tidymut
API Reference
tidymut.cleaners package
tidymut.core package
tidymut.utils package
tidymut
Index
Index
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
K
|
L
|
M
|
N
|
P
|
R
|
S
|
T
|
V
|
W
A
add_delayed_step() (tidymut.core.Pipeline method)
(tidymut.core.pipeline.Pipeline method)
add_mutation() (tidymut.core.mutation.MutationSet method)
add_mutation_set() (tidymut.core.dataset.MutationDataset method)
(tidymut.core.MutationDataset method)
add_mutation_sets() (tidymut.core.dataset.MutationDataset method)
(tidymut.core.MutationDataset method)
add_reference_sequence() (tidymut.core.dataset.MutationDataset method)
(tidymut.core.MutationDataset method)
add_sequences_to_dataset() (in module tidymut.cleaners.human_domainome_custom_cleaners)
AminoAcidMutation (class in tidymut.core.mutation)
AminoAcidMutationSet (class in tidymut.core)
(class in tidymut.core.mutation)
apply() (tidymut.core.Pipeline method)
(tidymut.core.pipeline.Pipeline method)
apply_mutation() (tidymut.core.sequence.BaseSequence method)
apply_mutations_to_sequences() (in module tidymut.cleaners.basic_cleaners)
apply_single_mutation() (in module tidymut.utils.cleaner_workers)
artifacts (tidymut.core.Pipeline property)
(tidymut.core.pipeline.Pipeline property)
assign() (tidymut.core.Pipeline method)
(tidymut.core.pipeline.Pipeline method)
B
back_transcribe() (tidymut.core.RNASequence method)
(tidymut.core.sequence.RNASequence method)
BaseAlphabet (class in tidymut.core.alphabet)
BaseCleanerConfig (class in tidymut.cleaners.base_config)
BaseMutation (class in tidymut.core.mutation)
BaseSequence (class in tidymut.core.sequence)
C
clean_human_domainome_dataset() (in module tidymut.cleaners)
(in module tidymut.cleaners.human_domainome_cleaner)
clean_k50_dataset() (in module tidymut.cleaners)
(in module tidymut.cleaners.k50_cleaner)
clean_protein_gym_dataset() (in module tidymut.cleaners)
(in module tidymut.cleaners.protein_gym_cleaner)
CodonMutation (class in tidymut.core.mutation)
CodonMutationSet (class in tidymut.core)
(class in tidymut.core.mutation)
CodonTable (class in tidymut.core)
(class in tidymut.core.codon)
column_mapping (tidymut.cleaners.human_domainome_cleaner.HumanDomainomeCleanerConfig attribute)
,
[1]
(tidymut.cleaners.HumanDomainomeCleanerConfig attribute)
,
[1]
(tidymut.cleaners.k50_cleaner.K50CleanerConfig attribute)
,
[1]
(tidymut.cleaners.K50CleanerConfig attribute)
,
[1]
(tidymut.cleaners.protein_gym_cleaner.ProteinGymCleanerConfig attribute)
,
[1]
(tidymut.cleaners.ProteinGymCleanerConfig attribute)
,
[1]
convert_codon_to_amino_acid_sets() (tidymut.core.dataset.MutationDataset method)
(tidymut.core.MutationDataset method)
convert_data_types() (in module tidymut.cleaners.basic_cleaners)
(in module tidymut.utils.type_converter)
convert_data_types_batch() (in module tidymut.utils.type_converter)
convert_format_1() (in module tidymut.utils.dataset_builders)
convert_format_2() (in module tidymut.utils.dataset_builders)
convert_to_boolean() (in module tidymut.utils.type_converter)
convert_to_mutation_dataset_format() (in module tidymut.cleaners.basic_cleaners)
copy() (tidymut.core.Pipeline method)
(tidymut.core.pipeline.Pipeline method)
count_by_effect_type() (tidymut.core.AminoAcidMutationSet method)
(tidymut.core.mutation.AminoAcidMutationSet method)
create_human_domainome_cleaner() (in module tidymut.cleaners)
(in module tidymut.cleaners.human_domainome_cleaner)
create_k50_cleaner() (in module tidymut.cleaners)
