seqgra.simulator.simulator module

MIT - CSAIL - Gifford Lab - seqgra

Generates synthetic sequences based on grammar

@author: Konstantin Krismer

class Simulator(data_definition: seqgra.model.data.datadefinition.DataDefinition, output_dir: str, silent: bool = False)

Bases: object

check_grammar() → bool

check_invalid_distances() → bool

check_invalid_positions() → bool

check_invalid_sequence_elements() → bool

check_missing_alphabet_distributions() → bool

check_mutually_exclusive_probabilities() → bool

check_overlapping_sequence_elements() → bool

check_spacing_contraint_se_refs() → bool

check_unused_conditions() → bool

check_unused_sequence_elements() → bool

create_empirical_similarity_score_matrix(padding_size: int = 100, num_examples: int = 100) → None

create_grammar_heatmap(set_name: str) → None

create_motif_info() → None

create_motif_kl_divergence_matrix() → None

simulate_data() → None

write_session_info() → None