Index

A

add_single_instance() (inmotifin.Inserter method) add_single_motif_probabilities() (inmotifin.Inserter method) assign_frequencies() (inmotifin.Frequencer method) assign_group_frequencies() (inmotifin.Frequencer method)

assign_group_group_trans_probs() (inmotifin.Frequencer method) assign_iid_probs() (inmotifin.Backgrounder method) assign_motif_frequencies() (inmotifin.Frequencer method) assign_motifs_to_groups() (inmotifin.Grouper method)

B

Backgrounder (class in inmotifin) BackgroundParams (class in inmotifin)

Backgrounds (class in inmotifin) BackgroundSampler (class in inmotifin) BasicParams (class in inmotifin)

C

calc_position_probabilities() (inmotifin.Markover method) check_alphabet() (inmotifin.Motifs method) check_central_positions() (inmotifin.Positioner method) check_lengths() (inmotifin.Positioner method) check_overlap() (inmotifin.Positioner method) Controller (class in inmotifin) convert_jaspardict_to_ppm() (inmotifin.Reader method) create_a_multimer() (inmotifin.Multimerer method) create_backgrounds() (inmotifin.Backgrounder method) (inmotifin.Controller method)

create_groups() (inmotifin.Grouper method) create_insert_positions() (inmotifin.Inserter method) create_motif_in_seq() (inmotifin.Controller method) create_motifs() (inmotifin.Controller method) (inmotifin.Motifer method) create_multimers() (inmotifin.Controller method) (inmotifin.Multimerer method) create_reverse_complement() (in module inmotifin) create_reverse_complement_motif() (in module inmotifin)

D

data_to_bed() (inmotifin.Writer method) define_complementary_map_motif_array() (in module inmotifin)

dict_of_dict_to_json() (inmotifin.Writer method) dict_to_fasta() (inmotifin.Writer method) dict_to_tsv() (inmotifin.Writer method)

F

fetch_motif_from_jaspar() (inmotifin.Reader method) fit_markov() (inmotifin.Backgrounder method) fit_model() (inmotifin.Markover method)

FreqParams (class in inmotifin) Frequencer (class in inmotifin) Frequencies (class in inmotifin) FrequencySampler (class in inmotifin)

G

generate_motif_in_sequence() (inmotifin.Inserter method) generate_probabilistic_motif_in_sequence() (inmotifin.Inserter method) get_b_alphabet() (inmotifin.BackgroundSampler method) get_b_alphabet_prior() (inmotifin.BackgroundSampler method) get_background_ids() (inmotifin.BackgroundSampler method) get_backgrounds() (inmotifin.Backgrounder method) (inmotifin.BackgroundSampler method) get_backgrounds_seq() (inmotifin.Backgrounder method) get_frequencies() (inmotifin.Frequencer method) get_groups() (inmotifin.Grouper method) get_motifs() (inmotifin.Motifer method) get_multimers() (inmotifin.Multimerer method)

get_one_new_instance() (inmotifin.MotifInstancer method) get_outfolder() (inmotifin.Writer method) get_positions() (inmotifin.Positioner method) get_probabilities() (inmotifin.Markover method) get_pwms() (inmotifin.Motifer method) get_single_background() (inmotifin.BackgroundSampler method) get_str_sequence() (inmotifin.Markover method) get_title() (inmotifin.Writer method) get_to_replace() (inmotifin.Positioner method) Grouper (class in inmotifin) GroupParams (class in inmotifin) Groups (class in inmotifin)

I

Inserter (class in inmotifin)

L

list_to_file() (inmotifin.Writer method)

M

main() (inmotifin.Multimerer method) markov_backgrounds() (inmotifin.Backgrounder method) Markover (class in inmotifin) mask_motif_in_seq() (inmotifin.Controller method) membership_assignment() (inmotifin.Grouper method) motif_to_meme() (inmotifin.Writer method)

Motifer (class in inmotifin) MotifInstancer (class in inmotifin) MotifParams (class in inmotifin) Motifs (class in inmotifin) motived_and_plain_to_fasta() (inmotifin.Writer method) Multimerer (class in inmotifin) MultimerParams (class in inmotifin)

O

onehot_to_str() (in module inmotifin)

orient_motif() (inmotifin.MotifInstancer method)

P

pairs_random() (inmotifin.Frequencer method) pairs_uniform() (inmotifin.Frequencer method) pandas_to_tsv() (inmotifin.Writer method)

Positioner (class in inmotifin) PositionParams (class in inmotifin) Positions (class in inmotifin)

R

read_backgrounds() (inmotifin.Backgrounder method) read_fasta() (inmotifin.Reader method) read_group_freq() (inmotifin.Frequencer method) read_group_group_trans() (inmotifin.Frequencer method) read_groups() (inmotifin.Grouper method) read_in_motifs() (inmotifin.Reader method) read_jaspar() (inmotifin.Reader method) read_meme() (inmotifin.Reader method) read_motif() (inmotifin.Reader method)

read_motif_freq_per_group() (inmotifin.Frequencer method) read_motifs() (inmotifin.Motifer method) (inmotifin.Multimerer method) read_multimer_rules() (inmotifin.Multimerer method) read_multimerisation_tsv() (inmotifin.Reader method) read_tsv_to_pandas() (inmotifin.Reader method) read_twocolumn_tsv() (inmotifin.Reader method) Reader (class in inmotifin) run_inmotifin() (inmotifin.Controller method) run_sampling() (inmotifin.Controller method)

S

sample_from_model() (inmotifin.Markover method) sample_instances() (inmotifin.MotifInstancer method) sample_str_and_prob() (inmotifin.Markover method) SamplingParams (class in inmotifin) save_dagsim_data() (inmotifin.Writer method) save_dictionary_with_numpy_to_npz() (inmotifin.Writer method) save_multimers() (inmotifin.Multimerer method) save_outputs() (inmotifin.Controller method) select_central_position() (inmotifin.Positioner method) select_gaussian_inserted() (inmotifin.Positioner method) select_group_sizes_binomial() (inmotifin.Grouper method) select_groups() (inmotifin.FrequencySampler method) select_leftcentral_position() (inmotifin.Positioner method) select_motifs_from_groups() (inmotifin.FrequencySampler method) select_positions() (inmotifin.Positioner method) select_positions_inserted() (inmotifin.Positioner method) select_positions_replace() (inmotifin.Positioner method) select_rightcentral_position() (inmotifin.Positioner method)

select_single_position_replacer() (inmotifin.Positioner method) set_motifs() (inmotifin.Multimerer method) set_positions() (inmotifin.Positioner method) set_to_replace() (inmotifin.Inserter method) setup_dirs() (inmotifin.Writer method) setup_simulation() (inmotifin.Controller method) shuffle_backgrounds() (inmotifin.Backgrounder method) shuffle_seq_random_nucleotide() (inmotifin.Shuffler method) Shuffler (class in inmotifin) simulate_background_freq() (inmotifin.Frequencer method) simulate_background_freq_random() (inmotifin.Frequencer method) simulate_background_freq_uniform() (inmotifin.Frequencer method) simulate_backgrounds() (inmotifin.Controller method) simulate_groups() (inmotifin.Grouper method) simulate_iid_backgrounds() (inmotifin.Backgrounder method) simulate_markov() (inmotifin.Backgrounder method) simulate_motifs() (inmotifin.Motifer method) simulate_one_motif() (inmotifin.Motifer method)

W

Writer (class in inmotifin)