(in module tidymut.cleaners.k50_cleaner)
create_pipeline() (in module tidymut.core)
(in module tidymut.core.pipeline)
create_protein_gym_cleaner() (in module tidymut.cleaners)
(in module tidymut.cleaners.protein_gym_cleaner)
D
data (tidymut.core.Pipeline property)
(tidymut.core.pipeline.Pipeline property)
delayed_then() (tidymut.core.Pipeline method)
(tidymut.core.pipeline.Pipeline method)
DNAAlphabet (class in tidymut.core)
(class in tidymut.core.alphabet)
DNASequence (class in tidymut.core)
(class in tidymut.core.sequence)
drop_na_columns (tidymut.cleaners.human_domainome_cleaner.HumanDomainomeCleanerConfig attribute)
,
[1]
(tidymut.cleaners.HumanDomainomeCleanerConfig attribute)
,
[1]
E
effect_type (tidymut.core.mutation.AminoAcidMutation property)
execute() (tidymut.core.Pipeline method)
(tidymut.core.pipeline.Pipeline method)
extract_and_rename_columns() (in module tidymut.cleaners.basic_cleaners)
extract_domain_sequences() (in module tidymut.cleaners.human_domainome_custom_cleaners)
F
filter() (tidymut.core.Pipeline method)
(tidymut.core.pipeline.Pipeline method)
filter_and_clean_data() (in module tidymut.cleaners.basic_cleaners)
filter_by_category() (tidymut.core.mutation.MutationSet method)
filter_by_effect_type() (tidymut.core.dataset.MutationDataset method)
(tidymut.core.MutationDataset method)
filter_by_mutation_type() (tidymut.core.dataset.MutationDataset method)
(tidymut.core.MutationDataset method)
filter_by_reference() (tidymut.core.dataset.MutationDataset method)
(tidymut.core.MutationDataset method)
filters (tidymut.cleaners.k50_cleaner.K50CleanerConfig attribute)
,
[1]
(tidymut.cleaners.K50CleanerConfig attribute)
,
[1]
(tidymut.cleaners.protein_gym_cleaner.ProteinGymCleanerConfig attribute)
,
[1]
(tidymut.cleaners.ProteinGymCleanerConfig attribute)
,
[1]
find_motif() (tidymut.core.ProteinSequence method)
(tidymut.core.sequence.ProteinSequence method)
from_dataframe() (tidymut.core.dataset.MutationDataset class method)
(tidymut.core.MutationDataset class method)
from_dict() (tidymut.cleaners.base_config.BaseCleanerConfig class method)
from_json() (tidymut.cleaners.base_config.BaseCleanerConfig class method)
from_string() (tidymut.core.mutation.AminoAcidMutation class method)
(tidymut.core.mutation.BaseMutation class method)
(tidymut.core.mutation.CodonMutation class method)
(tidymut.core.mutation.MutationSet class method)
G
get_all_artifacts() (tidymut.core.Pipeline method)
(tidymut.core.pipeline.Pipeline method)
get_artifact() (tidymut.core.Pipeline method)
(tidymut.core.pipeline.Pipeline method)
get_conversion_function() (in module tidymut.utils.type_converter)
get_data() (tidymut.core.Pipeline method)
(tidymut.core.pipeline.Pipeline method)
get_delayed_steps_info() (tidymut.core.Pipeline method)
(tidymut.core.pipeline.Pipeline method)
get_execution_summary() (tidymut.core.Pipeline method)
(tidymut.core.pipeline.Pipeline method)
get_invalid_chars() (tidymut.core.alphabet.BaseAlphabet method)
get_missense_mutations() (tidymut.core.AminoAcidMutationSet method)
(tidymut.core.mutation.AminoAcidMutationSet method)
get_mutation_at() (tidymut.core.mutation.MutationSet method)
get_mutation_categories() (tidymut.core.mutation.MutationSet method)
get_mutation_category() (tidymut.core.mutation.AminoAcidMutation method)
(tidymut.core.mutation.BaseMutation method)
(tidymut.core.mutation.CodonMutation method)
get_mutation_count() (tidymut.core.mutation.MutationSet method)
