LICENSE
MANIFEST.in
README.md
setup.py
abritamr/AmrSetup.py
abritamr/Collate.py
abritamr/CustomLog.py
abritamr/RunFinder.py
abritamr/Update.py
abritamr/__init__.py
abritamr/abritamr.py
abritamr/species_config.json
abritamr/version.py
abritamr.egg-info/PKG-INFO
abritamr.egg-info/SOURCES.txt
abritamr.egg-info/dependency_links.txt
abritamr.egg-info/entry_points.txt
abritamr.egg-info/not-zip-safe
abritamr.egg-info/requires.txt
abritamr.egg-info/top_level.txt
abritamr/control/GCA_00129350.fa
abritamr/control/GCA_001441225.fa
abritamr/control/GCA_001647755.fa
abritamr/control/GCA_001931555.fa
abritamr/control/contigs.fa
abritamr/db/refgenes_latest.csv
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR.LIB
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR.LIB.h3f
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR.LIB.h3i
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR.LIB.h3m
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR.LIB.h3p
abritamr/db/amrfinderplus/data/2026-05-15.1/AMRProt-mutation.tsv
abritamr/db/amrfinderplus/data/2026-05-15.1/AMRProt-suppress.tsv
abritamr/db/amrfinderplus/data/2026-05-15.1/AMRProt-susceptible.fa
abritamr/db/amrfinderplus/data/2026-05-15.1/AMRProt-susceptible.tsv
abritamr/db/amrfinderplus/data/2026-05-15.1/AMRProt.fa
abritamr/db/amrfinderplus/data/2026-05-15.1/AMRProt.fa.pdb
abritamr/db/amrfinderplus/data/2026-05-15.1/AMRProt.fa.phr
abritamr/db/amrfinderplus/data/2026-05-15.1/AMRProt.fa.pin
abritamr/db/amrfinderplus/data/2026-05-15.1/AMRProt.fa.pjs
abritamr/db/amrfinderplus/data/2026-05-15.1/AMRProt.fa.pot
abritamr/db/amrfinderplus/data/2026-05-15.1/AMRProt.fa.psq
abritamr/db/amrfinderplus/data/2026-05-15.1/AMRProt.fa.ptf
abritamr/db/amrfinderplus/data/2026-05-15.1/AMRProt.fa.pto
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_CDS.fa
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_CDS.fa.ndb
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_CDS.fa.nhr
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_CDS.fa.nin
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_CDS.fa.njs
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_CDS.fa.not
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_CDS.fa.nsq
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_CDS.fa.ntf
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_CDS.fa.nto
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Acinetobacter_baumannii.fa
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Acinetobacter_baumannii.fa.ndb
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Acinetobacter_baumannii.fa.nhr
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Acinetobacter_baumannii.fa.nin
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Acinetobacter_baumannii.fa.njs
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Acinetobacter_baumannii.fa.not
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Acinetobacter_baumannii.fa.nsq
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Acinetobacter_baumannii.fa.ntf
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Acinetobacter_baumannii.fa.nto
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Acinetobacter_baumannii.tsv
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Bordetella_pertussis.fa
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Bordetella_pertussis.fa.ndb
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Bordetella_pertussis.fa.nhr
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Bordetella_pertussis.fa.nin
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Bordetella_pertussis.fa.njs
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Bordetella_pertussis.fa.not
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Bordetella_pertussis.fa.nsq
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Bordetella_pertussis.fa.ntf
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Bordetella_pertussis.fa.nto
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Bordetella_pertussis.tsv
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Campylobacter.fa
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Campylobacter.fa.ndb
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Campylobacter.fa.nhr
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Campylobacter.fa.nin
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Campylobacter.fa.njs
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Campylobacter.fa.not
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Campylobacter.fa.nsq
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Campylobacter.fa.ntf
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Campylobacter.fa.nto
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Campylobacter.tsv
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Clostridioides_difficile.fa
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Clostridioides_difficile.fa.ndb
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Clostridioides_difficile.fa.nhr
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Clostridioides_difficile.fa.nin
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Clostridioides_difficile.fa.njs
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Clostridioides_difficile.fa.not
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Clostridioides_difficile.fa.nsq
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Clostridioides_difficile.fa.ntf
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Clostridioides_difficile.fa.nto
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Clostridioides_difficile.tsv
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Enterococcus_faecalis.fa
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Enterococcus_faecalis.fa.ndb
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Enterococcus_faecalis.fa.nhr
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Enterococcus_faecalis.fa.nin
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Enterococcus_faecalis.fa.njs
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Enterococcus_faecalis.fa.not
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Enterococcus_faecalis.fa.nsq
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Enterococcus_faecalis.fa.ntf
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Enterococcus_faecalis.fa.nto
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Enterococcus_faecalis.tsv
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Enterococcus_faecium.fa
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Enterococcus_faecium.fa.ndb
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Enterococcus_faecium.fa.nhr
