Index

_

__add__() (poolparty.Pool method) __enter__() (poolparty.Party method) __eq__() (poolparty.Region method) __exit__() (poolparty.Party method) __getitem__() (poolparty.Pool method) __hash__() (poolparty.Region method) __init__() (poolparty.FixedOp method) (poolparty.FromIupacOp method) (poolparty.FromMotifOp method) (poolparty.FromSeqsOp method) (poolparty.GetKmersOp method) (poolparty.MutagenizeOp method) (poolparty.MutagenizeOrfOp method) (poolparty.Operation method) (poolparty.Party method) (poolparty.Pool method) (poolparty.RecombineOp method) (poolparty.Region method) (poolparty.RepeatOp method) (poolparty.SampleOp method) (poolparty.SeqShuffleOp method) (poolparty.StackOp method) (poolparty.StateShuffleOp method) (poolparty.StateSliceOp method) (poolparty.StylizeOp method)

__mul__() (poolparty.Pool method) __post_init__() (poolparty.Region method) __rmul__() (poolparty.Pool method) _id (poolparty.Region attribute)

A

action_uniquely_determined_by_state (poolparty.Operation property)

add_region() (poolparty.Pool method) apply_at_region() (in module poolparty)

B

build_pool_counter() (poolparty.Operation method) (poolparty.SampleOp method) (poolparty.StackOp method) (poolparty.StateShuffleOp method) (poolparty.StateSliceOp method)

C

clear_annotation() (in module poolparty) clear_gaps() (in module poolparty) clear_pools() (in module poolparty) (poolparty.Party method) codon_table (poolparty.Party property)

compute() (poolparty.Operation method) compute_name_contributions() (poolparty.FromSeqsOp method) (poolparty.Operation method) configure_logging() (in module poolparty) copy() (poolparty.Operation method) (poolparty.Pool method)

D

deepcopy() (poolparty.Operation method) (poolparty.Pool method) deletion_multiscan() (in module poolparty) deletion_scan() (in module poolparty) design_card_keys (poolparty.FixedOp attribute) (poolparty.FromIupacOp attribute) (poolparty.FromMotifOp attribute) (poolparty.FromSeqsOp attribute) (poolparty.GetKmersOp attribute) (poolparty.MutagenizeOp attribute) (poolparty.MutagenizeOrfOp attribute) (poolparty.Operation attribute) (poolparty.RecombineOp attribute) (poolparty.RepeatOp attribute) (poolparty.SampleOp attribute) (poolparty.SeqShuffleOp attribute) (poolparty.StackOp attribute) (poolparty.StateShuffleOp attribute) (poolparty.StateSliceOp attribute) (poolparty.StylizeOp attribute)

E

extract_region() (in module poolparty)

F

factory_name (poolparty.FixedOp attribute) (poolparty.FromIupacOp attribute) (poolparty.FromMotifOp attribute) (poolparty.FromSeqsOp attribute) (poolparty.GetKmersOp attribute) (poolparty.MutagenizeOp attribute) (poolparty.MutagenizeOrfOp attribute) (poolparty.Operation attribute) (poolparty.RecombineOp attribute) (poolparty.RepeatOp attribute) (poolparty.SampleOp attribute) (poolparty.SeqShuffleOp attribute) (poolparty.StackOp attribute) (poolparty.StateShuffleOp attribute) (poolparty.StateSliceOp attribute) (poolparty.StylizeOp attribute)

FixedOp (class in poolparty) from_fasta() (in module poolparty) from_iupac() (in module poolparty) from_motif() (in module poolparty) from_seq() (in module poolparty) from_seqs() (in module poolparty) FromIupacOp (class in poolparty) FromMotifOp (class in poolparty) FromSeqsOp (class in poolparty)

G

generate_library() (in module poolparty) (poolparty.Pool method) get_active_party() (in module poolparty) get_effective_seq_length() (poolparty.Party method) get_kmers() (in module poolparty) get_length_without_tags() (poolparty.Party method) get_molecular_positions() (poolparty.Party method)

get_op_by_id() (poolparty.Party method) get_op_by_name() (poolparty.Party method) get_pool_by_id() (poolparty.Party method) get_pool_by_name() (poolparty.Party method) get_region() (poolparty.Party method) get_region_by_id() (poolparty.Party method) get_region_by_name() (poolparty.Party method) GetKmersOp (class in poolparty)

H

has_cards (poolparty.Operation property)

has_region() (poolparty.Party method) (poolparty.Pool method)

I

id (poolparty.Operation property) init() (in module poolparty) insert_tags() (in module poolparty) insertion_multiscan() (in module poolparty)

insertion_scan() (in module poolparty) is_variable_length (poolparty.Region property) is_zero_length (poolparty.Region property) iter_order (poolparty.Operation property) (poolparty.Pool property)

J

join() (in module poolparty)

L

lower() (in module poolparty)

M

max_num_sequential_states (poolparty.Operation attribute) mutagenize() (in module poolparty) mutagenize_orf() (in module poolparty)

mutagenize_scan() (in module poolparty) MutagenizeOp (class in poolparty) MutagenizeOrfOp (class in poolparty)

N

name (poolparty.Operation property) (poolparty.Pool property) (poolparty.Region attribute), [1]

named() (poolparty.Pool method) natural_num_states (poolparty.Operation property) num_states (poolparty.Pool property)

O

Operation (class in poolparty)

output() (poolparty.Party method)

P

parents (poolparty.Pool property) Party (class in poolparty) Pool (class in poolparty) poolparty.BASES (built-in variable) poolparty.COMPLEMENT (built-in variable) poolparty.IGNORE_CHARS (built-in variable)

poolparty.IUPAC_TO_DNA (built-in variable) poolparty.VALID_CHARS (built-in variable) print_dag() (poolparty.Operation method) (poolparty.Pool method) print_graph() (poolparty.Party method) print_library() (poolparty.Pool method) print_named_colors() (in module poolparty)

R

rc() (in module poolparty) recombine() (in module poolparty) RecombineOp (class in poolparty) Region (class in poolparty) region_multiscan() (in module poolparty) region_scan() (in module poolparty) regions (poolparty.Pool property)

register_orf_region() (poolparty.Party method) register_region() (poolparty.Party method) remove_tags() (in module poolparty) repeat() (in module poolparty) RepeatOp (class in poolparty) replace_region() (in module poolparty) replacement_multiscan() (in module poolparty) replacement_scan() (in module poolparty)

S

sample() (in module poolparty) SampleOp (class in poolparty) seq_length (poolparty.Operation property) (poolparty.Pool property) (poolparty.Region attribute), [1] SeqShuffleOp (class in poolparty) set_genetic_code() (poolparty.Party method) shuffle_scan() (in module poolparty) shuffle_seq() (in module poolparty) slice_seq() (in module poolparty) stack() (in module poolparty) StackOp (class in poolparty)

state_manager (poolparty.Party property) state_shuffle() (in module poolparty) state_slice() (in module poolparty) StateShuffleOp (class in poolparty) StateSliceOp (class in poolparty) stylize() (in module poolparty) StylizeOp (class in poolparty) subseq_scan() (in module poolparty) suppress_cards (poolparty.Party property) suppress_styles (poolparty.Party property) swapcase() (in module poolparty) sync() (in module poolparty)

T

toggle_cards() (in module poolparty)

toggle_styles() (in module poolparty)

U

upgrade_to_orf_region() (poolparty.Party method)

upper() (in module poolparty) uses_custom_column_names (poolparty.Operation property)

V

validate_num_states() (poolparty.Operation class method)