get_mutation_set_label() (tidymut.core.dataset.MutationDataset method)
(tidymut.core.MutationDataset method)
get_mutation_set_reference() (tidymut.core.dataset.MutationDataset method)
(tidymut.core.MutationDataset method)
get_nonsense_mutations() (tidymut.core.AminoAcidMutationSet method)
(tidymut.core.mutation.AminoAcidMutationSet method)
get_one_letter_code() (tidymut.core.alphabet.ProteinAlphabet method)
(tidymut.core.ProteinAlphabet method)
get_position_coverage() (tidymut.core.dataset.MutationDataset method)
(tidymut.core.MutationDataset method)
get_positions() (tidymut.core.mutation.MutationSet method)
get_positions_set() (tidymut.core.mutation.MutationSet method)
get_reference_sequence() (tidymut.core.dataset.MutationDataset method)
(tidymut.core.MutationDataset method)
get_residue() (tidymut.core.ProteinSequence method)
(tidymut.core.sequence.ProteinSequence method)
get_sorted_by_position() (tidymut.core.mutation.MutationSet method)
get_standard_table() (tidymut.core.codon.CodonTable class method)
(tidymut.core.CodonTable class method)
get_statistics() (tidymut.core.dataset.MutationDataset method)
(tidymut.core.MutationDataset method)
get_step_result() (tidymut.core.Pipeline method)
(tidymut.core.pipeline.Pipeline method)
get_subsequence() (tidymut.core.sequence.BaseSequence method)
get_summary() (tidymut.cleaners.base_config.BaseCleanerConfig method)
get_synonymous_mutations() (tidymut.core.AminoAcidMutationSet method)
(tidymut.core.mutation.AminoAcidMutationSet method)
get_table_by_name() (tidymut.core.codon.CodonTable class method)
(tidymut.core.CodonTable class method)
get_three_letter_code() (tidymut.core.alphabet.ProteinAlphabet method)
(tidymut.core.ProteinAlphabet method)
H
handle_multiple_wt (tidymut.cleaners.k50_cleaner.K50CleanerConfig attribute)
,
[1]
(tidymut.cleaners.K50CleanerConfig attribute)
,
[1]
(tidymut.cleaners.protein_gym_cleaner.ProteinGymCleanerConfig attribute)
,
[1]
(tidymut.cleaners.ProteinGymCleanerConfig attribute)
,
[1]
has_mutation_at() (tidymut.core.mutation.MutationSet method)
has_pending_steps (tidymut.core.Pipeline property)
(tidymut.core.pipeline.Pipeline property)
has_stop_codon_mutations() (tidymut.core.AminoAcidMutationSet method)
(tidymut.core.mutation.AminoAcidMutationSet method)
header_parser (tidymut.cleaners.human_domainome_cleaner.HumanDomainomeCleanerConfig attribute)
(tidymut.cleaners.HumanDomainomeCleanerConfig attribute)
header_parser() (tidymut.cleaners.human_domainome_cleaner.HumanDomainomeCleanerConfig method)
(tidymut.cleaners.HumanDomainomeCleanerConfig method)
HumanDomainomeCleanerConfig (class in tidymut.cleaners)
(class in tidymut.cleaners.human_domainome_cleaner)
I
infer_wildtype_sequences() (in module tidymut.cleaners.basic_cleaners)
infer_wt_sequence_grouped() (in module tidymut.utils.cleaner_workers)
infer_wt_workers (tidymut.cleaners.k50_cleaner.K50CleanerConfig attribute)
,
[1]
(tidymut.cleaners.K50CleanerConfig attribute)
,
[1]
(tidymut.cleaners.protein_gym_cleaner.ProteinGymCleanerConfig attribute)
,
[1]
(tidymut.cleaners.ProteinGymCleanerConfig attribute)
,
[1]
invert_mutation() (in module tidymut.utils.mutation_converter)
invert_mutation_set() (in module tidymut.utils.mutation_converter)
is_missense() (tidymut.core.mutation.AminoAcidMutation method)
is_multiple_mutations() (tidymut.core.mutation.MutationSet method)
is_nonsense() (tidymut.core.mutation.AminoAcidMutation method)
