data/ShigaPass_DataBases/MLST/purA_len.fasta
kleborate/modules/escherichia__pathovar/data/ShigaPass_DataBases/MLST/purA_len.fasta.njs
kleborate/modules/escherichia__pathovar/data/ShigaPass_DataBases/MLST/recA_len.fasta
kleborate/modules/escherichia__pathovar/data/ShigaPass_DataBases/MLST/recA_len.fasta.njs
kleborate/modules/escherichia__pathovar/data/ShigaPass_DataBases/RFB/POAC-genes_150-mers.fasta
kleborate/modules/escherichia__pathovar/data/ShigaPass_DataBases/RFB/POAC-genes_150-mers.fasta.njs
kleborate/modules/escherichia__pathovar/data/ShigaPass_DataBases/RFB/RFB_A16_150-mers_v2.fasta
kleborate/modules/escherichia__pathovar/data/ShigaPass_DataBases/RFB/RFB_A16_150-mers_v2.fasta.njs
kleborate/modules/escherichia__pathovar/data/ShigaPass_DataBases/RFB/RFB_AprovBEDP02-5104_150-mers.fasta
kleborate/modules/escherichia__pathovar/data/ShigaPass_DataBases/RFB/RFB_AprovBEDP02-5104_150-mers.fasta.njs
kleborate/modules/escherichia__pathovar/data/ShigaPass_DataBases/RFB/RFB_serogroup_D_150-mers.fasta
kleborate/modules/escherichia__pathovar/data/ShigaPass_DataBases/RFB/RFB_serogroup_D_150-mers.fasta.njs
kleborate/modules/escherichia__pathovar/data/ShigaPass_DataBases/RFB/RFB_serotypes_AtoC_150-mers_v2.fasta
kleborate/modules/escherichia__pathovar/data/ShigaPass_DataBases/RFB/RFB_serotypes_AtoC_150-mers_v2.fasta.njs
kleborate/modules/escherichia__pathovar/data/ShigaPass_DataBases/RFB/galF_SB1.fasta
kleborate/modules/escherichia__pathovar/data/ShigaPass_DataBases/RFB/galF_SB1.fasta.njs
kleborate/modules/escherichia__pathovar/data/ShigaPass_DataBases/RFB/taurine_SB6.fasta
kleborate/modules/escherichia__pathovar/data/ShigaPass_DataBases/RFB/taurine_SB6.fasta.njs
kleborate/modules/escherichia__pks/__init__.py
kleborate/modules/escherichia__pks/escherichia__pks.py
kleborate/modules/escherichia__pks/data/clbB.fasta
kleborate/modules/escherichia__stxtyper/__init__.py
kleborate/modules/escherichia__stxtyper/escherichia__stxtyper.py
kleborate/modules/escherichia__vfdb/__init__.py
kleborate/modules/escherichia__vfdb/escherichia__vfdb.py
kleborate/modules/escherichia__vfdb/vfdb.py
kleborate/modules/escherichia__vfdb/data/notes.txt
kleborate/modules/escherichia__vfdb/data/virulence_ecoli.fsa
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/general__species/__init__.py
kleborate/modules/general__species/general__species.py
kleborate/modules/general__species/test_general__species.py
kleborate/modules/general__species/data/species_mash_sketches.msh
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__peg-344/__init__.py
kleborate/modules/klebsiella__peg-344/klebsiella__peg-344.py
kleborate/modules/klebsiella__peg-344/data/peg-344.fasta
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/rmpADC_calling.py
kleborate/modules/klebsiella__rmst/test_klebsiella__rmst.py
kleborate/modules/klebsiella__rmst/data/argR.fasta
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/rmpA_polyG_status.txt
kleborate/modules/klebsiella__rmst/data/rmpC.fasta
kleborate/modules/klebsiella__rmst/data/rmpC_polyG_status.txt
kleborate/modules/klebsiella__rmst/data/rmpD.fasta
kleborate/modules/klebsiella__rmst/data/rmpD_polyA_status.txt
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/kosc__kaptive/__init__.py
kleborate/modules/kosc__kaptive/kosc__kaptive.py
kleborate/modules/kosc__kaptive/data/KoSC_K_locus_database.gbk
kleborate/modules/kosc__kaptive/data/KoSC_O_locus_database.gbk
kleborate/modules/kosc__mlst/__init__.py
kleborate/modules/kosc__mlst/kosc__mlst.py
kleborate/modules/kosc__mlst/test_kosc__mlst.py
kleborate/modules/kosc__mlst/data/download.sh
kleborate/modules/kosc__mlst/data/gapA.fasta
