tidymut package
Subpackages
- tidymut.cleaners package
- Submodules
- tidymut.cleaners.base_config module
- tidymut.cleaners.basic_cleaners module
- tidymut.cleaners.human_domainome_cleaner module
- tidymut.cleaners.human_domainome_custom_cleaners module
- tidymut.cleaners.k50_cleaner module
- tidymut.cleaners.protein_gym_cleaner module
- tidymut.cleaners.protein_gym_custom_cleaners module
- Module contents
HumanDomainomeCleanerConfig
HumanDomainomeCleanerConfig.sequence_dict_path
HumanDomainomeCleanerConfig.header_parser
HumanDomainomeCleanerConfig.column_mapping
HumanDomainomeCleanerConfig.type_conversions
HumanDomainomeCleanerConfig.drop_na_columns
HumanDomainomeCleanerConfig.is_zero_based
HumanDomainomeCleanerConfig.process_workers
HumanDomainomeCleanerConfig.label_columns
HumanDomainomeCleanerConfig.primary_label_column
HumanDomainomeCleanerConfig.column_mapping
HumanDomainomeCleanerConfig.drop_na_columns
HumanDomainomeCleanerConfig.header_parser()
HumanDomainomeCleanerConfig.is_zero_based
HumanDomainomeCleanerConfig.label_columns
HumanDomainomeCleanerConfig.pipeline_name
HumanDomainomeCleanerConfig.primary_label_column
HumanDomainomeCleanerConfig.process_workers
HumanDomainomeCleanerConfig.sequence_dict_path
HumanDomainomeCleanerConfig.type_conversions
HumanDomainomeCleanerConfig.validate()
K50CleanerConfig
K50CleanerConfig.column_mapping
K50CleanerConfig.filters
K50CleanerConfig.type_conversions
K50CleanerConfig.validation_workers
K50CleanerConfig.infer_wt_workers
K50CleanerConfig.handle_multiple_wt
K50CleanerConfig.label_columns
K50CleanerConfig.primary_label_column
K50CleanerConfig.column_mapping
K50CleanerConfig.filters
K50CleanerConfig.handle_multiple_wt
K50CleanerConfig.infer_wt_workers
K50CleanerConfig.label_columns
K50CleanerConfig.pipeline_name
K50CleanerConfig.primary_label_column
K50CleanerConfig.type_conversions
K50CleanerConfig.validate()
K50CleanerConfig.validation_workers
ProteinGymCleanerConfig
ProteinGymCleanerConfig.column_mapping
ProteinGymCleanerConfig.filters
ProteinGymCleanerConfig.type_conversions
ProteinGymCleanerConfig.is_zero_based
ProteinGymCleanerConfig.validation_workers
ProteinGymCleanerConfig.infer_wt_workers
ProteinGymCleanerConfig.handle_multiple_wt
ProteinGymCleanerConfig.label_columns
ProteinGymCleanerConfig.primary_label_column
ProteinGymCleanerConfig.column_mapping
ProteinGymCleanerConfig.filters
ProteinGymCleanerConfig.handle_multiple_wt
ProteinGymCleanerConfig.infer_wt_workers
ProteinGymCleanerConfig.label_columns
ProteinGymCleanerConfig.pipeline_name
ProteinGymCleanerConfig.primary_label_column
ProteinGymCleanerConfig.type_conversions
ProteinGymCleanerConfig.validate()
ProteinGymCleanerConfig.validation_workers
clean_human_domainome_dataset()
clean_k50_dataset()
clean_protein_gym_dataset()
create_human_domainome_cleaner()
create_k50_cleaner()
create_protein_gym_cleaner()
- Submodules
- tidymut.core package
- Submodules
- Module contents
AminoAcidMutationSet
CodonMutationSet
CodonTable
DNAAlphabet
DNASequence
MutationDataset
MutationDataset.add_mutation_set()
MutationDataset.add_mutation_sets()
MutationDataset.add_reference_sequence()
MutationDataset.convert_codon_to_amino_acid_sets()
MutationDataset.filter_by_effect_type()
MutationDataset.filter_by_mutation_type()
MutationDataset.filter_by_reference()
MutationDataset.from_dataframe()
MutationDataset.get_mutation_set_label()
MutationDataset.get_mutation_set_reference()
MutationDataset.get_position_coverage()
MutationDataset.get_reference_sequence()
MutationDataset.get_statistics()
MutationDataset.list_reference_sequences()
MutationDataset.load()
MutationDataset.load_by_reference()
MutationDataset.remove_mutation_set()
MutationDataset.remove_reference_sequence()
MutationDataset.save()
MutationDataset.save_by_reference()
MutationDataset.set_mutation_set_label()
MutationDataset.set_mutation_set_reference()
MutationDataset.to_dataframe()
MutationDataset.validate_against_references()
Pipeline
Pipeline.add_delayed_step()
Pipeline.apply()
Pipeline.artifacts
Pipeline.assign()
Pipeline.copy()
Pipeline.data
Pipeline.delayed_then()
Pipeline.execute()
Pipeline.filter()
Pipeline.get_all_artifacts()
Pipeline.get_artifact()
Pipeline.get_data()
Pipeline.get_delayed_steps_info()
Pipeline.get_execution_summary()
Pipeline.get_step_result()
Pipeline.has_pending_steps
Pipeline.load()
Pipeline.load_structured_data()
Pipeline.peek()
Pipeline.remove_delayed_step()
Pipeline.save()
Pipeline.save_artifacts()
Pipeline.save_structured_data()
Pipeline.store()
Pipeline.structured_data
Pipeline.then()
Pipeline.transform()
Pipeline.validate()
Pipeline.visualize_pipeline()
ProteinAlphabet
ProteinSequence
RNAAlphabet
RNASequence
create_pipeline()
multiout_step()
pipeline_step()
- tidymut.utils package
Module contents
TidyMut: A Python package for cleaning protein mutation data