pyrion 0.1.0__tar.gz

pyrion-0.1.0/API_REFERENCE.md

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+# Pyrion API Reference
+
+**Generated:** 2025-08-02 19:53:00
+
+Complete API reference with full docstrings and signatures.
+
+## Table of Contents
+
+- [pyrion](#pyrion)
+  - [cite](#cite)
+  - [get_version](#get_version)
+  - [get_version_info](#get_version_info)
+  - [quick_start](#quick_start)
+- [pyrion._bed12parser](#pyrion_bed12parser)
+- [pyrion._chainparser](#pyrion_chainparser)
+- [pyrion._faiparser](#pyrion_faiparser)
+- [pyrion._fastaparser](#pyrion_fastaparser)
+- [pyrion._gtfparser](#pyrion_gtfparser)
+- [pyrion._narrowbedparser](#pyrion_narrowbedparser)
+- [pyrion._version](#pyrion_version)
+- [pyrion.config](#pyrionconfig)
+  - [PyrionConfig](#pyrionconfig)
+
+---
+
+# pyrion
+
+Pyrion: A Fast and Efficient Bioinformatics Library for Genomic Data Processing
+
+
+## Functions
+
+### cite
+
+**Signature:** `()`
+
+Get citation information.
+
+
+### get_version
+
+**Signature:** `()`
+
+Get pyrion version.
+
+
+### get_version_info
+
+**Signature:** `()`
+
+Get pyrion version as tuple.
+
+
+### quick_start
+
+**Signature:** `()`
+
+
+---
+
+# pyrion._bed12parser
+
+
+---
+
+# pyrion._chainparser
+
+
+---
+
+# pyrion._faiparser
+
+Fast FASTA indexer for generating FAI entries - Production optimized
+
+
+---
+
+# pyrion._fastaparser
+
+Fast FASTA file parser with numpy integration - Production optimized
+
+
+---
+
+# pyrion._gtfparser
+
+High-performance GTF parser
+
+
+---
+
+# pyrion._narrowbedparser
+
+
+---
+
+# pyrion._version
+
+Version information for pyrion.
+
+
+---
+
+# pyrion.config
+
+Global configuration for pyrion library.
+
+
+## Classes
+
+### PyrionConfig
+
+Global configuration for pyrion library.
+
+Manages parallelization settings and other global options.
+
+**Signature:** `(self)`
+
+#### Methods
+
+**__init__**
+
+*Signature:* `(self)`
+
+Initialize self.  See help(type(self)) for accurate signature.
+
+
+**disable_parallel**
+
+*Signature:* `(self) -> None`
+
+Disable all parallel processing by setting max_cores to 0.
+
+
+**enable_parallel**
+
+*Signature:* `(self, max_cores: Optional[int] = None) -> None`
+
+Enable parallel processing.
+
+Args:
+    max_cores: Maximum cores to use. If None, uses default (min(available, 8)).
+
+
+**get_optimal_processes**
+
+*Signature:* `(self, n_items: int, max_processes: Optional[int] = None) -> int`
+
+Determine optimal number of processes based on data size and configuration.
+
+Args:
+    n_items: Number of items to process
+    max_processes: Override max processes for this call
+
+Returns:
+    Optimal number of processes (0 means use sequential processing)
+
+
+**summary**
+
+*Signature:* `(self) -> dict`
+
+Get a summary of current configuration.
+
+
+#### Properties
+
+**available_cores** -> `int`
+
+Get the number of available CPU cores (read-only).
+
+
+**max_cores** -> `int`
+
+Get the maximum number of cores to use for parallel processing.
+
+
+**min_items_for_parallel** -> `int`
+
+Get the minimum number of items required to use parallel processing.
+
+
+**multiprocessing_available** -> `bool`
+
+Check if multiprocessing is available (read-only).
+
+
+
+## Functions
+
+### disable_parallel
+
+**Signature:** `() -> None`
+
+Disable all parallel processing.
+
+
+### enable_parallel
+
+**Signature:** `(max_cores: Optional[int] = None) -> None`
+
+Enable parallel processing with optional core limit.
+
+
+### get_available_cores
+
+**Signature:** `() -> int`
+
+Get the number of available CPU cores.
+
+
+### get_config_summary
+
+**Signature:** `() -> dict`
+
+Get a summary of current configuration.
+
+
+### get_max_cores
+
+**Signature:** `() -> int`
+
+Get the current maximum number of cores for parallel processing.
+
+
+### get_min_items_for_parallel
+
+**Signature:** `() -> int`
+
+Get the minimum number of items required for parallel processing.
+
+
+### is_multiprocessing_available
+
+**Signature:** `() -> bool`
+
+Check if multiprocessing is available.
+
+
+### set_max_cores
+
+**Signature:** `(cores: int) -> None`
+
+Set the maximum number of cores to use for parallel processing.
+
+Args:
+    cores: Number of cores to use (1 to available_cores, or 0 to disable)
+
+
+### set_min_items_for_parallel
+
+**Signature:** `(items: int) -> None`
+
+Set the minimum number of items required for parallel processing.
+
+
+---
+
+# pyrion.constants
+
+
+---
+
+# pyrion.core
+
+Core genomics data structures and types.
+
+
+---
+
+# pyrion.core.amino_acid_auxiliary
+
+Auxiliary functions for amino acid sequence objects.
+
+
+## Functions
+
+### calculate_molecular_weight
+
+**Signature:** `(sequence) -> float`
+
+Calculate approximate molecular weight in Daltons.
+
+
+### count_amino_acids_in_sequence
+
+**Signature:** `(sequence) -> Dict[str, int]`
+
+Count occurrences of each amino acid type (ignoring masking).
+
+
+### get_amino_acid_composition
+
+**Signature:** `(sequence) -> Dict[str, float]`
+
+
+---
+
+# pyrion.core.amino_acid_sequences
+
+Amino acid sequence representations and storage.
+
+
+## Classes
+
+### AminoAcidSequence
+
+AminoAcidSequence(data: 'np.ndarray', metadata: 'Optional[Metadata]' = None)
+
+**Signature:** `(self, data: 'np.ndarray', metadata: 'Optional[Metadata]' = None) -> None`
+
+#### Methods
+
+**__init__**
+
+*Signature:* `(self, data: 'np.ndarray', metadata: 'Optional[Metadata]' = None) -> None`
+
+Initialize self.  See help(type(self)) for accurate signature.
+
+
+**__repr__**
+
+*Signature:* `(self) -> 'str'`
+
+Return repr(self).
+
+
+**__str__**
+
+*Signature:* `(self) -> 'str'`
+
+Return str(self).
+
+
+**apply_masking**
+
+*Signature:* `(self) -> "'AminoAcidSequence'"`
+
+
+**count_amino_acids**
+
+*Signature:* `(self) -> 'dict'`
+
+Count occurrences of each amino acid type (ignoring masking) using vectorized operations.
+
+
+**find_stop_codons**
+
+*Signature:* `(self) -> 'np.ndarray'`
+
+Find positions of stop codons in the sequence.
+
+
+**from_string**
+
+*Signature:* `(sequence: 'str', metadata: 'Optional[Metadata]' = None) -> "'AminoAcidSequence'"`
+
+
+**get_amino_acid_content**
+
+*Signature:* `(self) -> 'dict'`
+
+Get amino acid composition as percentages.
+
+
+**get_gap_positions**
+
+*Signature:* `(self) -> 'np.ndarray'`
+
+Get boolean array indicating which positions are gaps.
+
+
+**get_masked_positions**
+
+*Signature:* `(self) -> 'np.ndarray'`
+
+Get boolean array indicating which positions are masked.
+
+
+**get_stop_positions**
+
+*Signature:* `(self) -> 'np.ndarray'`
+
+Get boolean array indicating which positions are stop codons.
+
+
+**molecular_weight**
+
+*Signature:* `(self) -> 'float'`
+
+Calculate approximate molecular weight in Daltons.
+
+
+**remove_gaps**
+
+*Signature:* `(self) -> "'AminoAcidSequence'"`
+
+
+**remove_masking**
+
+*Signature:* `(self) -> "'AminoAcidSequence'"`
+
+
+**reverse**
+
+*Signature:* `(self) -> "'AminoAcidSequence'"`
+
+
+**slice**
+
+*Signature:* `(self, start: 'int', end: 'int') -> "'AminoAcidSequence'"`
+
+
+**to_fasta_string**
+
+*Signature:* `(self, width: 'int' = 80, header: 'Optional[str]' = None) -> 'str'`
+
+
+**to_string**
+
+*Signature:* `(self) -> 'str'`
+
+
+
+---
+
+# pyrion.core.canonizer
+
+Canonizer functions for selecting canonical transcripts from transcript lists.
+
+
+## Functions
+
+### DEFAULT_CANONIZER
+
+**Signature:** `(transcripts: List, **kwargs) -> Optional[str]`
+
+Default canonizer that selects the transcript with the longest total exonic length.
+
+
+### first_transcript_canonizer
+
+**Signature:** `(transcripts: List, **kwargs) -> Optional[str]`
+
+
+### longest_cds_canonizer
+
+**Signature:** `(transcripts: List, **kwargs) -> Optional[str]`
+
+
+### longest_isoform_canonizer
+
+**Signature:** `(transcripts: List, **kwargs) -> Optional[str]`
+
+Default canonizer that selects the transcript with the longest total exonic length.
+
+
+### longest_transcript_span_canonizer
+
+**Signature:** `(transcripts: List, **kwargs) -> Optional[str]`
+
+
+### most_exons_canonizer
+
+**Signature:** `(transcripts: List, **kwargs) -> Optional[str]`
+
+
+---
+
+# pyrion.core.codons
+
+Codon and codon sequence representations for genomic analysis.
+
+
+## Classes
+
+### Codon
+
+Codon representation holding 1-3 non-gap symbols (incomplete codons allowed).
+
+**Signature:** `(self, symbols: numpy.ndarray, is_rna: bool = False) -> None`
+
+#### Methods
+
+**__init__**
+
+*Signature:* `(self, symbols: numpy.ndarray, is_rna: bool = False) -> None`
+
+Initialize self.  See help(type(self)) for accurate signature.
+
+
+**__repr__**
+
+*Signature:* `(self) -> str`
+
+Return repr(self).
+
+
+**__str__**
+
+*Signature:* `(self) -> str`
+
+Return str(self).
+
+
+**is_complete**
+
+*Signature:* `(self) -> bool`
+
+Check if codon has exactly 3 non-gap symbols.
+
+
+**to_string**
+
+*Signature:* `(self) -> str`
+
+
+**translate**
+
+*Signature:* `(self, translation_table=None) -> str`
+
+
+
+### CodonSequence
+
+Codon sequence wrapper around NucleotideSequence with codon-wise operations.
