README.md
pyproject.toml
setup.cfg
src/depht/__init__.py
src/depht/__main__.py
src/depht/data.py
src/depht/fetch_model.py
src/depht.egg-info/PKG-INFO
src/depht.egg-info/SOURCES.txt
src/depht.egg-info/dependency_links.txt
src/depht.egg-info/entry_points.txt
src/depht.egg-info/requires.txt
src/depht.egg-info/top_level.txt
src/depht/classes/__init__.py
src/depht/classes/contig.py
src/depht/classes/file_translator.py
src/depht/classes/hhresult.py
src/depht/classes/progress.py
src/depht/classes/prophage.py
src/depht/classes/prophage_classifier.py
src/depht/functions/__init__.py
src/depht/functions/annotation.py
src/depht/functions/att.py
src/depht/functions/blastn.py
src/depht/functions/fasta.py
src/depht/functions/find_homologs.py
src/depht/functions/mmseqs.py
src/depht/functions/multiprocess.py
src/depht/functions/prophage_prediction.py
src/depht/functions/sliding_window.py
src/depht/functions/sniff_format.py
src/depht/functions/statistics.py
src/depht/functions/subprocess.py
src/depht/functions/visualization.py
src/depht_train/__init__.py
src/depht_train/__main__.py
src/depht_train/data.py
src/depht_train/run.py
src/depht_train/classes/__init__.py
src/depht_train/classes/database.py
src/depht_train/classes/kfold.py
src/depht_train/functions/__init__.py
src/depht_train/functions/blastdb.py
src/depht_train/functions/clustalo.py
src/depht_train/functions/config_handling.py
src/depht_train/functions/entrez.py
src/depht_train/functions/fileio.py
src/depht_train/functions/hhsuitedb.py
src/depht_train/functions/train_classifier.py
src/depht_train/pipelines/__init__.py
src/depht_train/pipelines/benchmark_output.py
src/depht_train/pipelines/build_HMM_db.py
src/depht_train/pipelines/build_reference_db.py
src/depht_train/pipelines/create_model.py
src/depht_train/pipelines/curate_gene_clusters.py
src/depht_train/pipelines/index_sequences.py
src/depht_train/pipelines/phamerate.py
src/depht_train/pipelines/plot_gene_density.py
src/depht_train/pipelines/pull_sequences.py
src/depht_train/pipelines/recut_fasta.py
src/depht_train/pipelines/screen_conserved_phams.py
src/depht_train/pipelines/train_model.py