LICENSE
README-pypi.md
README.md
pyproject.toml
CheckAMG/__init__.py
CheckAMG/__main__.py
CheckAMG/files/AMG_categories.tsv
CheckAMG/files/AMG_filters.tsv
CheckAMG/files/AMGs.tsv
CheckAMG/files/AMGs_categorized.tsv
CheckAMG/files/APG_categories.tsv
CheckAMG/files/APG_filters.tsv
CheckAMG/files/APGs.tsv
CheckAMG/files/APGs_categorized.tsv
CheckAMG/files/AReG_categories.tsv
CheckAMG/files/AReG_filters.tsv
CheckAMG/files/AReGs.tsv
CheckAMG/files/AReGs_categorized.tsv
CheckAMG/files/FOAM.tsv
CheckAMG/files/hmm_id_to_name.tsv
CheckAMG/files/lgbm_feature_names.joblib
CheckAMG/files/lgbm_model.joblib
CheckAMG/files/lgbm_thresholds.joblib
CheckAMG/files/mobile_genes.tsv
CheckAMG/files/pst_thresholds.json
CheckAMG/files/viral_hallmark_genes.tsv
CheckAMG/files/vscores.tsv
CheckAMG/scripts/aggregate/aggregate.py
CheckAMG/scripts/aggregate/aggregate_results.py
CheckAMG/scripts/aggregate/cli.py
CheckAMG/scripts/aggregate/workflow.smk
CheckAMG/scripts/annotate/__init__.py
CheckAMG/scripts/annotate/add_annots.py
CheckAMG/scripts/annotate/annotate.py
CheckAMG/scripts/annotate/check_circular.py
CheckAMG/scripts/annotate/cli.py
CheckAMG/scripts/annotate/curate_annots.py
CheckAMG/scripts/annotate/filter_by_cds.py
CheckAMG/scripts/annotate/filter_by_length.py
CheckAMG/scripts/annotate/genome_context.py
CheckAMG/scripts/annotate/hmm_annotate.py
CheckAMG/scripts/annotate/make_final_tables.py
CheckAMG/scripts/annotate/map_protein_data.py
CheckAMG/scripts/annotate/organize_proteins.py
CheckAMG/scripts/annotate/utils.py
CheckAMG/scripts/annotate/workflow.smk
CheckAMG/scripts/common/__init__.py
CheckAMG/scripts/common/args_formatter_logging.py
CheckAMG/scripts/common/checkAMG_ASCII.py
CheckAMG/scripts/common/db_paths.py
CheckAMG/scripts/common/fasta_io.py
CheckAMG/scripts/common/mem_limit.py
CheckAMG/scripts/common/resources.py
CheckAMG/scripts/common/run_pyrodigal.py
CheckAMG/scripts/common/runner_logging.py
CheckAMG/scripts/common/set_up_snakemake.py
CheckAMG/scripts/common/snakemake_logging.py
CheckAMG/scripts/common/validate_fasta.py
CheckAMG/scripts/denovo/__init__.py
CheckAMG/scripts/denovo/anchored_view.py
CheckAMG/scripts/denovo/cli.py
CheckAMG/scripts/denovo/config.py
CheckAMG/scripts/denovo/constants.py
CheckAMG/scripts/denovo/data.py
CheckAMG/scripts/denovo/denovo.py
CheckAMG/scripts/denovo/embed.py
CheckAMG/scripts/denovo/esm2_to_pst_embed.py
CheckAMG/scripts/denovo/fasta_to_esm2.py
CheckAMG/scripts/denovo/filter_prots.py
CheckAMG/scripts/denovo/loss.py
CheckAMG/scripts/denovo/model.py
CheckAMG/scripts/denovo/pst_embed_to_inference.py
CheckAMG/scripts/denovo/utils.py
CheckAMG/scripts/denovo/workflow.smk
CheckAMG/scripts/download/__init__.py
CheckAMG/scripts/download/cli.py
CheckAMG/scripts/download/download_dbs.py
CheckAMG/scripts/end_to_end/__init__.py
CheckAMG/scripts/end_to_end/cli.py
CheckAMG/scripts/end_to_end/end_to_end.py
CheckAMG/scripts/train_pst/cli.py
CheckAMG/scripts/train_pst/embed_train_data.py
CheckAMG/scripts/train_pst/train.py
CheckAMG/scripts/train_pst/train_pst_model.py
CheckAMG/scripts/train_pst/workflow.smk
checkamg.egg-info/PKG-INFO
checkamg.egg-info/SOURCES.txt
checkamg.egg-info/dependency_links.txt
checkamg.egg-info/entry_points.txt
checkamg.egg-info/requires.txt
checkamg.egg-info/top_level.txt