Crate cyanea_seq 

Sequence I/O and manipulation for the Cyanea bioinformatics ecosystem.

Provides strongly-typed, validated biological sequence types with full IUPAC alphabet support, plus FASTA/FASTQ parsing:

• Alphabets — DnaAlphabet, RnaAlphabet, ProteinAlphabet
• Sequences — DnaSequence, RnaSequence, ProteinSequence
• Codon translation — Standard genetic code (NCBI Table 1)
• K-mer iteration — Zero-allocation KmerIter
• Quality scores — QualityScores with Phred+33/64 support
• FASTA parsing — FastaStats via parse_fasta_stats
• FASTQ parsing — FastqRecord, FastqStats via parse_fastq_file

Example

use cyanea_seq::{DnaSequence, RnaSequence, ProteinSequence};
use cyanea_core::Sequence;

// Create a DNA sequence (lowercased input is normalized)
let dna = DnaSequence::new(b"atgaaagcttaa").unwrap();
assert_eq!(dna.as_bytes(), b"ATGAAAGCTTAA");

// Reverse complement
let rc = dna.reverse_complement();
assert_eq!(rc.as_bytes(), b"TTAAGCTTTCAT");

// Transcribe DNA → RNA
let rna = dna.transcribe();
assert_eq!(rna.as_bytes(), b"AUGAAAGCUUAA");

// Translate RNA → Protein (stops at UAA)
let protein = rna.translate().unwrap();
assert_eq!(protein.as_bytes(), b"MKA");

Re-exports

pub use alphabet::Alphabet;

pub use alphabet::DnaAlphabet;

pub use alphabet::ProteinAlphabet;

pub use alphabet::RnaAlphabet;

pub use seq::ValidatedSeq;

pub use types::DnaSequence;

pub use types::ProteinSequence;

pub use types::RnaSequence;

pub use codon::classify_substitution;

pub use codon::codon_adaptation_index;

pub use codon::count_syn_nonsyn_sites;

pub use codon::translate_codon;

pub use codon::translate_sequence;

pub use codon::CodonUsage;

pub use codon::GeneticCode;

pub use codon::GeneticCodeId;

pub use codon::SubstitutionClass;

pub use kmer::KmerIter;

pub use quality::PhredEncoding;

pub use quality::QualityScores;

pub use fasta::parse_fasta_stats;

pub use fasta::FastaStats;

pub use fasta_index::FastaIndex;

pub use fasta_index::FastaIndexEntry;

pub use fasta_index::IndexedFastaReader;

pub use fastq::parse_fastq_file;

pub use fastq::parse_fastq_stats;

pub use fastq::FastqRecord;

pub use fastq::FastqStats;

pub use twobit::TwoBitSequence;

pub use suffix::SuffixArray;

pub use fm_index::FmIndex;

pub use fmd_index::FmdIndex;

pub use fmd_index::BiInterval;

pub use minhash::MinHash;

pub use minhash::FracMinHash;

pub use pattern::bndm;

pub use pattern::bom;

pub use pattern::horspool;

pub use pattern::kmp;

pub use pattern::myers_bitparallel;

pub use pattern::shift_and;

pub use pattern::ukkonen;

pub use pssm::dna_mapping;

pub use pssm::protein_mapping;

pub use pssm::Pssm;

pub use pssm::PssmDna;

pub use pssm::PssmProtein;

pub use orf::find_orfs;

pub use orf::find_orfs_both_strands;

pub use orf::find_orfs_with_codons;

pub use orf::OrfResult;

pub use orf::Strand;

pub use bwt::Bwt;

pub use trim::TrimPipeline;

pub use trim::TrimRange;

pub use trim::TrimReport;

pub use trim::OrphanPolicy;

pub use trim::PairedTrimReport;

pub use trim::PairedTrimResult;

pub use paired::deinterleave_fastq_file;

pub use paired::interleave_fastq_files;

pub use paired::parse_interleaved_fastq;

pub use paired::parse_paired_fastq_files;

pub use paired::parse_paired_fastq_stats;

pub use paired::strip_read_suffix;

pub use paired::validate_mate_pair;

pub use paired::validate_mate_pair_strict;

pub use paired::write_interleaved_fastq;

pub use paired::write_paired_fastq;

pub use paired::MateValidation;

pub use paired::PairedFastqRecord;

pub use paired::PairedFastqStats;

pub use protein_properties::amino_acid_composition;

pub use protein_properties::chou_fasman;

pub use protein_properties::extinction_coefficient;

pub use protein_properties::gor;