+
+**Signature:** `(self, nucleotide_sequence)`
+
+#### Methods
+
+**__init__**
+
+*Signature:* `(self, nucleotide_sequence)`
+
+Initialize from a NucleotideSequence object.
+
+
+**__repr__**
+
+*Signature:* `(self) -> str`
+
+Return repr(self).
+
+
+**__str__**
+
+*Signature:* `(self) -> str`
+
+Return str(self).
+
+
+**get_codons**
+
+*Signature:* `(self, preserve_gaps: bool = False) -> List[pyrion.core.codons.Codon]`
+
+
+**get_frameshift_positions**
+
+*Signature:* `(self) -> List[Tuple[int, int]]`
+
+
+**insert_frameshift**
+
+*Signature:* `(self, position: int) -> None`
+
+Insert frameshift after the Nth valid nucleotide (atgcnATGCN) (0-based).
+
+
+**remove_frameshift**
+
+*Signature:* `(self, position: int) -> None`
+
+Remove frameshift after the Nth valid nucleotide (atgcnATGCN).
+
+
+**remove_gaps**
+
+*Signature:* `(self) -> None`
+
+
+**to_fasta_string**
+
+*Signature:* `(self, width: int = 80, header: Optional[str] = None) -> str`
+
+
+**translate**
+
+*Signature:* `(self, translation_table=None)`
+
+
+#### Properties
+
+**data** -> `ndarray`
+
+Access to underlying data array.
+
+
+
+---
+
+# pyrion.core.fai
+
+FASTA index (FAI) functionality for efficient random access to large FASTA files.
+
+
+## Classes
+
+### FaiEntry
+
+FASTA index entry for a single sequence.
+
+**Signature:** `(self, name: 'str', length: 'int', offset: 'int', line_bases: 'int', line_bytes: 'int') -> None`
+
+#### Methods
+
+**__init__**
+
+*Signature:* `(self, name: 'str', length: 'int', offset: 'int', line_bases: 'int', line_bytes: 'int') -> None`
+
+Initialize self.  See help(type(self)) for accurate signature.
+
+
+**__repr__**
+
+*Signature:* `(self) -> 'str'`
+
+Return repr(self).
+
+
+**__str__**
+
+*Signature:* `(self) -> 'str'`
+
+Format as FAI file line.
+
+
+**from_fai_line**
+
+*Signature:* `(line: 'str') -> "'FaiEntry'"`
+
+
+**get_sequence_end_offset**
+
+*Signature:* `(self) -> 'int'`
+
+
+
+### FaiStore
+
+Container for FASTA index entries with dict interface.
+
+**Signature:** `(self, entries: 'Optional[Dict[str, FaiEntry]]' = None)`
+
+#### Methods
+
+**__init__**
+
+*Signature:* `(self, entries: 'Optional[Dict[str, FaiEntry]]' = None)`
+
+Initialize self.  See help(type(self)) for accurate signature.
+
+
+**__repr__**
+
+*Signature:* `(self) -> 'str'`
+
+Return repr(self).
+
+
+**get_total_bases**
+
+*Signature:* `(self) -> 'int'`
+
+
+**load_from_file**
+
+*Signature:* `(filename: 'Union[str, Path]') -> "'FaiStore'"`
+
+
+**save_to_file**
+
+*Signature:* `(self, filename: 'Union[str, Path]') -> 'None'`
+
+
+
+---
+
+# pyrion.core.gene_data
+
+Gene data storage with multiple mappings.
+
+
+## Classes
+
+### GeneData
+
+Gene data container with optional mappings for gene-transcript relationships, biotypes, and names.
+
+**Signature:** `(self, source_file: Optional[str] = None)`
+
+#### Methods
+
+**__init__**
+
+*Signature:* `(self, source_file: Optional[str] = None)`
+
+Initialize self.  See help(type(self)) for accurate signature.
+
+
+**__repr__**
+
+*Signature:* `(self) -> str`
+
+Return repr(self).
+
+
+**add_gene_name**
+
+*Signature:* `(self, gene_id: str, gene_name: str) -> None`
+
+
+**add_gene_transcript_mapping**
+
+*Signature:* `(self, gene_id: str, transcript_id: str) -> None`
+
+
+**add_transcript_biotype**
+
+*Signature:* `(self, transcript_id: str, biotype: str) -> None`
+
+
+**get_biotype_count**
+
+*Signature:* `(self) -> int`
+
+
+**get_gene**
+
+*Signature:* `(self, transcript_id: str) -> Optional[str]`
+
+
+**get_gene_name**
+
+*Signature:* `(self, gene_id: str) -> Optional[str]`
+
+
+**get_gene_name_count**
+
+*Signature:* `(self) -> int`
+
+
+**get_gene_transcript_count**
+
+*Signature:* `(self) -> int`
+
+
+**get_genes_by_name**
+
+*Signature:* `(self, gene_name: str) -> Set[str]`
+
+
+**get_transcript_biotype**
+
+*Signature:* `(self, transcript_id: str) -> Optional[str]`
+
+
+**get_transcripts**
+
+*Signature:* `(self, gene_id: str) -> Set[str]`
+
+
+**has_biotype_mapping**
+
+*Signature:* `(self) -> bool`
+
+
+**has_gene**
+
+*Signature:* `(self, gene_id: str) -> bool`
+
+
+**has_gene_name_mapping**
+
+*Signature:* `(self) -> bool`
+
+
+**has_gene_transcript_mapping**
+
+*Signature:* `(self) -> bool`
+
+
+**has_transcript**
+
+*Signature:* `(self, transcript_id: str) -> bool`
+
+
+**summary**
+
+*Signature:* `(self) -> str`
+
+
+#### Properties
+
+**gene_ids** -> `Set`
+
+
+**transcript_ids** -> `Set`
+
+
+
+---
+
+# pyrion.core.genes
+
+Gene and transcript representations.
+
+
+## Classes
+
+### Gene
+
+Gene containing multiple transcripts with computed genomic bounds.
+
+**Signature:** `(self, gene_id: str, transcripts: List[pyrion.core.genes.Transcript], gene_name: Optional[str] = None)`
+
+#### Methods
+
+**__init__**
+
+*Signature:* `(self, gene_id: str, transcripts: List[pyrion.core.genes.Transcript], gene_name: Optional[str] = None)`
+
+Initialize self.  See help(type(self)) for accurate signature.
+
+
+**__repr__**
+
+*Signature:* `(self) -> str`
+
+Return repr(self).
+
+
+**apply_canonizer**
+
+*Signature:* `(self, canonizer_func: Optional[Callable] = None, **kwargs) -> None`
+
+Set the canonical transcript using a canonizer function.
+
+Args:
+    canonizer_func: Function that takes transcripts list and returns canonical transcript ID.
+                  If None, uses the default longest_isoform_canonizer.
+    **kwargs: Additional arguments passed to the canonizer function.
+
+
+**clear_canonical_transcript**
+
+*Signature:* `(self) -> None`
+
+
+**get_transcript**
+
+*Signature:* `(self, transcript_id: str) -> Optional[pyrion.core.genes.Transcript]`
+
+
+**has_transcript**
+
+*Signature:* `(self, transcript_id: str) -> bool`
+
+
+**set_canonical_transcript**
+
+*Signature:* `(self, transcript_id: str) -> None`
+
+
+#### Properties
+
+**canonical_transcript** -> `Optional`
+
+
+**canonical_transcript_id** -> `Optional`
+
+
+**chrom** -> `str`
+
+
+**has_canonical_transcript** -> `bool`
+
+
+**is_coding** -> `bool`
+
+Check if gene has any coding transcripts.
+
+
+**length** -> `int`
+
+
+**strand** -> `Strand`
+
+
+**transcript_ids** -> `Set`
+
+
+**transcripts** -> `List`
+
+
+
+### Transcript
+
+Transcript(blocks: numpy.ndarray, strand: pyrion.core.strand.Strand, chrom: str, id: str, cds_start: Optional[int] = None, cds_end: Optional[int] = None, biotype: Optional[str] = None)
+
+**Signature:** `(self, blocks: numpy.ndarray, strand: pyrion.core.strand.Strand, chrom: str, id: str, cds_start: Optional[int] = None, cds_end: Optional[int] = None, biotype: Optional[str] = None) -> None`
+
+#### Methods
+
+**__init__**
+
+*Signature:* `(self, blocks: numpy.ndarray, strand: pyrion.core.strand.Strand, chrom: str, id: str, cds_start: Optional[int] = None, cds_end: Optional[int] = None, biotype: Optional[str] = None) -> None`
+
+Initialize self.  See help(type(self)) for accurate signature.
+
+
+**__repr__**
+
+*Signature:* `(self) -> str`
+
+Return repr(self).
+
+
+**__str__**
+
+*Signature:* `(self) -> str`
+
+Return str(self).
+
+
+**compute_flanks**
+
+*Signature:* `(self, flank_size: int, chrom_sizes: Dict[str, int]) -> Tuple[Optional[pyrion.core.intervals.GenomicInterval], Optional[pyrion.core.intervals.GenomicInterval]]`
+
+
+**contains_interval**
+
+*Signature:* `(self, interval: pyrion.core.intervals.GenomicInterval) -> bool`
+
+
+**get_annotated_regions**
+
+*Signature:* `(self, chrom_sizes: dict, flank_size: int = 5000) -> pyrion.core.intervals.AnnotatedIntervalSet`
+
+
+**splice_junctions**
+
+*Signature:* `(self)`
+
+Generator yielding splice junction coordinates (donor, acceptor) for transcript.
+
+
+#### Properties
+
+**is_coding** -> `bool`
+
+
+
+### TranscriptsCollection
+
+Container for many transcripts.
+
+**Signature:** `(self, transcripts: Optional[List[pyrion.core.genes.Transcript]] = None, source_file: Optional[str] = None)`
+
+#### Methods
+
+**__init__**
+
+*Signature:* `(self, transcripts: Optional[List[pyrion.core.genes.Transcript]] = None, source_file: Optional[str] = None)`
+
+Initialize self.  See help(type(self)) for accurate signature.
+
+
+**__repr__**
+
+*Signature:* `(self) -> str`
+
+Return repr(self).
+
+
+**__str__**
+
+*Signature:* `(self) -> str`
+
+Return str(self).
+
+
+**apply_gene_canonical_mapping**
+
+*Signature:* `(self, gene_to_canonical: Dict[str, str]) -> None`
+
+gene_to_canonical: Dictionary mapping gene IDs to canonical transcript IDs
+
+
+**bind_gene_data**
+
+*Signature:* `(self, gene_data: 'GeneData') -> None`
+
+
+**canonize_transcripts**
+
+*Signature:* `(self, canonizer_func: Optional[Callable] = None, **kwargs) -> None`
+
+
+**from_json**
+
+*Signature:* `(file_path: Union[str, pathlib.Path]) -> 'TranscriptsCollection'`
+
+
+**get_all_chromosomes**
+
+*Signature:* `(self) -> List[str]`
+
+
+**get_by_chrom**
+
+*Signature:* `(self, chrom: str) -> List[pyrion.core.genes.Transcript]`
+
+
+**get_by_gene_name**
+
+*Signature:* `(self, gene_name: str) -> List[pyrion.core.genes.Gene]`
+
+Get Gene objects by gene name. Multiple genes can have the same name.
