LICENSE.txt
MANIFEST.in
README.md
pyproject.toml
setup.cfg
src/paras.egg-info/PKG-INFO
src/paras.egg-info/SOURCES.txt
src/paras.egg-info/dependency_links.txt
src/paras.egg-info/entry_points.txt
src/paras.egg-info/not-zip-safe
src/paras.egg-info/requires.txt
src/paras.egg-info/top_level.txt
src/parasect/__init__.py
src/parasect/api.py
src/parasect/cli_paras.py
src/parasect/cli_parasect.py
src/parasect/version.py
src/parasect/core/__init__.py
src/parasect/core/chem.py
src/parasect/core/constants.py
src/parasect/core/domain.py
src/parasect/core/featurisation.py
src/parasect/core/genbank.py
src/parasect/core/github.py
src/parasect/core/helpers.py
src/parasect/core/hmmer.py
src/parasect/core/muscle.py
src/parasect/core/parasect_result.py
src/parasect/core/parsing.py
src/parasect/core/pca.py
src/parasect/core/tabular.py
src/parasect/core/taxonomy.py
src/parasect/core/writers.py
src/parasect/data/AMP-binding_full.hmm
src/parasect/data/AMP-binding_full.hmm.h3f
src/parasect/data/AMP-binding_full.hmm.h3i
src/parasect/data/AMP-binding_full.hmm.h3m
src/parasect/data/AMP-binding_full.hmm.h3p
src/parasect/data/AMP-binding_hmmer2.hmm
src/parasect/data/__init__.py
src/parasect/data/active_site.txt
src/parasect/data/active_site_hmm2.txt
src/parasect/data/fingerprints.txt
src/parasect/data/fingerprints_bacterial.txt
src/parasect/data/hashes.txt
src/parasect/data/included_substrates.txt
src/parasect/data/included_substrates_bacterial.txt
src/parasect/data/physicochemical_properties.txt
src/parasect/data/stachelhaus.txt
src/parasect/data/stachelhaus_hmm2.txt
src/parasect/data/structure_alignment.fasta
src/parasect/data/database_files/domain_substrate_mapping.txt
src/parasect/data/database_files/domains.fasta
src/parasect/data/database_files/extended_signatures.fasta
src/parasect/data/database_files/parasect_dataset.txt
src/parasect/data/database_files/proteins.fasta
src/parasect/data/database_files/signatures.fasta
src/parasect/data/database_files/smiles.tsv
src/parasect/data/database_files/taxonomy.txt
src/parasect/data/database_files/signature_positions/positions.txt
src/parasect/data/database_files/signature_positions/relative_positions.txt
src/parasect/database/__init__.py
src/parasect/database/add_user_submissions.py
src/parasect/database/build_database.py
src/parasect/database/extract_signature_positions.py
src/parasect/database/flatfiles_from_db.py
src/parasect/database/get_substrate_mapping.py
src/parasect/database/populate_database.py
src/parasect/database/process_substrate_corrections.py
src/parasect/database/protein_identifiers.py
src/parasect/database/query_database.py
src/parasect/model_training/__init__.py
src/parasect/model_training/data_processing/__init__.py
src/parasect/model_training/data_processing/get_domain_fasta.py
src/parasect/model_training/data_processing/get_new_domains.py
src/parasect/model_training/data_processing/subtract_domains.py
src/parasect/model_training/data_processing/data_analysis/__init__.py
src/parasect/model_training/data_processing/data_analysis/alluvial_table_from_database.py
src/parasect/model_training/data_processing/data_analysis/analyse_domain_groups.py
src/parasect/model_training/data_processing/data_analysis/benchmark_paras_parasect.py
src/parasect/model_training/data_processing/data_analysis/cytoscape.py
src/parasect/model_training/data_processing/data_analysis/explore_data_splits.py
src/parasect/model_training/data_processing/data_analysis/get_promiscuous_domains.py
src/parasect/model_training/data_processing/data_analysis/parasect_performance.py
src/parasect/model_training/data_processing/data_analysis/summarise_crossvalidation.py
src/parasect/model_training/data_processing/data_analysis/taxonomic_distribution_sandpuma.py
src/parasect/model_training/data_processing/plotting/__init__.py
src/parasect/model_training/data_processing/plotting/confusion_matrix.py
src/parasect/model_training/data_processing/plotting/plot_violins.py
src/parasect/model_training/data_processing/taxonomy/__init__.py
src/parasect/model_training/data_processing/taxonomy/add_species_and_strains.py
src/parasect/model_training/data_processing/taxonomy/condense_taxonomy.py
src/parasect/model_training/data_processing/taxonomy/get_rank.py
src/parasect/model_training/data_processing/taxonomy/get_species.py
src/parasect/model_training/data_processing/taxonomy/get_taxonomy.py
src/parasect/model_training/data_processing/taxonomy/map_taxonomy_to_all_synonyms.py
src/parasect/model_training/data_processing/taxonomy/split_by_clade.py
src/parasect/model_training/data_processing/taxonomy/split_fungal_bacterial.py
src/parasect/model_training/pca/__init__.py
src/parasect/model_training/pca/apply_pca.py
src/parasect/model_training/pca/build_pca.py
src/parasect/model_training/pca/visualize_pca.py
src/parasect/model_training/rf/__init__.py
src/parasect/model_training/rf/crossvalidation.py
src/parasect/model_training/rf/test_rf.py
src/parasect/model_training/rf/train_rf.py
src/parasect/model_training/train_test_splits/__init__.py
src/parasect/model_training/train_test_splits/crossvalidation.py
src/parasect/model_training/train_test_splits/domain_scope.py
src/parasect/model_training/train_test_splits/multilabel_stratification.py
src/parasect/model_training/train_test_splits/split_on_rank.py
src/parasect/model_training/train_test_splits/split_on_substrate.py
src/parasect/model_training/train_test_splits/substrate_selection.py