Crate fastxgz

This crate is an implementation of a simple fasta and fastq parser. It handles decompression of a gzipped file. Fasta files with reads on multiple lines are supported. This crate also provides functions to iterate over kmers or their hash values.

Examples:

Iterating over the reads of a fasta file:

use fastxgz::fasta_reads;

let reads = fasta_reads("data/tests/data.fa").expect("The file cannot be opened.");
for read in reads {
    println!("{}", String::from_utf8(read).unwrap());
}

Iterating over the kmers of the reads of a gzipped fastq file:

use fastxgz::fastq_reads;
use fastxgz::KmerIterator;

let reads = fastq_reads("data/tests/data.fq.gz").expect("The file cannot be opened.");
let kmers = KmerIterator::from(reads, 31);
for kmer in kmers {
    println!("{}", String::from_utf8(kmer).unwrap());
}

Iterating over the hash of the kmers of the reads of a gzipped fastq file:

use fastxgz::fastq_reads;
use fastxgz::KmerIterator;
use fastxgz::HashIterator;

let reads = fastq_reads("data/tests/data.fq.gz").expect("The file cannot be opened.");
let kmers = KmerIterator::from(reads, 31);
let hashes = HashIterator::from(kmers);
for hash in hashes {
    println!("{}", hash);
}

Structs

• HashIterator
  An iterator taking a sequence of kmers and yielding their hash.
• KmerIterator
  An iterator taking a sequence of string and yielding their kmers.
• ResultLinesIterator

Functions

• fasta_reads
  Return an iterator over the reads of a (potentially gzipped) fasta file. Reads can be on multiple lines.
• fastq_reads
  Return an iterator over the reads of a (potentially gzipped) fastq file.
• lines_iterator
  Return an iterator over the lines of a (potentially gzipped) file.
• simple_fasta_reads
  Return an iterator over the reads of a (potentially gzipped) fastq file. The reads must be on a single line.