genome_entropy
  • Installation
    • Requirements
    • PyPI
    • Optional extras
    • Development checkout
    • External get_orfs dependency
    • CPU, NVIDIA, AMD, and Apple
    • Model downloads and offline use
    • Verification
  • Quick start
    • Prerequisites
    • Complete pipeline
    • Step-by-step workflow
    • Protein-only workflow
    • Model and device selection
    • Next steps
  • User guide
    • Pipeline concepts
    • ORFs and genetic codes
    • Structural-state encodings
    • Shannon entropy
    • Choosing an input workflow
    • Performance and reproducibility
    • Interpretation limits
  • Models and structural-state encodings
    • Authoritative model registry
    • Output semantics
    • Loading, security, and cache behaviour
    • Devices, precision, and multi-GPU
    • Citations and provenance
  • Data formats, coordinates, and entropy
    • Input formats
    • Unified pipeline JSON
    • Coordinates and identifiers
    • GenBank matching and in_genbank
    • Raw and normalised entropy
    • Intermediate and backward-compatible formats
  • Machine-learning workflow
    • Purpose and interpretation
    • Models
    • Feature matrix and missing values
    • Splitting and reproducibility
    • Training, evaluation, and persistence
    • Prediction
    • Devices
    • Reference
  • GPU and HPC operation
    • Platform semantics
    • Scheduler discovery and visibility
    • Installation and offline jobs
    • Monitoring
    • ML caveat
  • Command-line reference
    • Global options
    • run
    • orf
    • translate
    • fasta-to-protein
    • encode3di
    • entropy
    • download
    • estimate-tokens
    • ml train
    • ml predict
    • Exit behaviour
    • Environment variables
  • Python API reference
    • ORF discovery
      • find_orfs()
      • reverse_complement()
      • OrfRecord
        • OrfRecord.parent_id
        • OrfRecord.orf_id
        • OrfRecord.start
        • OrfRecord.end
        • OrfRecord.strand
        • OrfRecord.frame
        • OrfRecord.nt_sequence
        • OrfRecord.aa_sequence
        • OrfRecord.table_id
        • OrfRecord.has_start_codon
        • OrfRecord.has_stop_codon
        • OrfRecord.in_genbank
        • OrfRecord.__post_init__()
        • OrfRecord.__init__()
    • Translation
      • ProteinRecord
        • ProteinRecord.orf
        • ProteinRecord.aa_sequence
        • ProteinRecord.aa_length
        • ProteinRecord.__post_init__()
        • ProteinRecord.__init__()
      • translate_orf()
      • translate_orfs()
    • Structural-state encoding
      • ThreeDiRecord
        • ThreeDiRecord.protein
        • ThreeDiRecord.three_di
        • ThreeDiRecord.method
        • ThreeDiRecord.model_name
        • ThreeDiRecord.inference_device
        • ThreeDiRecord.twelve_state
        • ThreeDiRecord.__init__()
      • StructuralEncoding
        • StructuralEncoding.three_di
        • StructuralEncoding.twelve_state
        • StructuralEncoding.__init__()
      • IndexedSeq
        • IndexedSeq.idx
        • IndexedSeq.seq
        • IndexedSeq.__init__()
      • ProstT5ThreeDiEncoder
        • ProstT5ThreeDiEncoder.__init__()
        • ProstT5ThreeDiEncoder.token_budget_batches()
        • ProstT5ThreeDiEncoder.encode()
        • ProstT5ThreeDiEncoder.encode_proteins()
      • ModernProstThreeDiEncoder
        • ModernProstThreeDiEncoder.__init__()
        • ModernProstThreeDiEncoder.token_budget_batches()
        • ModernProstThreeDiEncoder.encode()
        • ModernProstThreeDiEncoder.encode_proteins()
      • MultiGPUEncoder
        • MultiGPUEncoder.__init__()
        • MultiGPUEncoder.num_gpus
        • MultiGPUEncoder.is_multi_gpu()
        • MultiGPUEncoder.encode_batch_async()