+
+
+**get_by_id**
+
+*Signature:* `(self, transcript_id: str) -> Optional[pyrion.core.genes.Transcript]`
+
+
+**get_canonical_transcripts**
+
+*Signature:* `(self) -> 'TranscriptsCollection'`
+
+
+**get_gene_by_id**
+
+*Signature:* `(self, gene_id: str) -> Optional[pyrion.core.genes.Gene]`
+
+
+**get_gene_by_transcript_id**
+
+*Signature:* `(self, transcript_id: str) -> Optional[pyrion.core.genes.Gene]`
+
+
+**get_genes_without_canonical_transcript**
+
+*Signature:* `(self) -> List[pyrion.core.genes.Gene]`
+
+
+**get_transcript_ids_by_chrom**
+
+*Signature:* `(self, chrom: str) -> List[str]`
+
+
+**get_transcripts_in_interval**
+
+*Signature:* `(self, interval: pyrion.core.intervals.GenomicInterval, include_partial: bool = True) -> 'TranscriptsCollection'`
+
+
+**save_to_bed12**
+
+*Signature:* `(self, file_path: Union[str, pathlib.Path]) -> None`
+
+
+**save_to_json**
+
+*Signature:* `(self, file_path: Union[str, pathlib.Path]) -> None`
+
+
+**summary**
+
+*Signature:* `(self) -> str`
+
+
+**to_bed12_string**
+
+*Signature:* `(self) -> str`
+
+
+#### Properties
+
+**applied_biotypes** -> `bool`
+
+
+**applied_gene_names** -> `bool`
+
+
+**available_data_mappings** -> `List`
+
+
+**gene_ids** -> `Set`
+
+
+**genes** -> `List`
+
+
+**has_gene_mapping** -> `bool`
+
+
+
+---
+
+# pyrion.core.genes_auxiliary
+
+Auxiliary functions for gene and transcript objects.
+
+
+## Functions
+
+### build_annotated_regions
+
+**Signature:** `(transcript, chrom_sizes: dict, flank_size: int = 5000) -> pyrion.core.intervals.AnnotatedIntervalSet`
+
+
+### compute_flanks
+
+**Signature:** `(transcript, flank_size: int, chrom_sizes: Dict[str, int]) -> Tuple[Optional[pyrion.core.intervals.GenomicInterval], Optional[pyrion.core.intervals.GenomicInterval]]`
+
+Get flanking regions of specified size around a transcript.
+
+
+### filter_transcripts_in_interval
+
+**Signature:** `(transcripts_collection, interval: pyrion.core.intervals.GenomicInterval, include_partial: bool = True)`
+
+Filter transcripts that are within or intersect with a genomic interval.
+
+
+### get_canonical_transcripts_from_collection
+
+**Signature:** `(transcripts_collection, canonizer_func: Optional[Callable] = None, **kwargs)`
+
+Get a new collection containing only canonical transcripts.
+
+
+### get_canonical_transcripts_only_from_collection
+
+**Signature:** `(transcripts_collection)`
+
+Get a new collection containing only already-set canonical transcripts.
+
+
+### get_cds_blocks
+
+**Signature:** `(transcript) -> numpy.ndarray`
+
+Get CDS blocks from transcript using slice operations.
+
+
+### get_genes_with_canonical_transcripts_from_collection
+
+**Signature:** `(transcripts_collection) -> List`
+
+Get all genes that have canonical transcripts set.
+
+
+### get_left_utr_blocks
+
+**Signature:** `(transcript) -> numpy.ndarray`
+
+Get UTR blocks to the left of CDS (chromosomally before CDS start).
+
+
+### get_right_utr_blocks
+
+**Signature:** `(transcript) -> numpy.ndarray`
+
+Get UTR blocks to the right of CDS (chromosomally after CDS end).
+
+
+### get_transcript_cds_interval
+
+**Signature:** `(transcript) -> Optional[pyrion.core.intervals.GenomicInterval]`
+
+Get genomic interval spanning the CDS region.
+
+
+### get_transcript_interval
+
+**Signature:** `(transcript) -> pyrion.core.intervals.GenomicInterval`
+
+Get genomic interval spanning the entire transcript.
+
+
+### get_utr3_blocks
+
+**Signature:** `(transcript) -> numpy.ndarray`
+
+
+### get_utr5_blocks
+
+**Signature:** `(transcript) -> numpy.ndarray`
+
+
+### set_canonical_transcripts_for_collection
+
+**Signature:** `(transcripts_collection, canonizer_func: Optional[Callable] = None, **kwargs) -> None`
+
+Set canonical transcripts for all genes in a collection using a canonizer function.
+
+
+---
+
+# pyrion.core.genome_alignment
+
+
+## Classes
+
+### GenomeAlignment
+
+GenomeAlignment(chain_id: int, score: int, t_chrom: str, t_strand: int, t_size: int, q_chrom: str, q_strand: int, q_size: int, blocks: numpy.ndarray, child_id: Optional[int] = None)
+
+**Signature:** `(self, chain_id: int, score: int, t_chrom: str, t_strand: int, t_size: int, q_chrom: str, q_strand: int, q_size: int, blocks: numpy.ndarray, child_id: Optional[int] = None) -> None`
+
+#### Methods
+
+**__init__**
+
+*Signature:* `(self, chain_id: int, score: int, t_chrom: str, t_strand: int, t_size: int, q_chrom: str, q_strand: int, q_size: int, blocks: numpy.ndarray, child_id: Optional[int] = None) -> None`
+
+Initialize self.  See help(type(self)) for accurate signature.
+
+
+**__repr__**
+
+*Signature:* `(self) -> str`
+
+Return repr(self).
+
+
+**aligned_length**
+
+*Signature:* `(self) -> int`
+
+
+**blocks_in_query**
+
+*Signature:* `(self) -> numpy.ndarray`
+
+
+**blocks_in_target**
+
+*Signature:* `(self) -> numpy.ndarray`
+
+
+**q_length**
+
+*Signature:* `(self) -> int`
+
+
+**t_length**
+
+*Signature:* `(self) -> int`
+
+
+
+### GenomeAlignmentsCollection
+
+Container for many genome alignments.
+
+**Signature:** `(self, alignments: Optional[List[pyrion.core.genome_alignment.GenomeAlignment]] = None, source_file: Optional[str] = None)`
+
+#### Methods
+
+**__init__**
+
+*Signature:* `(self, alignments: Optional[List[pyrion.core.genome_alignment.GenomeAlignment]] = None, source_file: Optional[str] = None)`
+
+Initialize self.  See help(type(self)) for accurate signature.
+
+
+**__repr__**
+
+*Signature:* `(self) -> str`
+
+Return repr(self).
+
+
+**__str__**
+
+*Signature:* `(self) -> str`
+
+String representation with summary.
+
+
+**from_json**
+
+*Signature:* `(file_path: Union[str, pathlib.Path]) -> 'GenomeAlignmentsCollection'`
+
+
+**get_alignments_fully_contained**
+
+*Signature:* `(self, interval: 'GenomicInterval') -> List[pyrion.core.genome_alignment.GenomeAlignment]`
+
+
+**get_alignments_in_interval**
+
+*Signature:* `(self, interval: 'GenomicInterval', include_partial: bool = True) -> List[pyrion.core.genome_alignment.GenomeAlignment]`
+
+
+**get_alignments_overlapping_query_interval**
+
+*Signature:* `(self, interval: 'GenomicInterval', include_partial: bool = True) -> List[pyrion.core.genome_alignment.GenomeAlignment]`
+
+
+**get_alignments_overlapping_target_interval**
+
+*Signature:* `(self, interval: 'GenomicInterval', include_partial: bool = True) -> List[pyrion.core.genome_alignment.GenomeAlignment]`
+
+
+**get_by_chain_id**
+
+*Signature:* `(self, chain_id: int) -> Optional[pyrion.core.genome_alignment.GenomeAlignment]`
+
+
+**get_by_query_chrom**
+
+*Signature:* `(self, chrom: str) -> List[pyrion.core.genome_alignment.GenomeAlignment]`
+
+
+**get_by_target_chrom**
+
+*Signature:* `(self, chrom: str) -> List[pyrion.core.genome_alignment.GenomeAlignment]`
+
+
+**get_chain_ids_by_query_chrom**
+
+*Signature:* `(self, chrom: str) -> List[int]`
+
+
+**get_chain_ids_by_target_chrom**
+
+*Signature:* `(self, chrom: str) -> List[int]`
+
+
+**get_query_chromosomes**
+
+*Signature:* `(self) -> List[str]`
+
+
+**get_reference_chromosomes**
+
+*Signature:* `(self) -> List[str]`
+
+
+**save_to_chain**
+
+*Signature:* `(self, file_path: Union[str, pathlib.Path]) -> None`
+
+
+**save_to_json**
+
+*Signature:* `(self, file_path: Union[str, pathlib.Path]) -> None`
+
+
+**sort_by_score**
+
+*Signature:* `(self, max_elems: Optional[int] = None) -> List[Tuple[int, int]]`
+
+
+**summary**
+
+*Signature:* `(self) -> str`
+
+
+
+---
+
+# pyrion.core.genome_alignment_auxiliary
+
+Auxiliary functions for genome alignment objects.
+
+
+## Functions
+
+### sort_alignments_by_score
+
+**Signature:** `(alignments_collection, max_elems: Optional[int] = None) -> List[Tuple[int, int]]`
+
+
+---
+
+# pyrion.core.intervals
+
+Genomic interval representations.
+
+
+## Classes
+
+### AnnotatedIntervalSet
+
+AnnotatedIntervalSet(intervals: numpy.ndarray, region_types: numpy.ndarray)
+
+**Signature:** `(self, intervals: numpy.ndarray, region_types: numpy.ndarray) -> None`
+
+#### Methods
+
+**__init__**
+
+*Signature:* `(self, intervals: numpy.ndarray, region_types: numpy.ndarray) -> None`
+
+Initialize self.  See help(type(self)) for accurate signature.
+
+
+**__repr__**
+
+*Signature:* `(self) -> str`
+
+Return repr(self).
+
+
+
+### GenomicInterval
+
+Single genomic interval with strand information and optional ID.
