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/2024-07-22.1/AMR.LIB
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR.LIB.h3f
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR.LIB.h3i
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR.LIB.h3m
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR.LIB.h3p
abritamr/db/amrfinderplus/data/2024-07-22.1/AMRProt
abritamr/db/amrfinderplus/data/2024-07-22.1/AMRProt-mutation.tab
abritamr/db/amrfinderplus/data/2024-07-22.1/AMRProt-suppress
abritamr/db/amrfinderplus/data/2024-07-22.1/AMRProt-susceptible.tab
abritamr/db/amrfinderplus/data/2024-07-22.1/AMRProt.pdb
abritamr/db/amrfinderplus/data/2024-07-22.1/AMRProt.phr
abritamr/db/amrfinderplus/data/2024-07-22.1/AMRProt.pin
abritamr/db/amrfinderplus/data/2024-07-22.1/AMRProt.pjs
abritamr/db/amrfinderplus/data/2024-07-22.1/AMRProt.pot
abritamr/db/amrfinderplus/data/2024-07-22.1/AMRProt.psq
abritamr/db/amrfinderplus/data/2024-07-22.1/AMRProt.ptf
abritamr/db/amrfinderplus/data/2024-07-22.1/AMRProt.pto
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_CDS
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_CDS.ndb
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_CDS.nhr
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_CDS.nin
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_CDS.njs
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_CDS.not
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_CDS.nsq
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_CDS.ntf
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_CDS.nto
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Acinetobacter_baumannii
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Acinetobacter_baumannii.ndb
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Acinetobacter_baumannii.nhr
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Acinetobacter_baumannii.nin
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Acinetobacter_baumannii.njs
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Acinetobacter_baumannii.not
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Acinetobacter_baumannii.nsq
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Acinetobacter_baumannii.ntf
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Acinetobacter_baumannii.nto
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Acinetobacter_baumannii.tab
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Campylobacter
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Campylobacter.ndb
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Campylobacter.nhr
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Campylobacter.nin
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Campylobacter.njs
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Campylobacter.not
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Campylobacter.nsq
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Campylobacter.ntf
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Campylobacter.nto
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Campylobacter.tab
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Clostridioides_difficile
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Clostridioides_difficile.ndb
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Clostridioides_difficile.nhr
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Clostridioides_difficile.nin
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Clostridioides_difficile.njs
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Clostridioides_difficile.not
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Clostridioides_difficile.nsq
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Clostridioides_difficile.ntf
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Clostridioides_difficile.nto
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Clostridioides_difficile.tab
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Enterococcus_faecalis
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Enterococcus_faecalis.ndb
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Enterococcus_faecalis.nhr
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Enterococcus_faecalis.nin
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Enterococcus_faecalis.njs
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Enterococcus_faecalis.not
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Enterococcus_faecalis.nsq
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Enterococcus_faecalis.ntf
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Enterococcus_faecalis.nto
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Enterococcus_faecalis.tab
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Enterococcus_faecium
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Enterococcus_faecium.ndb
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Enterococcus_faecium.nhr
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Enterococcus_faecium.nin
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Enterococcus_faecium.njs
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Enterococcus_faecium.not
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Enterococcus_faecium.nsq
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Enterococcus_faecium.ntf
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Enterococcus_faecium.nto
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Enterococcus_faecium.tab
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Escherichia
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Escherichia.ndb
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Escherichia.nhr
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Escherichia.nin
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Escherichia.njs
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Escherichia.not
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Escherichia.nsq
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Escherichia.ntf
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Escherichia.nto
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Escherichia.tab
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Klebsiella_oxytoca
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Klebsiella_oxytoca.ndb
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Klebsiella_oxytoca.nhr
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Klebsiella_oxytoca.nin
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Klebsiella_oxytoca.njs
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Klebsiella_oxytoca.not
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Klebsiella_oxytoca.nsq
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Klebsiella_oxytoca.ntf
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Klebsiella_oxytoca.nto
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Klebsiella_oxytoca.tab
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Klebsiella_pneumoniae
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Klebsiella_pneumoniae.ndb
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Klebsiella_pneumoniae.nhr
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Klebsiella_pneumoniae.nin
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Klebsiella_pneumoniae.njs
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Klebsiella_pneumoniae.not
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Klebsiella_pneumoniae.nsq
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Klebsiella_pneumoniae.ntf
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Klebsiella_pneumoniae.nto
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Klebsiella_pneumoniae.tab
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Neisseria_gonorrhoeae
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Neisseria_gonorrhoeae.ndb
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Neisseria_gonorrhoeae.nhr
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Neisseria_gonorrhoeae.nin
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Neisseria_gonorrhoeae.njs
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Neisseria_gonorrhoeae.not
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Neisseria_gonorrhoeae.nsq
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Neisseria_gonorrhoeae.ntf
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Neisseria_gonorrhoeae.nto
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Neisseria_gonorrhoeae.tab
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Salmonella
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Salmonella.ndb
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Salmonella.nhr
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Salmonella.nin
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Salmonella.njs
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Salmonella.not
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Salmonella.nsq
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Salmonella.ntf
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Salmonella.nto
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Salmonella.tab
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Staphylococcus_aureus
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Staphylococcus_aureus.ndb
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Staphylococcus_aureus.nhr
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Staphylococcus_aureus.nin
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Staphylococcus_aureus.njs
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Staphylococcus_aureus.not
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Staphylococcus_aureus.nsq
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Staphylococcus_aureus.ntf
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Staphylococcus_aureus.nto
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Staphylococcus_aureus.tab
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Streptococcus_pneumoniae
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Streptococcus_pneumoniae.ndb
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Streptococcus_pneumoniae.nhr
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Streptococcus_pneumoniae.nin
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Streptococcus_pneumoniae.njs
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Streptococcus_pneumoniae.not
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Streptococcus_pneumoniae.nsq
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Streptococcus_pneumoniae.ntf
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Streptococcus_pneumoniae.nto
abritamr/db/amrfinderplus/data/2024-07-22.1/AMR_DNA-Streptococcus_pneumoniae.tab
abritamr/db/amrfinderplus/data/2024-07-22.1/changes.txt
abritamr/db/amrfinderplus/data/2024-07-22.1/database_format_version.txt
abritamr/db/amrfinderplus/data/2024-07-22.1/fam.tab
abritamr/db/amrfinderplus/data/2024-07-22.1/taxgroup.tab
abritamr/db/amrfinderplus/data/2024-07-22.1/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