        • MultiGPUEncoder.encode_all_batches_async()
        • MultiGPUEncoder.encode_multi_gpu()
      • discover_available_gpus()
      • select_device_for_gpu()
      • validate_gpu_availability()
      • generate_random_protein()
      • generate_combined_proteins()
      • estimate_token_size()
    • Entropy
      • normalise_entropy()
      • normalise_dna_entropy()
      • normalise_protein_entropy()
      • normalise_three_di_entropy()
      • normalise_twelve_state_entropy()
      • EntropyReport
        • EntropyReport.dna_entropy_global
        • EntropyReport.orf_nt_entropy
        • EntropyReport.protein_aa_entropy
        • EntropyReport.three_di_entropy
        • EntropyReport.alphabet_sizes
        • EntropyReport.twelve_state_entropy
        • EntropyReport.__init__()
      • shannon_entropy()
      • calculate_sequence_entropy()
      • calculate_entropies_for_sequences()
    • Pipeline and schemas
      • PipelineResult
        • PipelineResult.input_id
        • PipelineResult.input_dna_length
        • PipelineResult.orfs
        • PipelineResult.proteins
        • PipelineResult.three_dis
        • PipelineResult.entropy
        • PipelineResult.__init__()
      • run_pipeline()
      • calculate_pipeline_entropy()
      • FeatureLocation
        • FeatureLocation.start
        • FeatureLocation.end
        • FeatureLocation.strand
        • FeatureLocation.frame
        • FeatureLocation.__init__()
      • FeatureDNA
        • FeatureDNA.nt_sequence
        • FeatureDNA.length
        • FeatureDNA.__init__()
      • FeatureProtein
        • FeatureProtein.aa_sequence
        • FeatureProtein.length
        • FeatureProtein.__init__()
      • FeatureThreeDi
        • FeatureThreeDi.encoding
        • FeatureThreeDi.length
        • FeatureThreeDi.method
        • FeatureThreeDi.model_name
        • FeatureThreeDi.inference_device
        • FeatureThreeDi.__init__()
      • FeatureTwelveState
        • FeatureTwelveState.encoding
        • FeatureTwelveState.length
        • FeatureTwelveState.__init__()
      • FeatureMetadata
        • FeatureMetadata.parent_id
        • FeatureMetadata.table_id
        • FeatureMetadata.has_start_codon
        • FeatureMetadata.has_stop_codon
        • FeatureMetadata.in_genbank
        • FeatureMetadata.__init__()
      • FeatureEntropy
        • FeatureEntropy.dna_entropy
        • FeatureEntropy.protein_entropy
        • FeatureEntropy.three_di_entropy
        • FeatureEntropy.twelve_state_entropy
        • FeatureEntropy.__init__()
      • UnifiedFeature
        • UnifiedFeature.orf_id
        • UnifiedFeature.location
        • UnifiedFeature.dna
        • UnifiedFeature.protein
        • UnifiedFeature.three_di
        • UnifiedFeature.metadata
        • UnifiedFeature.entropy
        • UnifiedFeature.twelve_state
        • UnifiedFeature.__init__()
      • UnifiedPipelineResult
        • UnifiedPipelineResult.schema_version
        • UnifiedPipelineResult.input_id
        • UnifiedPipelineResult.input_dna_length
        • UnifiedPipelineResult.dna_entropy_global
        • UnifiedPipelineResult.alphabet_sizes
        • UnifiedPipelineResult.features
        • UnifiedPipelineResult.__init__()
    • I/O
      • read_fasta()
      • read_fasta_iter()
      • write_fasta()
      • CodingInterval
        • CodingInterval.start
        • CodingInterval.end
        • CodingInterval.strand
        • CodingInterval.length
        • CodingInterval.__init__()
      • CdsMatchResult
        • CdsMatchResult.matched
        • CdsMatchResult.overlap_nt
        • CdsMatchResult.overlap_fraction
        • CdsMatchResult.compared_aa
        • CdsMatchResult.compatible_aa
        • CdsMatchResult.wildcard_aa
        • CdsMatchResult.identity