+
+**Signature:** `(self, chrom: str, start: int, end: int, strand: pyrion.core.strand.Strand = <Strand.UNKNOWN: 0>, id: Optional[str] = None) -> None`
+
+#### Methods
+
+**__init__**
+
+*Signature:* `(self, chrom: str, start: int, end: int, strand: pyrion.core.strand.Strand = <Strand.UNKNOWN: 0>, id: Optional[str] = None) -> None`
+
+Initialize self.  See help(type(self)) for accurate signature.
+
+
+**__repr__**
+
+*Signature:* `(self) -> str`
+
+Detailed representation for debugging.
+
+
+**__str__**
+
+*Signature:* `(self) -> str`
+
+Return str(self).
+
+
+**contains**
+
+*Signature:* `(self, pos: int) -> bool`
+
+
+**flip_strand**
+
+*Signature:* `(self) -> 'GenomicInterval'`
+
+
+**from_string**
+
+*Signature:* `(interval_string: str, id: Optional[str] = None) -> 'GenomicInterval'`
+
+Create GenomicInterval from string representation.
+
+Supported formats:
+- "chr1:100-200" (no strand)
+- "chr1:100-200:+" (plus strand)  
+- "chr1:100-200:-" (minus strand)
+- "chr1:1,000,000-2,000,000" (commas in numbers supported)
+- "chr11:118,300,000-118,400,000:+" (full example with commas)
+
+
+**intersects**
+
+*Signature:* `(self, other: 'GenomicInterval') -> bool`
+
+
+**length**
+
+*Signature:* `(self) -> int`
+
+
+**overlap**
+
+*Signature:* `(self, other: 'GenomicInterval') -> int`
+
+
+**to_bed6_string**
+
+*Signature:* `(self, score: int = 1000) -> str`
+
+Convert to BED6 format string.
+
+
+**union**
+
+*Signature:* `(self, other: 'GenomicInterval') -> Optional[ForwardRef('GenomicInterval')]`
+
+
+
+### GenomicIntervalsCollection
+
+GenomicIntervalsCollection(chrom: str, strand: pyrion.core.strand.Strand, array: numpy.ndarray, ids: numpy.ndarray)
+
+**Signature:** `(self, chrom: str, strand: pyrion.core.strand.Strand, array: numpy.ndarray, ids: numpy.ndarray) -> None`
+
+#### Methods
+
+**__init__**
+
+*Signature:* `(self, chrom: str, strand: pyrion.core.strand.Strand, array: numpy.ndarray, ids: numpy.ndarray) -> None`
+
+Initialize self.  See help(type(self)) for accurate signature.
+
+
+**__repr__**
+
+*Signature:* `(self) -> str`
+
+Return repr(self).
+
+
+**__str__**
+
+*Signature:* `(self) -> str`
+
+Return str(self).
+
+
+**filter_by**
+
+*Signature:* `(self, predicate: Callable[[pyrion.core.intervals.GenomicInterval], bool]) -> 'GenomicIntervalsCollection'`
+
+
+**from_array**
+
+*Signature:* `(array: numpy.ndarray, chrom: str, strand: Optional[pyrion.core.strand.Strand] = None, ids: Optional[List[str]] = None) -> 'GenomicIntervalsCollection'`
+
+Create collection from numpy array.
+
+
+**from_intervals**
+
+*Signature:* `(intervals: List[pyrion.core.intervals.GenomicInterval]) -> 'GenomicIntervalsCollection'`
+
+Create collection from list of GenomicInterval objects.
+
+
+**from_strings**
+
+*Signature:* `(interval_strings, ids: Optional[List[str]] = None) -> Dict[Tuple[str, pyrion.core.strand.Strand], ForwardRef('GenomicIntervalsCollection')]`
+
+
+**group_by_proximity**
+
+*Signature:* `(self, max_gap: int) -> List[ForwardRef('GenomicIntervalsCollection')]`
+
+
+**intersect**
+
+*Signature:* `(self, other: Union[ForwardRef('GenomicIntervalsCollection'), pyrion.core.intervals.GenomicInterval]) -> 'GenomicIntervalsCollection'`
+
+
+**is_empty**
+
+*Signature:* `(self) -> bool`
+
+
+**merge_close**
+
+*Signature:* `(self, max_gap: int = 0) -> 'GenomicIntervalsCollection'`
+
+
+**split_on_gaps**
+
+*Signature:* `(self, min_gap: int) -> List[ForwardRef('GenomicIntervalsCollection')]`
+
+
+**to_bed6_string**
+
+*Signature:* `(self, score: int = 1000) -> str`
+
+
+**to_intervals_list**
+
+*Signature:* `(self) -> List[pyrion.core.intervals.GenomicInterval]`
+
+
+
+### RegionType
+
+An enumeration.
+
+**Signature:** `(self, /, *args, **kwargs)`
+
+
+---
+
+# pyrion.core.intervals_auxiliary
+
+Auxiliary functions for interval objects.
+
+
+## Functions
+
+### create_intervals_collections_from_strings
+
+**Signature:** `(interval_strings, ids: Optional[List[str]] = None) -> Dict[Tuple[str, pyrion.core.strand.Strand], pyrion.core.intervals.GenomicIntervalsCollection]`
+
+Create collections from iterable of string representations, grouped by chromosome and strand.
+
+
+---
+
+# pyrion.core.nucleotide_sequences
+
+Sequence representations and storage.
+
+
+## Classes
+
+### NucleotideSequence
+
+NucleotideSequence(data: 'np.ndarray', is_rna: 'bool' = False, metadata: 'Optional[Metadata]' = None)
+
+**Signature:** `(self, data: 'np.ndarray', is_rna: 'bool' = False, metadata: 'Optional[Metadata]' = None) -> None`
+
+#### Methods
+
+**__init__**
+
+*Signature:* `(self, data: 'np.ndarray', is_rna: 'bool' = False, metadata: 'Optional[Metadata]' = None) -> None`
+
+Initialize self.  See help(type(self)) for accurate signature.
+
+
+**__repr__**
+
+*Signature:* `(self) -> 'str'`
+
+Return repr(self).
+
+
+**__str__**
+
+*Signature:* `(self) -> 'str'`
+
+Return str(self).
+
+
+**complement**
+
+*Signature:* `(self) -> "'NucleotideSequence'"`
+
+
+**from_string**
+
+*Signature:* `(sequence: 'str', is_rna: 'bool' = False, metadata: 'Optional[Metadata]' = None) -> "'NucleotideSequence'"`
+
+
+**get_masked_positions**
+
+*Signature:* `(self) -> 'np.ndarray'`
+
+
+**get_unmasked_positions**
+
+*Signature:* `(self) -> 'np.ndarray'`
+
+
+**is_position_masked**
+
+*Signature:* `(self, position: 'int') -> 'bool'`
+
+
+**mask**
+
+*Signature:* `(self, start: 'Optional[int]' = None, end: 'Optional[int]' = None) -> "'NucleotideSequence'"`
+
+
+**merge**
+
+*Signature:* `(self, other: "'NucleotideSequence'") -> "'NucleotideSequence'"`
+
+
+**remove_gaps**
+
+*Signature:* `(self) -> "'NucleotideSequence'"`
+
+
+**reverse**
+
+*Signature:* `(self) -> "'NucleotideSequence'"`
+
+
+**reverse_complement**
+
+*Signature:* `(self) -> "'NucleotideSequence'"`
+
+
+**slice**
+
+*Signature:* `(self, start: 'int', end: 'int') -> "'NucleotideSequence'"`
+
+
+**to_amino_acids**
+
+*Signature:* `(self, translation_table=None)`
+
+
+**to_codons**
+
+*Signature:* `(self)`
+
+
+**to_fasta_string**
+
+*Signature:* `(self, width: 'int' = 80, header: 'Optional[str]' = None) -> 'str'`
+
+
+**to_string**
+
+*Signature:* `(self) -> 'str'`
+
+
+**unmask**
+
+*Signature:* `(self, start: 'Optional[int]' = None, end: 'Optional[int]' = None) -> "'NucleotideSequence'"`
+
+
+#### Properties
+
+**masked_fraction** -> `float`
+
+
+
+### SequenceType
+
+Sequence type detection.
+
+**Signature:** `(self, /, *args, **kwargs)`
+
+
+---
+
+# pyrion.core.sequences_auxiliary
+
+Auxiliary functions for sequences objects.
+
+
+## Functions
+
+### mask_nucleotide_sequence_slice
+
+**Signature:** `(sequence, start: Optional[int] = None, end: Optional[int] = None)`
+
+
+### merge_nucleotide_sequences
+
+**Signature:** `(sequence1, sequence2)`
+
+
+### unmask_nucleotide_sequence_slice
+
+**Signature:** `(sequence, start: Optional[int] = None, end: Optional[int] = None)`
+
+
+---
+
+# pyrion.core.strand
+
+
+## Classes
+
+### Strand
+
+An enumeration.
+
+**Signature:** `(self, /, *args, **kwargs)`
+
+
+---
+
+# pyrion.core.translation
+
+Translation tables for genetic code.
+
+
+## Classes
+
+### TranslationTable
+
+TranslationTable(table_id: int, name: str, codon_table: Dict[tuple, int], start_codons: set[tuple], stop_codons: set[tuple])
+
+**Signature:** `(self, table_id: int, name: str, codon_table: Dict[tuple, int], start_codons: set[tuple], stop_codons: set[tuple]) -> None`
+
+#### Methods
+
+**__init__**
+
+*Signature:* `(self, table_id: int, name: str, codon_table: Dict[tuple, int], start_codons: set[tuple], stop_codons: set[tuple]) -> None`
+
+Initialize self.  See help(type(self)) for accurate signature.
+
+
+**__repr__**
+
+*Signature:* `(self) -> str`
+
+Return repr(self).
+
+
+**is_start_codon**
+
+*Signature:* `(self, codon_codes: Tuple[int, int, int]) -> bool`
+
+
+**is_stop_codon**
+
+*Signature:* `(self, codon_codes: Tuple[int, int, int]) -> bool`
+
+
+**mitochondrial**
+
+*Signature:* `() -> 'TranslationTable'`
+
+Mitochondrial genetic code (NCBI table 2).
+
+
+**standard**
+
+*Signature:* `() -> 'TranslationTable'`
+
+Standard genetic code (NCBI table 1).
+
+
+**translate_codon**
+
+*Signature:* `(self, codon_codes: Tuple[int, int, int]) -> int`
+
+
+
+---
+
+# pyrion.core_types
+
+Shared types, enums, and protocols for pyrion.
+
+
+## Classes
+
+### ExonType
+
+Enumeration for exon types in genomic annotations.
+
+**Signature:** `(self, /, *args, **kwargs)`
+
+
+---
+
+# pyrion.io
+
+I/O modules for various genomic file formats.
+
+
+---
+
+# pyrion.io.bed
+
+BED format I/O support.
