sbol-fasta

Pure-Rust FASTA → SBOL 3 importer for the sbol-rs ecosystem.

FASTA is the lowest-common-denominator sequence exchange format — NCBI BLAST, UniProt downloads, every genome project, and most bioinformatics tools either emit or accept it. This crate lets sbol-rs ingest that data with zero new transitive dependencies.

Each >header record becomes one sbol::Component paired with one sbol::Sequence. The component's biological type (DNA / RNA / protein) and the sequence's EDAM encoding are auto-detected from the alphabet of the sequence itself; the detection can be overridden with FastaImporter::with_alphabet when the data is ambiguous.

FASTA carries no feature annotations — what you get back is a Component with no SequenceFeatures. For annotated data, use sbol-genbank instead.

Quickstart

use sbol_fasta::FastaImporter;

let (document, report) =
    FastaImporter::new("https://example.org/lab")?.read_path("genome.fasta")?;

println!(
    "{} component(s) ({} DNA, {} RNA, {} protein)",
    report.components, report.dna_records, report.rna_records, report.protein_records
);
document.check()?;
# Ok::<(), Box<dyn std::error::Error>>(())

CLI

sbol import-fasta genome.fasta \
  --namespace https://example.org/lab \
  --to turtle \
  -o genome.ttl \
  --validate

# Override alphabet detection for ambiguous sequences:
sbol import-fasta peptide.fasta \
  --namespace https://example.org/lab \
  --alphabet protein \
  --to turtle -o peptide.ttl

Accepted extensions: .fasta, .fa, .fna, .faa.

Alphabet detection

This handles the ambiguous case of FASTA files whose sequence is pure A/C/G/T — these are also valid protein letters, but in practice overwhelmingly mean DNA. Override with --alphabet protein on the CLI or .with_alphabet(Alphabet::Protein) in the SDK when the data is genuinely a peptide.

Dependencies

sbol-fasta does not depend on a third-party FASTA parser; the ~100-line parser lives in src/parser.rs. Compared to pulling in noodles-fasta, this saves four transitive dependencies (bstr, memchr, noodles-bgzf, noodles-core) for what amounts to "split on >, concatenate continuation lines."