Index

_

__init__() (genome_entropy.encode3di.encoder.ProstT5ThreeDiEncoder method) (genome_entropy.encode3di.types.IndexedSeq method) (genome_entropy.encode3di.types.ThreeDiRecord method) (genome_entropy.entropy.shannon.EntropyReport method), [1] (genome_entropy.io.genbank.GenBankCDS method) (genome_entropy.orf.types.OrfRecord method), [1] (genome_entropy.translate.translator.ProteinRecord method), [1]

__post_init__() (genome_entropy.orf.types.OrfRecord method), [1] (genome_entropy.translate.translator.ProteinRecord method), [1]

A

aa_length (genome_entropy.translate.translator.ProteinRecord attribute), [1], [2], [3] aa_sequence (genome_entropy.orf.types.OrfRecord attribute), [1], [2], [3] (genome_entropy.translate.translator.ProteinRecord attribute), [1], [2], [3]

alphabet_sizes (genome_entropy.entropy.shannon.EntropyReport attribute), [1], [2], [3]

C

calculate_entropies_for_sequences() (in module genome_entropy.entropy.shannon), [1] calculate_sequence_entropy() (in module genome_entropy.entropy.shannon), [1]

ConfigurationError configure_logging() (in module genome_entropy.logging_config) convert_pipeline_result_to_unified() (in module genome_entropy.io.jsonio), [1]

D

DeviceError

dna_entropy_global (genome_entropy.entropy.shannon.EntropyReport attribute), [1], [2], [3]

E

encode() (genome_entropy.encode3di.encoder.ProstT5ThreeDiEncoder method) (in module genome_entropy.encode3di.encoding) encode_proteins() (genome_entropy.encode3di.encoder.ProstT5ThreeDiEncoder method) EncodingError

end (genome_entropy.io.genbank.GenBankCDS attribute), [1] (genome_entropy.orf.types.OrfRecord attribute), [1], [2], [3] EntropyReport (class in genome_entropy.entropy.shannon), [1] extract_cds_features() (in module genome_entropy.io.genbank)

F

find_orfs() (in module genome_entropy.orf.finder), [1]

format_seconds() (in module genome_entropy.encode3di.encoding) frame (genome_entropy.orf.types.OrfRecord attribute), [1], [2], [3]

G

GenBankCDS (class in genome_entropy.io.genbank) genome_entropy.config module genome_entropy.encode3di.encoder module genome_entropy.encode3di.encoding module genome_entropy.encode3di.types module genome_entropy.entropy module, [1] genome_entropy.entropy.shannon module, [1] genome_entropy.errors module genome_entropy.io module, [1] genome_entropy.io.fasta module, [1]

genome_entropy.io.genbank module genome_entropy.io.jsonio module, [1] genome_entropy.logging_config module genome_entropy.orf module, [1] genome_entropy.orf.finder module, [1] genome_entropy.orf.types module genome_entropy.translate module, [1] genome_entropy.translate.translator module, [1] get_log_file() (in module genome_entropy.logging_config) get_log_level() (in module genome_entropy.logging_config) get_logger() (in module genome_entropy.logging_config) get_memory_info() (in module genome_entropy.encode3di.encoding)

H

has_start_codon (genome_entropy.orf.types.OrfRecord attribute), [1], [2], [3]

has_stop_codon (genome_entropy.orf.types.OrfRecord attribute), [1], [2], [3]

I

idx (genome_entropy.encode3di.types.IndexedSeq attribute) in_genbank (genome_entropy.orf.types.OrfRecord attribute), [1], [2], [3] IndexedSeq (class in genome_entropy.encode3di.types)

inference_device (genome_entropy.encode3di.types.ThreeDiRecord attribute), [1] InputError is_configured() (in module genome_entropy.logging_config)

M

match_orf_to_genbank_cds() (in module genome_entropy.io.genbank) method (genome_entropy.encode3di.types.ThreeDiRecord attribute), [1] model_name (genome_entropy.encode3di.types.ThreeDiRecord attribute), [1] ModelError module genome_entropy.config genome_entropy.encode3di.encoder genome_entropy.encode3di.encoding genome_entropy.encode3di.types genome_entropy.entropy, [1] genome_entropy.entropy.shannon, [1] genome_entropy.errors genome_entropy.io, [1] genome_entropy.io.fasta, [1] genome_entropy.io.genbank genome_entropy.io.jsonio, [1] genome_entropy.logging_config genome_entropy.orf, [1] genome_entropy.orf.finder, [1] genome_entropy.orf.types genome_entropy.translate, [1] genome_entropy.translate.translator, [1]

N

nt_sequence (genome_entropy.orf.types.OrfRecord attribute), [1], [2], [3]

O

orf (genome_entropy.translate.translator.ProteinRecord attribute), [1], [2], [3] orf_id (genome_entropy.orf.types.OrfRecord attribute), [1], [2], [3] orf_nt_entropy (genome_entropy.entropy.shannon.EntropyReport attribute), [1], [2], [3]

OrfEntropyError OrfFinderError OrfRecord (class in genome_entropy.orf.types), [1]

P

parent_id (genome_entropy.io.genbank.GenBankCDS attribute), [1] (genome_entropy.orf.types.OrfRecord attribute), [1], [2], [3] PipelineError preprocess_sequences() (in module genome_entropy.encode3di.encoding) process_batches() (in module genome_entropy.encode3di.encoding)

ProstT5ThreeDiEncoder (class in genome_entropy.encode3di.encoder) protein (genome_entropy.encode3di.types.ThreeDiRecord attribute), [1] protein_aa_entropy (genome_entropy.entropy.shannon.EntropyReport attribute), [1], [2], [3] protein_sequence (genome_entropy.io.genbank.GenBankCDS attribute), [1] ProteinRecord (class in genome_entropy.translate.translator), [1]

R

read_fasta() (in module genome_entropy.io.fasta), [1] read_fasta_iter() (in module genome_entropy.io.fasta), [1]

read_genbank() (in module genome_entropy.io.genbank) read_json() (in module genome_entropy.io.jsonio), [1] reverse_complement() (in module genome_entropy.orf.finder), [1]

S

seq (genome_entropy.encode3di.types.IndexedSeq attribute) set_log_level() (in module genome_entropy.logging_config) shannon_entropy() (in module genome_entropy.entropy.shannon), [1]

start (genome_entropy.io.genbank.GenBankCDS attribute), [1] (genome_entropy.orf.types.OrfRecord attribute), [1], [2], [3] strand (genome_entropy.io.genbank.GenBankCDS attribute), [1] (genome_entropy.orf.types.OrfRecord attribute), [1], [2], [3]

T

table_id (genome_entropy.orf.types.OrfRecord attribute), [1], [2], [3] three_di (genome_entropy.encode3di.types.ThreeDiRecord attribute), [1] three_di_entropy (genome_entropy.entropy.shannon.EntropyReport attribute), [1], [2], [3] ThreeDiRecord (class in genome_entropy.encode3di.types)

to_json_dict() (in module genome_entropy.io.jsonio), [1] token_budget_batches() (genome_entropy.encode3di.encoder.ProstT5ThreeDiEncoder method) translate_orf() (in module genome_entropy.translate.translator), [1] translate_orfs() (in module genome_entropy.translate.translator), [1] TranslationError

W

write_fasta() (in module genome_entropy.io.fasta), [1]

write_json() (in module genome_entropy.io.jsonio), [1]