+
+
+## Functions
+
+### read_bed12_file
+
+**Signature:** `(file_path: Union[str, pathlib.Path]) -> pyrion.core.genes.TranscriptsCollection`
+
+Read BED12 file and return TranscriptsCollection.
+
+
+### read_narrow_bed_file
+
+**Signature:** `(file_path: Union[str, pathlib.Path]) -> List[pyrion.core.intervals.GenomicInterval]`
+
+Read a narrow BED file with 3-9 fields and return a list of GenomicInterval objects.
+
+
+---
+
+# pyrion.io.chain
+
+Chain format I/O support.
+
+
+## Functions
+
+### read_chain_file
+
+**Signature:** `(file_path: Union[str, pathlib.Path], min_score: Optional[int] = None) -> pyrion.core.genome_alignment.GenomeAlignmentsCollection`
+
+Read chain file and return GenomeAlignmentsCollection.
+
+
+---
+
+# pyrion.io.fai
+
+FASTA indexing functionality using fast C extension.
+
+
+## Functions
+
+### create_fasta_index
+
+**Signature:** `(fasta_file: 'Union[str, Path]', fai_file: 'Optional[Union[str, Path]]' = None) -> 'FaiStore'`
+
+
+### get_or_create_fasta_index
+
+**Signature:** `(fasta_file: 'Union[str, Path]', force_recreate: 'bool' = False) -> 'FaiStore'`
+
+
+### load_fasta_index
+
+**Signature:** `(fai_file: 'Union[str, Path]') -> 'FaiStore'`
+
+
+---
+
+# pyrion.io.fasta
+
+FASTA I/O operations.
+
+
+## Classes
+
+### FastaAccessor
+
+**Signature:** `(self, fasta_file: 'Union[str, Path]', fai_store: 'FaiStore')`
+
+#### Methods
+
+**__init__**
+
+*Signature:* `(self, fasta_file: 'Union[str, Path]', fai_store: 'FaiStore')`
+
+Initialize FastaAccessor with FASTA file and index.
+
+
+**__repr__**
+
+*Signature:* `(self) -> 'str'`
+
+Return repr(self).
+
+
+**get_multiple_sequences**
+
+*Signature:* `(self, regions: 'List[GenomicInterval]', is_rna: 'bool' = False) -> 'Dict[str, NucleotideSequence]'`
+
+
+**get_sequence**
+
+*Signature:* `(self, region: 'GenomicInterval', is_rna: 'bool' = False) -> 'NucleotideSequence'`
+
+
+**get_sequence_length**
+
+*Signature:* `(self, sequence_name: 'str') -> 'int'`
+
+
+**get_sequence_names**
+
+*Signature:* `(self) -> 'List[str]'`
+
+
+**has_sequence**
+
+*Signature:* `(self, sequence_name: 'str') -> 'bool'`
+
+
+
+## Functions
+
+### read_dna_fasta
+
+**Signature:** `(filename: 'Union[str, Path]', **kwargs) -> 'Dict[str, NucleotideSequence]'`
+
+
+### read_fasta
+
+**Signature:** `(filename: 'Union[str, Path]', sequence_type: 'SequenceType', return_dict: 'bool' = True) -> 'Union[Dict[str, Union[NucleotideSequence, AminoAcidSequence]], List[Union[NucleotideSequence, AminoAcidSequence]]]'`
+
+
+### read_protein_fasta
+
+**Signature:** `(filename: 'Union[str, Path]', **kwargs) -> 'Dict[str, AminoAcidSequence]'`
+
+Read protein sequences from FASTA file.
+
+
+### read_rna_fasta
+
+**Signature:** `(filename: 'Union[str, Path]', **kwargs) -> 'Dict[str, NucleotideSequence]'`
+
+
+### write_fasta
+
+**Signature:** `(sequences: 'Union[Dict[str, NucleotideSequence], List[NucleotideSequence]]', filename: 'Union[str, Path]', line_width: 'int' = 80) -> 'None'`
+
+
+---
+
+# pyrion.io.gene_data
+
+Gene data I/O support.
+
+
+## Functions
+
+### read_gene_data
+
+**Signature:** `(file_path: Union[str, pathlib.Path], gene_column: Union[int, str, NoneType] = None, transcript_id_column: Union[int, str, NoneType] = None, gene_name_column: Union[int, str, NoneType] = None, transcript_type_column: Union[int, str, NoneType] = None, separator: str = '\t', has_header: bool = True) -> pyrion.core.gene_data.GeneData`
+
+Read gene data from TSV/CSV file and build mappings.
+
+Args:
+    file_path: Path to the data file
+    gene_column: Gene ID column index (1-based) or name. Optional.
+    transcript_id_column: Transcript ID column index (1-based) or name. Optional.
+    gene_name_column: Gene name column index (1-based) or name. Optional.
+    transcript_type_column: Transcript type/biotype column index (1-based) or name. Optional.
+    separator: Column separator. Default: ' ' (tab)
+    has_header: Whether file has header row. If False, only numeric column indices work.
+
+Returns:
+    GeneData object with available mappings built from the data
+
+Examples:
+    # Build all mappings from biomart TSV with header
+    gene_data = read_gene_data(
+        "transcripts.tsv",
+        gene_column="Gene stable ID",
+        transcript_id_column="Transcript stable ID", 
+        gene_name_column="Gene name",
+        transcript_type_column="Transcript type",
+        has_header=True
+    )
+    
+    # Build from file without header using column indices (1-based)
+    gene_data = read_gene_data(
+        "file.tsv",
+        gene_column=1,
+        transcript_id_column=2,
+        gene_name_column=5,
+        transcript_type_column=6,
+        has_header=False
+    )
+    
+    # Build only transcript-biotype mapping
+    gene_data = read_gene_data(
+        "file.tsv",
+        transcript_id_column="transcript_id",
+        transcript_type_column="biotype"
+    )
+
+
+### resolve_index
+
+**Signature:** `(column_idx: Union[int, str], header: List[str]) -> int | None`
+
+
+---
+
+# pyrion.io.genepred
+
+GenePred format I/O support.
+
+
+## Functions
+
+### read_genepred_file
+
+**Signature:** `(file_path: Union[str, pathlib.Path], has_header: bool = False, extended: bool = False) -> pyrion.core.genes.TranscriptsCollection`
+
+Read genePred file and return TranscriptsCollection.
+
+
+### read_refflat_file
+
+**Signature:** `(file_path: Union[str, pathlib.Path], has_header: bool = False) -> pyrion.core.genes.TranscriptsCollection`
+
+Read refFlat file and return TranscriptsCollection.
+
+refFlat format is like genePred but with an additional first column for gene name:
+geneName name chrom strand txStart txEnd cdsStart cdsEnd exonCount exonStarts exonEnds.
+
+
+---
+
+# pyrion.io.gtf
+
+High-performance GTF format I/O support using C extension.
+
+
+## Classes
+
+### GTFChunkReader
+
+**Signature:** `(self, file_path: Union[str, pathlib.Path], chunk_size_mb: int = 512)`
+
+#### Methods
+
+**__init__**
+
+*Signature:* `(self, file_path: Union[str, pathlib.Path], chunk_size_mb: int = 512)`
+
+Initialize self.  See help(type(self)) for accurate signature.
+
+
+**read_gene_chunks**
+
+*Signature:* `(self) -> Iterator[List[str]]`
+
+
+
+## Functions
+
+### read_gtf
+
+**Signature:** `(file_path: Union[str, pathlib.Path], chunk_size_mb: int = 512) -> pyrion.core.genes.TranscriptsCollection`
+
+
+---
+
+# pyrion.io.twobit
+
+2bit file format support.
+
+
+## Classes
+
+### TwoBitAccessor
+
+Access sequences from 2bit files using py2bit.
+
+**Signature:** `(self, file_path: str)`
+
+#### Methods
+
+**__init__**
+
+*Signature:* `(self, file_path: str)`
+
+Initialize self.  See help(type(self)) for accurate signature.
+
+
+**__repr__**
+
+*Signature:* `(self) -> str`
+
+Return repr(self).
+
+
+**chrom_names**
+
+*Signature:* `(self) -> List[str]`
+
+
+**chrom_sizes**
+
+*Signature:* `(self) -> Dict[str, int]`
+
+
+**close**
+
+*Signature:* `(self)`
+
+
+**fetch**
+
+*Signature:* `(self, chrom: str, start: int, end: int, strand: pyrion.core.strand.Strand = <Strand.PLUS: 1>) -> pyrion.core.nucleotide_sequences.NucleotideSequence`
+
+
+**fetch_interval**
+
+*Signature:* `(self, interval: pyrion.core.intervals.GenomicInterval) -> pyrion.core.nucleotide_sequences.NucleotideSequence`
+
+
+**list_chromosomes**
+
+*Signature:* `(self) -> None`
+
+
+**validate_interval**
+
+*Signature:* `(self, chrom: str, start: int, end: int) -> bool`
+
+
+
+---
+
+# pyrion.ops
+
+Pyrion operations module.
+
+
+---
+
+# pyrion.ops.chain_serialization
+
+Genome alignment serialization operations for chain format and JSON.
+
+
+## Functions
+
+### genome_alignment_from_dict
+
+**Signature:** `(data: Dict[str, Any]) -> pyrion.core.genome_alignment.GenomeAlignment`
+
+
+### genome_alignment_to_chain_string
+
+**Signature:** `(alignment: pyrion.core.genome_alignment.GenomeAlignment) -> str`
+
+Convert a single GenomeAlignment to chain format string.
+
+Chain format:
+chain {score} {t_chrom} {t_size} {t_strand} {t_start} {t_end} {q_chrom} {q_size} {q_strand} {q_start} {q_end} {chain_id}
+{block_size} {dt} {dq}
+...
+{final_block_size}
+
+
+### genome_alignment_to_dict
+
+**Signature:** `(alignment: pyrion.core.genome_alignment.GenomeAlignment) -> Dict[str, Any]`
+
+
+### genome_alignments_collection_from_dict
+
+**Signature:** `(data: Dict[str, Any]) -> pyrion.core.genome_alignment.GenomeAlignmentsCollection`
+
+
+### genome_alignments_collection_summary_string
+
+**Signature:** `(collection: pyrion.core.genome_alignment.GenomeAlignmentsCollection) -> str`
+
+
+### genome_alignments_collection_to_chain_string
+
+**Signature:** `(collection: pyrion.core.genome_alignment.GenomeAlignmentsCollection) -> str`
+
+
+### genome_alignments_collection_to_dict
+
+**Signature:** `(collection: pyrion.core.genome_alignment.GenomeAlignmentsCollection) -> Dict[str, Any]`
+
+
+### load_genome_alignments_collection_from_json
+
+**Signature:** `(file_path: Union[str, pathlib.Path]) -> pyrion.core.genome_alignment.GenomeAlignmentsCollection`
+
+
+### save_genome_alignments_collection_to_chain
+
+**Signature:** `(collection: pyrion.core.genome_alignment.GenomeAlignmentsCollection, file_path: Union[str, pathlib.Path]) -> None`
+
+
+### save_genome_alignments_collection_to_json
+
+**Signature:** `(collection: pyrion.core.genome_alignment.GenomeAlignmentsCollection, file_path: Union[str, pathlib.Path]) -> None`
+
+
+---
+
+# pyrion.ops.chain_slicing
+
+Chain slicing operations with proper Q strand handling.
