Crate needletail

Needletail is a crate to quickly and easily parse FASTA and FASTQ sequences out of streams/files and manipulate and analyse that data.

A contrived example of how to use it:

extern crate needletail;
use needletail::{parse_fastx_file, Sequence, FastxReader};

fn main() {
    let filename = "tests/data/28S.fasta";

    let mut n_bases = 0;
    let mut n_valid_kmers = 0;
    let mut reader = parse_fastx_file(&filename).expect("valid path/file");
    while let Some(record) = reader.next() {
        let seqrec = record.expect("invalid record");
        // keep track of the total number of bases
        n_bases += seqrec.num_bases();
        // normalize to make sure all the bases are consistently capitalized and
        // that we remove the newlines since this is FASTA
        let norm_seq = seqrec.normalize(false);
        // we make a reverse complemented copy of the sequence first for
        // `canonical_kmers` to draw the complemented sequences from.
        let rc = norm_seq.reverse_complement();
        // now we keep track of the number of AAAAs (or TTTTs via
        // canonicalization) in the file; note we also get the position (i.0;
        // in the event there were `N`-containing kmers that were skipped)
        // and whether the sequence was complemented (i.2) in addition to
        // the canonical kmer (i.1)
        for (_, kmer, _) in norm_seq.canonical_kmers(4, &rc) {
            if kmer == b"AAAA" {
                n_valid_kmers += 1;
            }
        }
    }
    println!("There are {} bases in your file.", n_bases);
    println!("There are {} AAAAs in your file.", n_valid_kmers);
}

Re-exports

• pub use parser::parse_fastx_file;
• pub use parser::parse_fastx_reader;
• pub use parser::parse_fastx_stdin;
• pub use parser::FastxReader;
• pub use sequence::Sequence;

Modules

• bitkmer
  Compact binary representations of nucleic acid kmers
• errors
  The errors needletail can return; only when parsing FASTA/FASTQ files
• kmer
  Functions for splitting sequences into fixed-width moving windows (kmers) and utilities for dealing with these kmers.
• parser
  Handles all the FASTA/FASTQ parsing
• sequence
  Generic functions for working with (primarily nucleic acid) sequences