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Enterococcus_faecium.fa.nin
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Enterococcus_faecium.fa.njs
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Enterococcus_faecium.fa.not
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Enterococcus_faecium.fa.nsq
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Enterococcus_faecium.fa.ntf
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Enterococcus_faecium.fa.nto
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Enterococcus_faecium.tsv
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Escherichia.fa
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Escherichia.fa.ndb
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Escherichia.fa.nhr
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Escherichia.fa.nin
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Escherichia.fa.njs
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Escherichia.fa.not
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Escherichia.fa.nsq
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Escherichia.fa.ntf
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Escherichia.fa.nto
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Escherichia.tsv
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Klebsiella_oxytoca.fa
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Klebsiella_oxytoca.fa.ndb
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Klebsiella_oxytoca.fa.nhr
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Klebsiella_oxytoca.fa.nin
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Klebsiella_oxytoca.fa.njs
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Klebsiella_oxytoca.fa.not
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Klebsiella_oxytoca.fa.nsq
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Klebsiella_oxytoca.fa.ntf
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Klebsiella_oxytoca.fa.nto
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Klebsiella_oxytoca.tsv
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Klebsiella_pneumoniae.fa
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Klebsiella_pneumoniae.fa.ndb
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Klebsiella_pneumoniae.fa.nhr
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Klebsiella_pneumoniae.fa.nin
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Klebsiella_pneumoniae.fa.njs
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Klebsiella_pneumoniae.fa.not
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Klebsiella_pneumoniae.fa.nsq
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Klebsiella_pneumoniae.fa.ntf
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Klebsiella_pneumoniae.fa.nto
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Klebsiella_pneumoniae.tsv
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Neisseria_gonorrhoeae.fa
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Neisseria_gonorrhoeae.fa.ndb
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Neisseria_gonorrhoeae.fa.nhr
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Neisseria_gonorrhoeae.fa.nin
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Neisseria_gonorrhoeae.fa.njs
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Neisseria_gonorrhoeae.fa.not
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Neisseria_gonorrhoeae.fa.nsq
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Neisseria_gonorrhoeae.fa.ntf
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Neisseria_gonorrhoeae.fa.nto
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Neisseria_gonorrhoeae.tsv
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Salmonella.fa
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Salmonella.fa.ndb
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Salmonella.fa.nhr
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Salmonella.fa.nin
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Salmonella.fa.njs
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Salmonella.fa.not
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Salmonella.fa.nsq
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Salmonella.fa.ntf
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Salmonella.fa.nto
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Salmonella.tsv
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Staphylococcus_aureus.fa
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Staphylococcus_aureus.fa.ndb
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Staphylococcus_aureus.fa.nhr
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Staphylococcus_aureus.fa.nin
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Staphylococcus_aureus.fa.njs
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Staphylococcus_aureus.fa.not
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Staphylococcus_aureus.fa.nsq
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Staphylococcus_aureus.fa.ntf
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Staphylococcus_aureus.fa.nto
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Staphylococcus_aureus.tsv
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Streptococcus_pneumoniae.fa
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Streptococcus_pneumoniae.fa.ndb
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Streptococcus_pneumoniae.fa.nhr
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Streptococcus_pneumoniae.fa.nin
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Streptococcus_pneumoniae.fa.njs
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Streptococcus_pneumoniae.fa.not
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Streptococcus_pneumoniae.fa.nsq
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Streptococcus_pneumoniae.fa.ntf
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Streptococcus_pneumoniae.fa.nto
abritamr/db/amrfinderplus/data/2026-05-15.1/AMR_DNA-Streptococcus_pneumoniae.tsv
abritamr/db/amrfinderplus/data/2026-05-15.1/changes.txt
abritamr/db/amrfinderplus/data/2026-05-15.1/database_format_version.txt
abritamr/db/amrfinderplus/data/2026-05-15.1/fam.tsv
abritamr/db/amrfinderplus/data/2026-05-15.1/taxgroup.tsv
abritamr/db/amrfinderplus/data/2026-05-15.1/version.txt
tests/__init__.py
tests/amrfinder.out
tests/batch.txt
tests/batch_fail.txt
tests/contigs.fa
tests/mdu_qc_checked.csv
tests/summary_matches.txt
tests/summary_matches_shig.txt
tests/summary_partials.txt
tests/summary_partials_shig.txt
tests/test_abritamr.py