+
+
+## Functions
+
+### remove_chain_region_target_space
+
+**Signature:** `(chain: pyrion.core.genome_alignment.GenomeAlignment, start: int, end: int, use_numba: bool = True) -> pyrion.core.genome_alignment.GenomeAlignment`
+
+
+### slice_chain_query_space
+
+**Signature:** `(chain: pyrion.core.genome_alignment.GenomeAlignment, start: int, end: int, use_numba: bool = True) -> pyrion.core.genome_alignment.GenomeAlignment`
+
+
+### slice_chain_target_space
+
+**Signature:** `(chain: pyrion.core.genome_alignment.GenomeAlignment, start: int, end: int, use_numba: bool = True) -> pyrion.core.genome_alignment.GenomeAlignment`
+
+
+---
+
+# pyrion.ops.chains
+
+Chain alignment operations for projecting genomic intervals.
+
+
+## Functions
+
+### get_chain_q_end
+
+**Signature:** `(genome_alignment) -> int`
+
+
+### get_chain_q_start
+
+**Signature:** `(genome_alignment) -> int`
+
+
+### get_chain_query_interval
+
+**Signature:** `(genome_alignment) -> pyrion.core.intervals.GenomicInterval`
+
+
+### get_chain_t_end
+
+**Signature:** `(genome_alignment) -> int`
+
+
+### get_chain_t_start
+
+**Signature:** `(genome_alignment) -> int`
+
+
+### get_chain_target_interval
+
+**Signature:** `(genome_alignment) -> pyrion.core.intervals.GenomicInterval`
+
+
+### project_intervals_through_chain
+
+**Signature:** `(intervals: numpy.ndarray, chain_blocks: numpy.ndarray) -> List[numpy.ndarray]`
+
+
+### project_intervals_through_genome_alignment
+
+**Signature:** `(intervals: numpy.ndarray, genome_alignment) -> List[numpy.ndarray]`
+
+Convenience function to project intervals through a GenomeAlignment object.
+
+
+### project_intervals_through_genome_alignment_to_intervals
+
+**Signature:** `(intervals: numpy.ndarray, genome_alignment, target_chrom: Optional[str] = None, target_strand: Optional[pyrion.core.strand.Strand] = None) -> List[pyrion.core.intervals.GenomicInterval]`
+
+Project intervals through genome alignment and convert to GenomicInterval objects.
+
+Args:
+    intervals: Array of intervals to project, shape (N, 2)
+    genome_alignment: GenomeAlignment object to project through
+    target_chrom: Target chromosome name (auto-detected if None)
+    target_strand: Target strand (auto-detected if None)
+
+
+### project_transcript_through_chain
+
+**Signature:** `(transcript: pyrion.core.genes.Transcript, chain: pyrion.core.genome_alignment.GenomeAlignment, only_cds=False) -> pyrion.core.intervals.GenomicInterval | None`
+
+
+### split_genome_alignment
+
+**Signature:** `(chain: pyrion.core.genome_alignment.GenomeAlignment, intersected_transcripts: List[pyrion.core.genes.Transcript], window_size: int = 1000000, intergenic_margin: int = 10000) -> Tuple[List[pyrion.core.genome_alignment.GenomeAlignment], Dict[int, List[str]]]`
+
+
+---
+
+# pyrion.ops.data_consistency
+
+Data consistency checking utilities.
+
+
+## Functions
+
+### check_data_consistency
+
+**Signature:** `(transcripts_collection: pyrion.core.genes.TranscriptsCollection, detailed: bool = False) -> str`
+
+Check data consistency in a transcripts collection.
+
+Analyzes the consistency of applied gene data mappings and reports issues:
+- Transcripts without gene IDs (if gene-transcript mapping was applied)
+- Transcripts without biotypes (if biotype mapping was applied)
+- Genes without names (if gene names were applied)
+
+
+---
+
+# pyrion.ops.entity_ops
+
+Entity-specific operations for Transcripts and GenomeAlignments using low-level interval operations.
+
+
+## Functions
+
+### find_alignment_gaps
+
+**Signature:** `(alignment: pyrion.core.genome_alignment.GenomeAlignment, space: str = 'target', use_numba: bool = True) -> numpy.ndarray`
+
+Find gaps in a genome alignment.
+
+Args:
+    alignment: GenomeAlignment object
+    space: "target" or "query" - which coordinate space to find gaps in
+    use_numba: Whether to use numba-optimized operations
+    
+Returns:
+    Array of gap intervals
+
+
+### find_transcript_overlaps
+
+**Signature:** `(transcript1: pyrion.core.genes.Transcript, transcript2: pyrion.core.genes.Transcript, region_type: str = 'exon', use_numba: bool = True) -> numpy.ndarray`
+
+Find overlaps between specific regions of two transcripts.
+
+
+### get_transcript_cds_in_range
+
+**Signature:** `(transcript: pyrion.core.genes.Transcript, start: int, end: int, use_numba: bool = True) -> numpy.ndarray`
+
+Get CDS blocks within a specific genomic range using slice operations.
+
+
+### get_transcript_introns_in_range
+
+**Signature:** `(transcript: pyrion.core.genes.Transcript, start: int, end: int, use_numba: bool = True) -> numpy.ndarray`
+
+Get intron blocks within a specific genomic range.
+
+
+### get_transcript_utrs_in_range
+
+**Signature:** `(transcript: pyrion.core.genes.Transcript, start: int, end: int, utr_type: str = 'both', use_numba: bool = True) -> numpy.ndarray`
+
+Get UTR blocks within a specific genomic range.
+
+
+### intersect_alignment_with_intervals
+
+**Signature:** `(alignment: pyrion.core.genome_alignment.GenomeAlignment, intervals: numpy.ndarray, space: str = 'target', use_numba: bool = True) -> numpy.ndarray`
+
+Find intersections between alignment blocks and given intervals.
+
+Args:
+    alignment: GenomeAlignment object
+    intervals: Array of intervals to intersect with, shape (N, 2)
+    space: "target" or "query" - which coordinate space to use
+    use_numba: Whether to use numba-optimized operations
+    
+Returns:
+    Array of intersection intervals
+
+
+### merge_genome_alignments
+
+**Signature:** `(alignments: List[pyrion.core.genome_alignment.GenomeAlignment], space: str = 'target', use_numba: bool = True) -> numpy.ndarray`
+
+Merge blocks from multiple genome alignments.
+
+
+### merge_transcript_cds
+
+**Signature:** `(transcripts: List[pyrion.core.genes.Transcript], use_numba: bool = True) -> numpy.ndarray`
+
+Merge CDS blocks from multiple transcripts.
+
+
+### merge_transcript_utrs
+
+**Signature:** `(transcripts: List[pyrion.core.genes.Transcript], utr_type: str = 'both', use_numba: bool = True) -> numpy.ndarray`
+
+Merge UTR blocks from multiple transcripts.
+
+
+### subtract_transcript_regions
+
+**Signature:** `(transcript: pyrion.core.genes.Transcript, subtract_regions: numpy.ndarray, region_type: str = 'exon', use_numba: bool = True) -> numpy.ndarray`
+
+Subtract regions from specific parts of a transcript.
+
+
+---
+
+# pyrion.ops.genes
+
+Gene and transcript operations.
+
+
+## Classes
+
+### SequenceAccessor
+
+Protocol for sequence accessors (TwoBitAccessor, FastaAccessor).
+
+**Signature:** `(self, *args, **kwargs)`
+
+#### Methods
+
+**__init__**
+
+*Signature:* `(self, *args, **kwargs)`
+
+
+**fetch**
+
+*Signature:* `(self, chrom: str, start: int, end: int, strand: pyrion.core.strand.Strand) -> pyrion.core.nucleotide_sequences.NucleotideSequence`
+
+Fetch sequence from chrom:start-end.
+
+
+
+## Functions
+
+### extract_cds_sequence
+
+**Signature:** `(transcript: pyrion.core.genes.Transcript, accessor: pyrion.ops.genes.SequenceAccessor) -> pyrion.core.nucleotide_sequences.NucleotideSequence`
+
+
+### extract_exon_sequence
+
+**Signature:** `(transcript: pyrion.core.genes.Transcript, accessor: pyrion.ops.genes.SequenceAccessor) -> pyrion.core.nucleotide_sequences.NucleotideSequence`
+
+
+### extract_utr3_sequence
+
+**Signature:** `(transcript: pyrion.core.genes.Transcript, accessor: pyrion.ops.genes.SequenceAccessor) -> pyrion.core.nucleotide_sequences.NucleotideSequence`
+
+
+### extract_utr5_sequence
+
+**Signature:** `(transcript: pyrion.core.genes.Transcript, accessor: pyrion.ops.genes.SequenceAccessor) -> pyrion.core.nucleotide_sequences.NucleotideSequence`
+
+
+### merge_transcript_intervals
+
+**Signature:** `(transcripts: List[pyrion.core.genes.Transcript], cds_only: bool = False, use_numba: bool = True) -> List[pyrion.core.intervals.GenomicInterval]`
+
+Merge overlapping or adjacent intervals from multiple transcripts.
+
+
+---
+
+# pyrion.ops.interval_collection_ops
+
+Bulk operations for GenomicIntervalsCollection using vectorized numpy operations.
+
+
+## Functions
+
+### create_collections_from_mixed_intervals
+
+**Signature:** `(intervals: List[pyrion.core.intervals.GenomicInterval], consider_strand: bool = False) -> List[pyrion.core.intervals.GenomicIntervalsCollection]`
+
+
+### filter_collection
+
+**Signature:** `(collection: pyrion.core.intervals.GenomicIntervalsCollection, predicate: Callable[[pyrion.core.intervals.GenomicInterval], bool]) -> pyrion.core.intervals.GenomicIntervalsCollection`
+
+
+### group_intervals_by_proximity
+
+**Signature:** `(collection: pyrion.core.intervals.GenomicIntervalsCollection, max_gap: int) -> List[pyrion.core.intervals.GenomicIntervalsCollection]`
+
+
+### intersect_collections
+
+**Signature:** `(collection: pyrion.core.intervals.GenomicIntervalsCollection, other: Union[pyrion.core.intervals.GenomicIntervalsCollection, pyrion.core.intervals.GenomicInterval]) -> pyrion.core.intervals.GenomicIntervalsCollection`
+
+
+### merge_close_intervals
+
+**Signature:** `(collection: pyrion.core.intervals.GenomicIntervalsCollection, max_gap: int = 0) -> pyrion.core.intervals.GenomicIntervalsCollection`
+
+
+### split_intervals_on_gaps
+
+**Signature:** `(collection: pyrion.core.intervals.GenomicIntervalsCollection, min_gap: int) -> List[pyrion.core.intervals.GenomicIntervalsCollection]`
+
+
+---
+
+# pyrion.ops.interval_ops
+
+Additional low-level interval operations for merge, intersection, etc.