is_single_mutation() (tidymut.core.mutation.MutationSet method)
is_start_codon() (tidymut.core.codon.CodonTable method)
(tidymut.core.CodonTable method)
is_stop_codon() (tidymut.core.codon.CodonTable method)
(tidymut.core.CodonTable method)
is_synonymous() (tidymut.core.mutation.AminoAcidMutation method)
is_valid_char() (tidymut.core.alphabet.BaseAlphabet method)
is_valid_sequence() (tidymut.core.alphabet.BaseAlphabet method)
is_zero_based (tidymut.cleaners.human_domainome_cleaner.HumanDomainomeCleanerConfig attribute)
,
[1]
(tidymut.cleaners.HumanDomainomeCleanerConfig attribute)
,
[1]
(tidymut.cleaners.protein_gym_cleaner.ProteinGymCleanerConfig attribute)
(tidymut.cleaners.ProteinGymCleanerConfig attribute)
K
K50CleanerConfig (class in tidymut.cleaners)
(class in tidymut.cleaners.k50_cleaner)
L
label_columns (tidymut.cleaners.human_domainome_cleaner.HumanDomainomeCleanerConfig attribute)
,
[1]
(tidymut.cleaners.HumanDomainomeCleanerConfig attribute)
,
[1]
(tidymut.cleaners.k50_cleaner.K50CleanerConfig attribute)
,
[1]
(tidymut.cleaners.K50CleanerConfig attribute)
,
[1]
(tidymut.cleaners.protein_gym_cleaner.ProteinGymCleanerConfig attribute)
,
[1]
(tidymut.cleaners.ProteinGymCleanerConfig attribute)
,
[1]
list_reference_sequences() (tidymut.core.dataset.MutationDataset method)
(tidymut.core.MutationDataset method)
load() (tidymut.core.dataset.MutationDataset class method)
(tidymut.core.MutationDataset class method)
(tidymut.core.Pipeline class method)
(tidymut.core.pipeline.Pipeline class method)
load_by_reference() (tidymut.core.dataset.MutationDataset class method)
(tidymut.core.MutationDataset class method)
load_sequences() (in module tidymut.utils.sequence_io)
load_structured_data() (tidymut.core.Pipeline class method)
(tidymut.core.pipeline.Pipeline class method)
M
merge() (tidymut.cleaners.base_config.BaseCleanerConfig method)
merge_columns() (in module tidymut.cleaners.basic_cleaners)
module
tidymut
tidymut.cleaners
tidymut.cleaners.base_config
tidymut.cleaners.basic_cleaners
tidymut.cleaners.human_domainome_cleaner
tidymut.cleaners.human_domainome_custom_cleaners
tidymut.cleaners.k50_cleaner
tidymut.cleaners.protein_gym_cleaner
tidymut.cleaners.protein_gym_custom_cleaners
tidymut.core
tidymut.core.alphabet
tidymut.core.codon
tidymut.core.constants
tidymut.core.dataset
tidymut.core.mutation
tidymut.core.pipeline
tidymut.core.sequence
tidymut.core.types
tidymut.utils
tidymut.utils.cleaner_workers
tidymut.utils.dataset_builders
tidymut.utils.mutation_converter
tidymut.utils.sequence_io
tidymut.utils.type_converter
multiout_step() (in module tidymut.core)
(in module tidymut.core.pipeline)
mutation_subtype (tidymut.core.mutation.MutationSet property)
MutationDataset (class in tidymut.core)
(class in tidymut.core.dataset)
MutationSet (class in tidymut.core.mutation)
N
normalize_type_conversions() (in module tidymut.utils.type_converter)
num_workers (tidymut.cleaners.base_config.BaseCleanerConfig attribute)
,
[1]
P
parse_custom_delimiter_header() (in module tidymut.utils.sequence_io)
parse_fasta() (in module tidymut.utils.sequence_io)
parse_ncbi_header() (in module tidymut.utils.sequence_io)
parse_simple_header() (in module tidymut.utils.sequence_io)
parse_uniprot_header() (in module tidymut.utils.sequence_io)
peek() (tidymut.core.Pipeline method)
(tidymut.core.pipeline.Pipeline method)
Pipeline (class in tidymut.core)
(class in tidymut.core.pipeline)
