Struct MultiFastaProvider 

pub struct MultiFastaProvider { /* private fields */ }

Multi-FASTA reference provider

Provides efficient random access to sequences across multiple FASTA files. Useful for reference datasets split across files (e.g., RefSeq transcripts).

Example

use ferro_hgvs::reference::multi_fasta::MultiFastaProvider;

let provider = MultiFastaProvider::from_directory("reference_data/transcripts")?;
let seq = provider.get_sequence("NM_000546.6", 0, 100)?;

Implementations

impl MultiFastaProvider

pub fn from_directory<P: AsRef<Path>>(dir: P) -> Result<Self, FerroError>

Create a new multi-FASTA provider from a directory of FASTA files

Scans the directory for .fna and .fa files with accompanying .fai indexes.

pub fn from_directories<P: AsRef<Path>>(dirs: &[P]) -> Result<Self, FerroError>

Create a provider from multiple directories (e.g., transcripts + genome)

pub fn from_manifest<P: AsRef<Path>>( manifest_path: P, ) -> Result<Self, FerroError>

Create a provider from a manifest file

pub fn with_cdot<P: AsRef<Path>, Q: AsRef<Path>>( fasta_path: P, cdot_path: Q, ) -> Result<Self, FerroError>

Create a provider from a single FASTA file with cdot metadata

This is the recommended method for normalizing intronic variants, as it combines genomic sequence data (from FASTA) with transcript metadata (from cdot) needed for coordinate conversions.

Arguments

• fasta_path - Path to an indexed FASTA file (must have .fai index)
• cdot_path - Path to a cdot JSON file (can be gzipped)

Example

let provider = MultiFastaProvider::with_cdot(
    "reference.fa",
    "cdot-0.2.32.refseq.GRCh38.json.gz",
)?;

pub fn has_sequence(&self, name: &str) -> bool

Check if a sequence exists

pub fn sequence_length(&self, name: &str) -> Option<u64>

Get the length of a sequence

pub fn sequence_count(&self) -> usize

Get total number of sequences

Trait Implementations

impl ReferenceProvider for MultiFastaProvider

fn get_transcript(&self, id: &str) -> Result<Transcript, FerroError>

Get a transcript by its accession

fn get_sequence( &self, id: &str, start: u64, end: u64, ) -> Result<String, FerroError>

Get a sequence region

fn get_genomic_sequence( &self, contig: &str, start: u64, end: u64, ) -> Result<String, FerroError>

Get genomic sequence for a contig/chromosome

fn has_genomic_data(&self) -> bool

Check if this provider has genomic sequence data

fn has_transcript(&self, id: &str) -> bool

Check if a transcript exists

fn get_protein_sequence( &self, accession: &str, start: u64, end: u64, ) -> Result<String, FerroError>

Get protein sequence for a protein accession

fn has_protein_data(&self) -> bool

Check if this provider has protein sequence data