+
+
+## Functions
+
+### intersect_intervals
+
+**Signature:** `(intervals1: numpy.ndarray, intervals2: numpy.ndarray, use_numba: bool = True) -> numpy.ndarray`
+
+
+### intervals_union
+
+**Signature:** `(intervals_list: List[numpy.ndarray], use_numba: bool = True) -> numpy.ndarray`
+
+
+### merge_intervals
+
+**Signature:** `(intervals: numpy.ndarray, use_numba: bool = None) -> numpy.ndarray`
+
+
+### subtract_intervals
+
+**Signature:** `(intervals1: numpy.ndarray, intervals2: numpy.ndarray, use_numba: bool = True) -> numpy.ndarray`
+
+
+---
+
+# pyrion.ops.interval_serialization
+
+Genomic interval serialization operations for BED6 format.
+
+
+## Functions
+
+### genomic_interval_to_bed6_string
+
+**Signature:** `(interval: pyrion.core.intervals.GenomicInterval, score: int = 1000) -> str`
+
+Convert a single GenomicInterval to BED6 format string.
+
+
+### genomic_intervals_to_bed6_string
+
+**Signature:** `(intervals: List[pyrion.core.intervals.GenomicInterval], score: int = 1000) -> str`
+
+
+### save_genomic_intervals_to_bed6
+
+**Signature:** `(intervals: List[pyrion.core.intervals.GenomicInterval], file_path: Union[str, pathlib.Path], score: int = 1000) -> None`
+
+
+---
+
+# pyrion.ops.interval_slicing
+
+Low-level interval slicing and manipulation operations.
+
+
+## Functions
+
+### invert_intervals
+
+**Signature:** `(intervals: numpy.ndarray, span_start: int, span_end: int, use_numba: bool = None) -> numpy.ndarray`
+
+Get the inverse (gaps) of intervals within a given span.
+    
+Example:
+    exons = [[100, 150], [200, 210], [400, 600]]
+    invert_intervals(exons, 50, 700) -> [[50, 100], [150, 200], [210, 400], [600, 700]]
+
+
+### remove_intervals
+
+**Signature:** `(intervals: numpy.ndarray, remove_start: int, remove_end: int, use_numba: bool = None) -> numpy.ndarray`
+
+Remove a region from intervals, potentially splitting them.
+    
+Example:
+    blocks = [[10, 100], [150, 300]]
+    remove_intervals(blocks, 50, 200) -> [[10, 50], [200, 300]]
+
+
+### slice_intervals
+
+**Signature:** `(intervals: numpy.ndarray, slice_start: int, slice_end: int, use_numba: bool = None) -> numpy.ndarray`
+
+Slice intervals to get only parts that intersect with [slice_start, slice_end).
+
+Example:
+    blocks = [[10, 30], [100, 150], [200, 210], [400, 600]]
+    slice_intervals(blocks, 40, 450) -> [[100, 150], [200, 210], [400, 450]]
+
+
+---
+
+# pyrion.ops.intervals
+
+Interval operations for pyrion.
+
+
+## Functions
+
+### array_to_intervals
+
+**Signature:** `(array: numpy.ndarray, chrom: str) -> List`
+
+Convert 2D numpy array of [start, end] pairs to list of GenomicInterval objects.
+
+
+### chains_to_arrays
+
+**Signature:** `(chains: List, for_q: bool = False) -> Tuple[numpy.ndarray, numpy.ndarray]`
+
+
+### compute_overlap_size
+
+**Signature:** `(start1: int, end1: int, start2: int, end2: int) -> int`
+
+
+### find_intersections
+
+**Signature:** `(arr1: numpy.ndarray, arr2: numpy.ndarray, ids1: Optional[List] = None, ids2: Optional[List] = None) -> Dict[Any, List]`
+
+Find intersections between two arrays of intervals.
+
+
+### intervals_to_array
+
+**Signature:** `(intervals: List) -> numpy.ndarray`
+
+Convert list of GenomicInterval objects to 2D numpy array of [start, end] pairs.
+
+
+### projected_intervals_to_genomic_intervals
+
+**Signature:** `(projected_arrays: List[numpy.ndarray], target_chrom: str, target_strand: pyrion.core.strand.Strand = <Strand.UNKNOWN: 0>, ids: Optional[List[str]] = None) -> List[List[pyrion.core.intervals.GenomicInterval]]`
+
+Convert projected interval arrays to GenomicInterval objects.
+
+Convenience function to convert the output of project_intervals_through_genome_alignment
+into GenomicInterval objects.
+
+
+### transcripts_to_arrays
+
+**Signature:** `(transcripts: List) -> Tuple[numpy.ndarray, numpy.ndarray]`
+
+
+---
+
+# pyrion.ops.sequence_serialization
+
+Sequence serialization operations for FASTA format.
+
+
+## Functions
+
+### amino_acid_sequence_to_fasta_string
+
+**Signature:** `(sequence: pyrion.core.amino_acid_sequences.AminoAcidSequence, width: int = 80, header: Optional[str] = None) -> str`
+
+
+### codon_sequence_to_fasta_string
+
+**Signature:** `(sequence: pyrion.core.codons.CodonSequence, width: int = 80, header: Optional[str] = None) -> str`
+
+
+### format_fasta_sequence
+
+**Signature:** `(sequence_string: str, width: int = 80) -> str`
+
+Format sequence string with specified line width.
+
+
+### get_sequence_header
+
+**Signature:** `(sequence: Any, index: Optional[int] = None) -> str`
+
+Extract or generate FASTA header for a sequence object.
+
+
+### nucleotide_sequence_to_fasta_string
+
+**Signature:** `(sequence: pyrion.core.nucleotide_sequences.NucleotideSequence, width: int = 80, header: Optional[str] = None) -> str`
+
+
+### save_sequences_to_fasta
+
+**Signature:** `(sequences: List[Any], file_path: Union[str, pathlib.Path], width: int = 80) -> None`
+
+
+### sequence_to_fasta_string
+
+**Signature:** `(sequence: Any, width: int = 80, header: Optional[str] = None) -> str`
+
+
+### sequences_to_fasta_string
+
+**Signature:** `(sequences: List[Any], width: int = 80) -> str`
+
+
+---
+
+# pyrion.ops.transcript_serialization
+
+Transcript serialization operations for BED12 and JSON formats.
+
+
+## Functions
+
+### load_transcripts_collection_from_json
+
+**Signature:** `(file_path: Union[str, pathlib.Path]) -> pyrion.core.genes.TranscriptsCollection`
+
+
+### save_transcripts_collection_to_bed12
+
+**Signature:** `(collection: pyrion.core.genes.TranscriptsCollection, file_path: Union[str, pathlib.Path]) -> None`
+
+
+### save_transcripts_collection_to_json
+
+**Signature:** `(collection: pyrion.core.genes.TranscriptsCollection, file_path: Union[str, pathlib.Path]) -> None`
+
+
+### transcript_from_dict
+
+**Signature:** `(data: Dict[str, Any]) -> pyrion.core.genes.Transcript`
+
+
+### transcript_to_bed12_string
+
+**Signature:** `(transcript: pyrion.core.genes.Transcript) -> str`
+
+
+### transcript_to_dict
+
+**Signature:** `(transcript: pyrion.core.genes.Transcript) -> Dict[str, Any]`
+
+
+### transcripts_collection_from_dict
+
+**Signature:** `(data: Dict[str, Any]) -> pyrion.core.genes.TranscriptsCollection`
+
+
+### transcripts_collection_summary_string
+
+**Signature:** `(collection: pyrion.core.genes.TranscriptsCollection) -> str`
+
+
+### transcripts_collection_to_bed12_string
+
+**Signature:** `(collection: pyrion.core.genes.TranscriptsCollection) -> str`
+
+
+### transcripts_collection_to_dict
+
+**Signature:** `(collection: pyrion.core.genes.TranscriptsCollection) -> Dict[str, Any]`
+
+
+---
+
+# pyrion.ops.transcript_slicing
+
+Transcript slicing operations.
+
+
+## Functions
+
+### get_transcript_introns
+
+**Signature:** `(transcript: pyrion.core.genes.Transcript, use_numba: bool = True) -> numpy.ndarray`
+
+Get intron blocks (gaps between exons) within transcript span.
+
+
+### remove_transcript_region
+
+**Signature:** `(transcript: pyrion.core.genes.Transcript, start: int, end: int, use_numba: bool = True) -> pyrion.core.genes.Transcript`
+
+Remove a region from transcript, potentially splitting blocks.
+
+Args:
+    transcript: Transcript object
+    start: Start position to remove (inclusive)
+    end: End position to remove (exclusive)
+    use_numba: Whether to use numba-optimized operations
+
+Returns:
+    New Transcript with region removed
+
+
+### slice_transcript
+
+**Signature:** `(transcript: pyrion.core.genes.Transcript, start: int, end: int, use_numba: bool = True) -> pyrion.core.genes.Transcript`
+
+Slice transcript to get only blocks that intersect with [start, end).
+
+
+---
+
+# pyrion.utils
+
+Utility modules for pyrion.
+
+
+---
+
+# pyrion.utils.amino_acid_encoding
+
+Amino acid encoding utilities using prime-based multiplicative semantics.
+
+
+## Functions
+
+### apply_masking_aa
+
+**Signature:** `(encoded: numpy.ndarray) -> numpy.ndarray`
+
+Apply masking using multiplicative semantics (multiply by -1, gaps stay 0).
+
+
+### decode_amino_acids
+
+**Signature:** `(encoded: numpy.ndarray) -> str`
+
+Decode int8 array to amino acid sequence using prime-based multiplicative semantics.
+
+
+### encode_amino_acids
+
+**Signature:** `(sequence: str) -> numpy.ndarray`
+
+Encode amino acid sequence to int8 array using prime-based multiplicative semantics.
+
+
+### get_masking_status_aa
+
+**Signature:** `(encoded: numpy.ndarray) -> numpy.ndarray`
+
+Get boolean array indicating which positions are masked.
+
+
+### is_gap
+
+**Signature:** `(code: int) -> bool`
+
+Check if code represents a gap.
+
+
+### is_masked
+
+**Signature:** `(code: int) -> bool`
+
+Check if amino acid is masked (negative and not 0).
