Module seqio 

Sequence I/O Module

Provides unified reading capabilities for biological sequence files. Supports both FASTA and FASTQ formats, including gzip-compressed files.

Supported Formats

• FASTA: Standard sequence format with header and sequence lines
• FASTQ: Sequence format with quality scores (plain or gzipped)

Examples

use argenus::seqio::{FastaReader, FastqFile};

// Read FASTA file
let mut reader = FastaReader::open("sequences.fas").unwrap();
while let Some(record) = reader.read_next().unwrap() {
    println!("{}: {} bp", record.name, record.seq.len());
}

// Read FASTQ file (auto-detects gzip)
let mut reader = FastqFile::open("reads.fq.gz").unwrap();
while let Some(record) = reader.read_next().unwrap() {
    println!("{}: {} bp", record.name, record.seq.len());
}

Structs

FastaReader

Sequential reader for FASTA format files.

FastaRecord

A FASTA record containing sequence name and nucleotide sequence.

FastqReader

Generic FASTQ reader supporting any Read source.

FastqRecord

A FASTQ record containing sequence name, nucleotide sequence, and quality scores.

Enums

FastqFile

Auto-detecting FASTQ file reader.