ProstT5ThreeDiEncoder
ModernProstThreeDiEncoder
ThreeDiRecord
IndexedSeq
estimate_token_size()
generate_random_protein()
generate_combined_proteins()
PipelineResult
run_pipeline()
calculate_pipeline_entropy()
UnifiedPipelineResult
UnifiedFeature
FeatureLocation
FeatureDNA
FeatureProtein
FeatureThreeDi
FeatureMetadata
FeatureEntropy
OrfRecord
find_orfs()
reverse_complement()
ProteinRecord
translate_orf()
translate_orfs()
ProstT5ThreeDiEncoder.__init__()
ProstT5ThreeDiEncoder.token_budget_batches()
ProstT5ThreeDiEncoder.encode()
ProstT5ThreeDiEncoder.encode_proteins()
ModernProstThreeDiEncoder.__init__()
ModernProstThreeDiEncoder.token_budget_batches()
ModernProstThreeDiEncoder.encode()
ModernProstThreeDiEncoder.encode_proteins()
ThreeDiRecord.protein
ThreeDiRecord.three_di
ThreeDiRecord.method
ThreeDiRecord.model_name
ThreeDiRecord.inference_device
ThreeDiRecord.__init__()
IndexedSeq.idx
IndexedSeq.seq
IndexedSeq.__init__()
preprocess_sequences()
format_seconds()
get_memory_info()
process_batches()
encode()
EntropyReport
shannon_entropy()
calculate_sequence_entropy()
calculate_entropies_for_sequences()
PipelineResult.input_id
PipelineResult.input_dna_length
PipelineResult.orfs
PipelineResult.proteins
PipelineResult.three_dis
PipelineResult.entropy
PipelineResult.__init__()
UnifiedPipelineResult.schema_version
UnifiedPipelineResult.input_id
UnifiedPipelineResult.input_dna_length
UnifiedPipelineResult.dna_entropy_global
UnifiedPipelineResult.alphabet_sizes
UnifiedPipelineResult.features
UnifiedPipelineResult.__init__()
UnifiedFeature.orf_id
UnifiedFeature.location
UnifiedFeature.dna
UnifiedFeature.protein
UnifiedFeature.three_di
UnifiedFeature.metadata
UnifiedFeature.entropy
UnifiedFeature.__init__()
FeatureLocation.start
FeatureLocation.end
FeatureLocation.strand
FeatureLocation.frame
FeatureLocation.__init__()
FeatureDNA.nt_sequence
FeatureDNA.length
FeatureDNA.__init__()
FeatureProtein.aa_sequence
FeatureProtein.length
FeatureProtein.__init__()
FeatureThreeDi.encoding
FeatureThreeDi.length
FeatureThreeDi.method
FeatureThreeDi.model_name
FeatureThreeDi.inference_device
FeatureThreeDi.__init__()
FeatureMetadata.parent_id
FeatureMetadata.table_id
FeatureMetadata.has_start_codon
FeatureMetadata.has_stop_codon
FeatureMetadata.in_genbank
FeatureMetadata.__init__()
FeatureEntropy.dna_entropy
FeatureEntropy.protein_entropy
FeatureEntropy.three_di_entropy
FeatureEntropy.__init__()
read_fasta()
read_fasta_iter()
write_fasta()
to_json_dict()
convert_pipeline_result_to_unified()
write_json()
read_json()
OrfEntropyError
ConfigurationError
InputError
OrfFinderError
TranslationError
EncodingError
ModelError
DeviceError
PipelineError
configure_logging()
get_logger()
is_configured()
get_log_file()
get_log_level()
set_log_level()
ORF finding utilities.
Modules
finder
ORF finder wrapper using get_orfs binary.
types
Data types for ORF representation.