kleborate/modules/kosc__mlst/data/infB.fasta
kleborate/modules/kosc__mlst/data/mdh.fasta
kleborate/modules/kosc__mlst/data/pgi.fasta
kleborate/modules/kosc__mlst/data/phoE.fasta
kleborate/modules/kosc__mlst/data/profiles.tsv
kleborate/modules/kosc__mlst/data/rpoB.fasta
kleborate/modules/kosc__mlst/data/tonB.fasta
kleborate/modules/kpsc__amr/__init__.py
kleborate/modules/kpsc__amr/col_mutations.py
kleborate/modules/kpsc__amr/kpsc__amr.py
kleborate/modules/kpsc__amr/omp_mutations.py
kleborate/modules/kpsc__amr/qrdr_mutations.py
kleborate/modules/kpsc__amr/shv_mutations.py
kleborate/modules/kpsc__amr/data/Kleborate_AMRdb_v3.3.csv
kleborate/modules/kpsc__amr/data/Kleborate_AMRdb_v3.3.fasta
kleborate/modules/kpsc__amr/data/Kleborate_classes.csv
kleborate/modules/kpsc__amr/data/MgrB_and_PmrB.fasta
kleborate/modules/kpsc__amr/data/OmpK.fasta
kleborate/modules/kpsc__amr/data/QRDR_120.fasta
kleborate/modules/kpsc__amr/test/test_mgrb_pmrb_klebsiella_pneumo_complex__amr.py
kleborate/modules/kpsc__amr/test/test_omp_klebsiella_pneumo_complex__amr.py
kleborate/modules/kpsc__amr/test/test_qrdr_klebsiella_pneumo_complex__amr.py
kleborate/modules/kpsc__amr/test/test_res_aac_klebsiella_pneumo_complex__amr.py
kleborate/modules/kpsc__amr/test/test_shv_klebsiella_pneumo_complex__amr.py
kleborate/modules/kpsc__amr/test/test_tem_klebsiella_pneumo_complex__amr.py
kleborate/modules/kpsc__cgmlst/__init__.py
kleborate/modules/kpsc__cgmlst/kpsc__cgmlst.py
kleborate/modules/kpsc__cgmlst/data/mist_to_partial_lincode.py
kleborate/modules/kpsc__cipro_prediction/__init__.py
kleborate/modules/kpsc__cipro_prediction/kpsc__cipro_prediction.py
kleborate/modules/kpsc__kaptive/__init__.py
kleborate/modules/kpsc__kaptive/kpsc__kaptive.py
kleborate/modules/kpsc__mlst/__init__.py
kleborate/modules/kpsc__mlst/kpsc__mlst.py
kleborate/modules/kpsc__mlst/test_kpsc__mlst.py
kleborate/modules/kpsc__mlst/data/download.sh
kleborate/modules/kpsc__mlst/data/gapA.fasta
kleborate/modules/kpsc__mlst/data/infB.fasta
kleborate/modules/kpsc__mlst/data/mdh.fasta
kleborate/modules/kpsc__mlst/data/pgi.fasta
kleborate/modules/kpsc__mlst/data/phoE.fasta
kleborate/modules/kpsc__mlst/data/profiles.tsv
kleborate/modules/kpsc__mlst/data/rpoB.fasta
kleborate/modules/kpsc__mlst/data/tonB.fasta
kleborate/modules/kpsc__mrk/kpsc__mrk.py
kleborate/modules/kpsc__mrk/data/mrkA.fasta
kleborate/modules/kpsc__mrk/data/mrkB.fasta
kleborate/modules/kpsc__mrk/data/mrkC.fasta
kleborate/modules/kpsc__mrk/data/mrkD.fasta
kleborate/modules/kpsc__mrk/data/mrkF.fasta
kleborate/modules/kpsc__mrk/data/mrkH.fasta
kleborate/modules/kpsc__mrk/data/mrkI.fasta
kleborate/modules/kpsc__mrk/data/mrkJ.fasta
kleborate/modules/kpsc__mrk/data/profiles.tsv
kleborate/modules/kpsc__resistance_class_count/__init__.py
kleborate/modules/kpsc__resistance_class_count/kpsc__resistance_class_count.py
kleborate/modules/kpsc__resistance_gene_count/__init__.py
kleborate/modules/kpsc__resistance_gene_count/kpsc__resistance_gene_count.py
kleborate/modules/kpsc__resistance_score/__init__.py
kleborate/modules/kpsc__resistance_score/kpsc__resistance_score.py
kleborate/modules/kpsc__virulence_score/__init__.py
kleborate/modules/kpsc__virulence_score/kpsc__virulence_score.py
kleborate/modules/kpsc__virulence_score/test_kpsc__virulence_score.py
kleborate/modules/kpsc__wzi/__init__.py
kleborate/modules/kpsc__wzi/kpsc__wzi.py
kleborate/modules/kpsc__wzi/wzi.py
kleborate/modules/kpsc__wzi/data/wzi.fasta
kleborate/modules/kpsc__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/setup_cgmlst.py
kleborate/shared/setup_ecoli_cgmlst.py
kleborate/shared/setup_mlst.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