pub use protein_properties::gravy;

pub use protein_properties::hydrophobicity_profile;

pub use protein_properties::isoelectric_point;

pub use protein_properties::predict_disorder;

pub use protein_properties::AminoAcidComposition;

pub use protein_properties::DisorderPrediction;

pub use protein_properties::ExtinctionCoefficient;

pub use protein_properties::HydrophobicityScale;

pub use protein_properties::SecondaryStructure;

pub use protein_properties::SecondaryStructurePrediction;

pub use rna_structure::base_pair_distance;

pub use rna_structure::mccaskill;

pub use rna_structure::mountain_distance;

pub use rna_structure::nussinov;

pub use rna_structure::zuker_mfe;

pub use rna_structure::MfeResult;

pub use rna_structure::NussinovResult;

pub use rna_structure::PartitionResult;

pub use rna_structure::RnaSecondaryStructure;

pub use masking::apply_mask;

pub use masking::dust;

pub use masking::find_tandem_repeats;

pub use masking::mask_dust;

pub use masking::mask_seg;

pub use masking::seg;

pub use masking::DustParams;

pub use masking::MaskMode;

pub use masking::MaskResult;

pub use masking::MaskSource;

pub use masking::MaskedRegion;

pub use masking::SegParams;

pub use masking::TandemRepeatParams;

pub use debruijn::DeBruijnGraph;

pub use debruijn::Unitig;

pub use assembly::assembly_stats;

pub use assembly::nx_values;

pub use assembly::AssemblyStats;

pub use taxonomy::KmerClassifier;

pub use taxonomy::TaxonRank;

pub use taxonomy::TaxonomyNode;

pub use taxonomy::TaxonomyTree;

pub use restriction::common_enzymes;

pub use restriction::digest;

pub use restriction::find_cut_sites;

pub use restriction::fragment_sizes;

pub use restriction::CutSite;

pub use restriction::Fragment;

pub use restriction::Overhang;

pub use restriction::RestrictionEnzyme;

pub use motif::discover_motifs;

pub use motif::DiscoveredMotif;

pub use motif::Pwm;

pub use read_sim::simulate_reads;

pub use read_sim::ReadSimConfig;

pub use read_sim::SimulatedRead;

pub use motif_io::motif_similarity;

pub use motif_io::parse_jaspar;

pub use motif_io::parse_meme;

pub use motif_io::parse_transfac;

pub use motif_io::write_jaspar;

pub use motif_io::write_meme;

pub use motif_io::write_transfac;

pub use motif_io::Motif;

pub use motif_io::MotifAlphabet;

Modules

alphabet

Alphabet definitions for biological sequence validation.

assembly

Assembly quality-control metrics.

bwt

Burrows-Wheeler Transform (BWT) for arbitrary byte sequences.

codon

Codon translation, genetic codes, codon usage analysis, and CAI.

debruijn

De Bruijn graph construction and unitig extraction.

fasta

FASTA/FASTQ parsing and statistics.

fasta_index

Indexed FASTA reading with random access via .fai index files.

fastq

FASTQ record type and parsing.

fm_index

FM-Index for fast substring search on DNA sequences.

fmd_index

Bidirectional FM-Index (FMD-Index) for strand-aware DNA search.

kmer

Zero-allocation k-mer iterator.

masking

Low-complexity and repeat masking for biological sequences.

minhash

MinHash and FracMinHash sketching for rapid genome comparison.

motif

DNA motif discovery — PWM construction, scanning, and EM-based de novo discovery.

motif_io

Motif format I/O — MEME, TRANSFAC, and JASPAR parsers/writers plus PWM comparison.

orf

Open Reading Frame (ORF) finder.

paired

Paired-end FASTQ support.

pattern

Pattern matching algorithms for biological sequences.

protein_properties

Protein sequence property analysis.

pssm

Position-Specific Scoring Matrices (PSSMs) for motif representation and scanning.

quality

Phred quality scores for sequencing reads.

read_sim

Illumina-style short-read simulator.

restriction

Restriction enzyme recognition, cut-site finding, and in-silico digestion.

rna_structure

RNA secondary structure prediction.

seq

Generic validated sequence type.

suffix

Suffix array construction via the SA-IS algorithm.

taxonomy

Taxonomic classification — taxonomy trees, LCA queries, k-mer classifiers.

trim

Quality trimming, adapter removal, and read filtering for FASTQ records.

twobit

2-bit DNA encoding for compact storage.

types

Concrete sequence type aliases and biologically meaningful operations.