Module bioinformatics 

Bioinformatics file formats

Provides support for common bioinformatics file formats:

• FASTA: Nucleotide and protein sequences
• FASTQ: Sequences with quality scores
• SAM/BAM: Sequence alignment data
• VCF: Variant Call Format for genomic variations Bioinformatics file format support

This module provides support for common bioinformatics file formats used in genomics, proteomics, and molecular biology research.

Supported Formats

• FASTA: Standard format for nucleotide and protein sequences
• FASTQ: Sequences with per-base quality scores
• SAM/BAM: Sequence Alignment/Map format
• VCF: Variant Call Format for genomic variations

Examples

use scirs2_io::formats::bioinformatics::{FastaReader, FastqReader};

// Read FASTA file
let mut reader = FastaReader::open("sequences.fasta")?;
for record in reader.records() {
    let record = record?;
    println!(">{}", record.id());
    println!("{}", record.sequence());
}

// Read FASTQ file
let mut reader = FastqReader::open("reads.fastq")?;
for record in reader.records() {
    let record = record?;
    println!("@{}", record.id());
    println!("{}", record.sequence());
    println!("+");
    println!("{}", record.quality());
}

Modules

analysis

Sequence analysis utilities

Structs

FastaReader

FASTA file reader

FastaRecord

FASTA sequence record

FastaRecordIterator

Iterator over FASTA records

FastaWriter

FASTA file writer

FastqReader

FASTQ file reader

FastqRecord

FASTQ sequence record

FastqRecordIterator

Iterator over FASTQ records

FastqWriter

FASTQ file writer

Enums

QualityEncoding

FASTQ quality encoding

Functions

count_fastasequences

Count sequences in a FASTA file

count_fastqsequences

Count sequences in a FASTQ file