+
+
+### is_stop
+
+**Signature:** `(code: int) -> bool`
+
+Check if code represents a stop codon.
+
+
+### is_unknown
+
+**Signature:** `(code: int) -> bool`
+
+Check if code represents an unknown amino acid.
+
+
+### mask
+
+**Signature:** `(code: int) -> int`
+
+Apply masking by multiplying by -1.
+
+
+### remove_masking_aa
+
+**Signature:** `(encoded: numpy.ndarray) -> numpy.ndarray`
+
+Remove masking using multiplicative semantics (take absolute value).
+
+
+### unmask
+
+**Signature:** `(code: int) -> int`
+
+Remove masking by taking absolute value.
+
+
+---
+
+# pyrion.utils.encoding
+
+Encoding utilities for nucleotides using multiplicative semantics.
+
+
+## Functions
+
+### apply_complement
+
+**Signature:** `(encoded: numpy.ndarray) -> numpy.ndarray`
+
+Apply complement using multiplicative semantics (multiply by -1).
+
+
+### apply_masking
+
+**Signature:** `(encoded: numpy.ndarray) -> numpy.ndarray`
+
+Apply masking using multiplicative semantics (multiply by 5, gaps stay 0).
+
+
+### complement
+
+**Signature:** `(code: int) -> int`
+
+Get complement by multiplying by -1.
+
+
+### decode_nucleotides
+
+**Signature:** `(encoded: numpy.ndarray, is_rna: bool = False) -> str`
+
+Decode int8 array to nucleotide sequence using multiplicative semantics.
+
+
+### encode_nucleotides
+
+**Signature:** `(sequence: str) -> numpy.ndarray`
+
+Encode nucleotide sequence to int8 array using multiplicative semantics.
+
+
+### get_masking_status
+
+**Signature:** `(encoded: numpy.ndarray) -> numpy.ndarray`
+
+Get boolean array indicating which positions are masked.
+
+
+### is_frameshift
+
+**Signature:** `(code: int) -> bool`
+
+Check if code represents a frameshift.
+
+
+### is_gap
+
+**Signature:** `(code: int) -> bool`
+
+Check if code represents a gap.
+
+
+### is_masked
+
+**Signature:** `(code: int) -> bool`
+
+Check if nucleotide is masked using multiplicative test.
+
+
+### mask
+
+**Signature:** `(code: int) -> int`
+
+Apply masking by multiplying by 5.
+
+
+### remove_masking
+
+**Signature:** `(encoded: numpy.ndarray) -> numpy.ndarray`
+
+Remove masking using multiplicative semantics.
+
+
+### unmask
+
+**Signature:** `(code: int) -> int`
+
+Remove masking by dividing by 5.
+
+
+---
+
+# pyrion.utils.numpy_utils
+
+
+---
+
+# pyrion.visualization
+
+The visualization module was quickly prototyped in Cursor without thorough design.
+
+A cleaner architecture and improved visuals are planned for a future release.
+
+
+## Classes
+
+### AlignmentFeature
+
+Wrapper for GenomeAlignment.
+
+**Signature:** `(self, alignment: pyrion.core.genome_alignment.GenomeAlignment)`
+
+#### Methods
+
+**__init__**
+
+*Signature:* `(self, alignment: pyrion.core.genome_alignment.GenomeAlignment)`
+
+Initialize self.  See help(type(self)) for accurate signature.
+
+
+#### Properties
+
+**end** -> `int`
+
+
+**length** -> `int`
+
+
+**start** -> `int`
+
+
+
+### Band
+
+Holds non-overlapping features placed in same vertical band.
+
+**Signature:** `(self, index: int)`
+
+#### Methods
+
+**__init__**
+
+*Signature:* `(self, index: int)`
+
+Initialize self.  See help(type(self)) for accurate signature.
+
+
+**add_feature**
+
+*Signature:* `(self, feature: pyrion.visualization.GenomicFeature)`
+
+Add feature to this band.
+
+
+**can_add_feature**
+
+*Signature:* `(self, feature: pyrion.visualization.GenomicFeature) -> bool`
+
+Check if feature can be added without overlap.
+
+
+
+### GenomicFeature
+
+Abstract base class for genomic features with start/end coordinates.
+
+**Signature:** `(self, /, *args, **kwargs)`
+
+#### Properties
+
+**end** -> `int`
+
+
+**length** -> `int`
+
+
+**start** -> `int`
+
+
+
+### GenomicRuler
+
+Renders genomic coordinate ruler with fixed height.
+
+**Signature:** `(self, interval: pyrion.core.intervals.GenomicInterval, tick_count: int = 10, inverted: bool = False, height: float = 0.15)`
+
+#### Methods
+
+**__init__**
+
+*Signature:* `(self, interval: pyrion.core.intervals.GenomicInterval, tick_count: int = 10, inverted: bool = False, height: float = 0.15)`
+
+Initialize self.  See help(type(self)) for accurate signature.
+
+
+**draw**
+
+*Signature:* `(self, ax, y: float = 0.0)`
+
+Draw ruler at specified y position.
+
+
+
+### IntervalFeature
+
+Wrapper for GenomicInterval.
+
+**Signature:** `(self, interval: pyrion.core.intervals.GenomicInterval)`
+
+#### Methods
+
+**__init__**
+
+*Signature:* `(self, interval: pyrion.core.intervals.GenomicInterval)`
+
+Initialize self.  See help(type(self)) for accurate signature.
+
+
+#### Properties
+
+**end** -> `int`
+
+
+**length** -> `int`
+
+
+**start** -> `int`
+
+
+
+### LayoutManager
+
+Assigns tracks to levels and produces packed band layout.
+
+**Signature:** `(self)`
+
+#### Methods
+
+**__init__**
+
+*Signature:* `(self)`
+
+Initialize self.  See help(type(self)) for accurate signature.
+
+
+**add_track**
+
+*Signature:* `(self, track: 'Track')`
+
+Assign track to correct level based on type.
+
+
+**compute_layout**
+
+*Signature:* `(self)`
+
+Run layout logic for all levels.
+
+
+**get_total_bands**
+
+*Signature:* `(self) -> int`
+
+Get total number of bands across all levels.
+
+
+
+### Level
+
+Contains features of one type, produces non-overlapping bands.
+
+**Signature:** `(self)`
+
+#### Methods
+
+**__init__**
+
+*Signature:* `(self)`
+
+Initialize self.  See help(type(self)) for accurate signature.
+
+
+**add_features**
+
+*Signature:* `(self, features: List[pyrion.visualization.GenomicFeature])`
+
+Add features to this level.
+
+
+**compute_bands**
+
+*Signature:* `(self)`
+
+Greedy algorithm to assign features to non-overlapping bands.
+
+
+
+### Track
+
+Logical unit of data belonging to one category.
+
+**Signature:** `(self, name: str, features: List[pyrion.visualization.GenomicFeature], track_type: pyrion.visualization.TrackType)`
+
+#### Methods
+
+**__init__**
+
+*Signature:* `(self, name: str, features: List[pyrion.visualization.GenomicFeature], track_type: pyrion.visualization.TrackType)`
+
+Initialize self.  See help(type(self)) for accurate signature.
+
+
+
+### TrackType
+
+An enumeration.
+
+**Signature:** `(self, /, *args, **kwargs)`
+
+
+### TranscriptFeature
+
+Wrapper for Transcript.
+
+**Signature:** `(self, transcript: pyrion.core.genes.Transcript)`
+
+#### Methods
+
+**__init__**
+
+*Signature:* `(self, transcript: pyrion.core.genes.Transcript)`
+
+Initialize self.  See help(type(self)) for accurate signature.
+
+
+#### Properties
+
+**end** -> `int`
+
+
+**length** -> `int`
+
+
+**start** -> `int`
+
+
+
+### VisualizationWindow
+
+Entry point for rendering genomic data visualization.
+
+**Signature:** `(self, interval: pyrion.core.intervals.GenomicInterval, height: Optional[float] = None, band_height: float = 0.35, band_spacing: float = 0.05, level_spacing: float = 0.2, ruler_height: float = 0.4, label_height: float = 0.15, show_labels: bool = True, left_padding_width: int = 15000, show_feature_labels: bool = True)`
+
+#### Methods
+
+**__init__**
+
+*Signature:* `(self, interval: pyrion.core.intervals.GenomicInterval, height: Optional[float] = None, band_height: float = 0.35, band_spacing: float = 0.05, level_spacing: float = 0.2, ruler_height: float = 0.4, label_height: float = 0.15, show_labels: bool = True, left_padding_width: int = 15000, show_feature_labels: bool = True)`
+
+Initialize self.  See help(type(self)) for accurate signature.
+
+
+**add_track**
+
+*Signature:* `(self, track: pyrion.visualization.Track)`
+
+Add a track to the window.
+
+
+**show**
+
+*Signature:* `(self, figsize: tuple = (12, 6))`
+
+Trigger layout and rendering.
+
+
+
+## Functions
+
+### create_alignment_track
+
+**Signature:** `(name: str, alignments: List[pyrion.core.genome_alignment.GenomeAlignment]) -> pyrion.visualization.Track`
+
+Create an alignment track from a list of GenomeAlignment objects.
+
+
+### create_interval_track
+
+**Signature:** `(name: str, intervals: List[pyrion.core.intervals.GenomicInterval]) -> pyrion.visualization.Track`
+
+Create an interval track from a list of GenomicInterval objects.
+
+
+### create_transcript_track
+
+**Signature:** `(name: str, transcripts: List[pyrion.core.genes.Transcript]) -> pyrion.visualization.Track`
+
+Create a transcript track from a list of Transcript objects.
+
+
+### create_window_for_region
+
+**Signature:** `(chrom: str, start: int, end: int, **kwargs) -> pyrion.visualization.VisualizationWindow`
+
+Create a VisualizationWindow for a specific genomic region.
+
+
+### visualize_alignments
+
+**Signature:** `(alignments: List[pyrion.core.genome_alignment.GenomeAlignment], window_interval: pyrion.core.intervals.GenomicInterval = None, track_name: str = 'Alignments', band_height: float = 0.35, **kwargs)`
+
+Quick function to visualize a list of alignments.
+
+
+### visualize_intervals
+
+**Signature:** `(intervals: List[pyrion.core.intervals.GenomicInterval], window_interval: pyrion.core.intervals.GenomicInterval = None, track_name: str = 'Intervals', band_height: float = 0.35, **kwargs)`
+
+Quick function to visualize a list of intervals.
+
+
+### visualize_transcripts
+
+**Signature:** `(transcripts: List[pyrion.core.genes.Transcript], window_interval: pyrion.core.intervals.GenomicInterval = None, track_name: str = 'Transcripts', band_height: float = 0.35, **kwargs)`
+
+Quick function to visualize a list of transcripts.
+
+
+---
+