pipeline_name (tidymut.cleaners.base_config.BaseCleanerConfig attribute)
,
[1]
(tidymut.cleaners.human_domainome_cleaner.HumanDomainomeCleanerConfig attribute)
(tidymut.cleaners.HumanDomainomeCleanerConfig attribute)
(tidymut.cleaners.k50_cleaner.K50CleanerConfig attribute)
(tidymut.cleaners.K50CleanerConfig attribute)
(tidymut.cleaners.protein_gym_cleaner.ProteinGymCleanerConfig attribute)
(tidymut.cleaners.ProteinGymCleanerConfig attribute)
pipeline_step() (in module tidymut.core)
(in module tidymut.core.pipeline)
primary_label_column (tidymut.cleaners.human_domainome_cleaner.HumanDomainomeCleanerConfig attribute)
,
[1]
(tidymut.cleaners.HumanDomainomeCleanerConfig attribute)
,
[1]
(tidymut.cleaners.k50_cleaner.K50CleanerConfig attribute)
,
[1]
(tidymut.cleaners.K50CleanerConfig attribute)
,
[1]
(tidymut.cleaners.protein_gym_cleaner.ProteinGymCleanerConfig attribute)
,
[1]
(tidymut.cleaners.ProteinGymCleanerConfig attribute)
,
[1]
process_domain_positions() (in module tidymut.cleaners.human_domainome_custom_cleaners)
process_workers (tidymut.cleaners.human_domainome_cleaner.HumanDomainomeCleanerConfig attribute)
,
[1]
(tidymut.cleaners.HumanDomainomeCleanerConfig attribute)
,
[1]
ProteinAlphabet (class in tidymut.core)
(class in tidymut.core.alphabet)
ProteinGymCleanerConfig (class in tidymut.cleaners)
(class in tidymut.cleaners.protein_gym_cleaner)
ProteinSequence (class in tidymut.core)
(class in tidymut.core.sequence)
R
read_dataset() (in module tidymut.cleaners.basic_cleaners)
read_protein_gym_data() (in module tidymut.cleaners.protein_gym_custom_cleaners)
remove_delayed_step() (tidymut.core.Pipeline method)
(tidymut.core.pipeline.Pipeline method)
remove_mutation() (tidymut.core.mutation.MutationSet method)
remove_mutation_set() (tidymut.core.dataset.MutationDataset method)
(tidymut.core.MutationDataset method)
remove_reference_sequence() (tidymut.core.dataset.MutationDataset method)
(tidymut.core.MutationDataset method)
reverse_complement() (tidymut.core.DNASequence method)
(tidymut.core.RNASequence method)
(tidymut.core.sequence.DNASequence method)
(tidymut.core.sequence.RNASequence method)
RNAAlphabet (class in tidymut.core)
(class in tidymut.core.alphabet)
RNASequence (class in tidymut.core)
(class in tidymut.core.sequence)
S
save() (tidymut.core.dataset.MutationDataset method)
(tidymut.core.MutationDataset method)
(tidymut.core.Pipeline method)
(tidymut.core.pipeline.Pipeline method)
save_artifacts() (tidymut.core.Pipeline method)
(tidymut.core.pipeline.Pipeline method)
save_by_reference() (tidymut.core.dataset.MutationDataset method)
(tidymut.core.MutationDataset method)
save_structured_data() (tidymut.core.Pipeline method)
(tidymut.core.pipeline.Pipeline method)
seq_type (tidymut.core.CodonMutationSet property)
(tidymut.core.mutation.CodonMutationSet property)
sequence_dict_path (tidymut.cleaners.human_domainome_cleaner.HumanDomainomeCleanerConfig attribute)
,
[1]
(tidymut.cleaners.HumanDomainomeCleanerConfig attribute)
,
[1]
set_mutation_set_label() (tidymut.core.dataset.MutationDataset method)
(tidymut.core.MutationDataset method)
set_mutation_set_reference() (tidymut.core.dataset.MutationDataset method)
(tidymut.core.MutationDataset method)
sort_by_position() (tidymut.core.mutation.MutationSet method)
store() (tidymut.core.Pipeline method)
(tidymut.core.pipeline.Pipeline method)
strict_mode (tidymut.cleaners.base_config.BaseCleanerConfig attribute)
,
[1]
structured_data (tidymut.core.Pipeline property)