        • CdsMatchResult.phase_compatible
        • CdsMatchResult.reason
        • CdsMatchResult.__init__()
      • GenBankCDS
        • GenBankCDS.parent_id
        • GenBankCDS.start
        • GenBankCDS.end
        • GenBankCDS.strand
        • GenBankCDS.protein_sequence
        • GenBankCDS.record_length
        • GenBankCDS.feature_id
        • GenBankCDS.translation_table
        • GenBankCDS.codon_start
        • GenBankCDS.partial
        • GenBankCDS.skip_reason
        • GenBankCDS.__init__()
      • read_genbank()
      • extract_cds_features()
      • normalise_protein_sequence()
      • amino_acids_are_compatible()
      • normalise_orf_coordinates()
      • normalise_genbank_coordinates()
      • coding_phase_is_compatible()
      • calculate_interval_overlap()
      • compare_shared_translation()
      • evaluate_orf_genbank_cds_match()
      • orf_matches_genbank_cds()
      • match_orf_to_genbank_cds()
      • to_json_dict()
      • convert_pipeline_result_to_unified()
      • write_json()
      • read_json()
    • Machine learning
      • load_json_data()
      • load_json_file()
      • split_json_records()
      • extract_features()
      • filter_json_records_with_features()
      • GenbankClassifier
        • GenbankClassifier.__init__()
        • GenbankClassifier.fit()
        • GenbankClassifier.predict()
        • GenbankClassifier.predict_proba()
        • GenbankClassifier.evaluate()
        • GenbankClassifier.get_feature_importance()
        • GenbankClassifier.save()
        • GenbankClassifier.load()
      • split_json_files()
      • load_json_files()
      • train_with_file_split()
      • BaseModel
        • BaseModel.fit()
        • BaseModel.predict()
        • BaseModel.predict_proba()
        • BaseModel.evaluate()
        • BaseModel.save()
        • BaseModel.load()
        • BaseModel.get_feature_importance()
      • XGBoostModel
        • XGBoostModel.__init__()
        • XGBoostModel.fit()
        • XGBoostModel.predict()
        • XGBoostModel.predict_proba()
        • XGBoostModel.evaluate()
        • XGBoostModel.get_feature_importance()
        • XGBoostModel.save()
        • XGBoostModel.load()
      • NeuralNetModel
        • NeuralNetModel.__init__()
        • NeuralNetModel.fit()
        • NeuralNetModel.predict()
        • NeuralNetModel.predict_proba()
        • NeuralNetModel.evaluate()
        • NeuralNetModel.save()
        • NeuralNetModel.load()
    • Configuration, errors, and logging
      • ModelCapabilities
        • ModelCapabilities.model_name
        • ModelCapabilities.family
        • ModelCapabilities.supports_3di
        • ModelCapabilities.supports_12st
        • ModelCapabilities.supports_profiles
        • ModelCapabilities.deprecated
        • ModelCapabilities.description
        • ModelCapabilities.__init__()
      • resolve_model_name()
      • get_model_capabilities()
      • supported_models_help()
      • OrfEntropyError
      • ConfigurationError
      • InputError
      • OrfFinderError
      • TranslationError
      • EncodingError
      • ModelError
      • DeviceError
      • PipelineError
      • configure_logging()
      • get_logger()
      • is_configured()
      • get_log_file()
      • get_log_level()
      • set_log_level()
  • Encoding-budget estimation
    • CLI
    • Python API
  • Development guide
    • Environment
    • Source layout
    • Quality commands
    • Documentation
    • Integration tests
    • Release metadata
    • Contributing safely
  • Changelog
    • Unreleased
      • Fixes
      • Documentation
    • 0.1.0 — 19 January 2026
genome_entropy
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© Copyright 2026, Rob Edwards.

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