(tidymut.core.pipeline.Pipeline property)
T
then() (tidymut.core.Pipeline method)
(tidymut.core.pipeline.Pipeline method)
tidymut
module
tidymut.cleaners
module
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
tidymut.core
module
tidymut.core.alphabet
module
tidymut.core.codon
module
tidymut.core.constants
module
tidymut.core.dataset
module
tidymut.core.mutation
module
tidymut.core.pipeline
module
tidymut.core.sequence
module
tidymut.core.types
module
tidymut.utils
module
tidymut.utils.cleaner_workers
module
tidymut.utils.dataset_builders
module
tidymut.utils.mutation_converter
module
tidymut.utils.sequence_io
module
tidymut.utils.type_converter
module
to_amino_acid_mutation() (tidymut.core.mutation.CodonMutation method)
to_amino_acid_mutation_set() (tidymut.core.CodonMutationSet method)
(tidymut.core.mutation.CodonMutationSet method)
to_dataframe() (tidymut.core.dataset.MutationDataset method)
(tidymut.core.MutationDataset method)
to_dict() (tidymut.cleaners.base_config.BaseCleanerConfig method)
to_json() (tidymut.cleaners.base_config.BaseCleanerConfig method)
transcribe() (tidymut.core.DNASequence method)
(tidymut.core.sequence.DNASequence method)
transform() (tidymut.core.Pipeline method)
(tidymut.core.pipeline.Pipeline method)
translate() (tidymut.core.DNASequence method)
(tidymut.core.RNASequence method)
(tidymut.core.sequence.DNASequence method)
(tidymut.core.sequence.RNASequence method)
translate_codon() (tidymut.core.codon.CodonTable method)
(tidymut.core.CodonTable method)
type (tidymut.core.mutation.AminoAcidMutation property)
(tidymut.core.mutation.BaseMutation property)
(tidymut.core.mutation.CodonMutation property)
type_conversions (tidymut.cleaners.human_domainome_cleaner.HumanDomainomeCleanerConfig attribute)
,
[1]
(tidymut.cleaners.HumanDomainomeCleanerConfig attribute)
,
[1]
(tidymut.cleaners.k50_cleaner.K50CleanerConfig attribute)
,
[1]
(tidymut.cleaners.K50CleanerConfig attribute)
,
[1]
(tidymut.cleaners.protein_gym_cleaner.ProteinGymCleanerConfig attribute)
,
[1]
(tidymut.cleaners.ProteinGymCleanerConfig attribute)
,
[1]
V
valid_single_mutation() (in module tidymut.utils.cleaner_workers)
validate() (tidymut.cleaners.base_config.BaseCleanerConfig method)
(tidymut.cleaners.human_domainome_cleaner.HumanDomainomeCleanerConfig method)
(tidymut.cleaners.HumanDomainomeCleanerConfig method)
(tidymut.cleaners.k50_cleaner.K50CleanerConfig method)
(tidymut.cleaners.K50CleanerConfig method)
(tidymut.cleaners.protein_gym_cleaner.ProteinGymCleanerConfig method)
(tidymut.cleaners.ProteinGymCleanerConfig method)
(tidymut.core.Pipeline method)
(tidymut.core.pipeline.Pipeline method)
validate_against_references() (tidymut.core.dataset.MutationDataset method)
(tidymut.core.MutationDataset method)
validate_all() (tidymut.core.mutation.MutationSet method)
validate_config (tidymut.cleaners.base_config.BaseCleanerConfig attribute)
,
[1]
validate_mutations() (in module tidymut.cleaners.basic_cleaners)
validate_sequence() (tidymut.core.alphabet.BaseAlphabet method)
validation_workers (tidymut.cleaners.k50_cleaner.K50CleanerConfig attribute)
,
[1]
(tidymut.cleaners.K50CleanerConfig attribute)
,
[1]
(tidymut.cleaners.protein_gym_cleaner.ProteinGymCleanerConfig attribute)
,
[1]
(tidymut.cleaners.ProteinGymCleanerConfig attribute)
,
[1]
visualize_pipeline() (tidymut.core.Pipeline method)
(tidymut.core.pipeline.Pipeline method)
W
write_fasta() (in module tidymut.utils.sequence_io)