针尾鸟

针尾鸟是一个MIT许可的、最小复制FASTA/FASTQ解析器和k-mer处理库，适用于Rust。

目标是编写一组快速且经过良好测试的函数，这些函数可以被更专业的生物信息学程序使用。针尾鸟的目标是在解析FASTX文件时与readfq C库一样快，在k-mer计数时比等效的Python实现快得多（即25倍）。

示例

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);
}

安装

针尾鸟需要安装rust和cargo。请使用您本地的包管理器（homebrew、apt-get、pacman等）或通过rustup安装这些。

一旦您设置了Rust，您可以在Cargo.toml文件中包含needletail，如下所示

[dependencies]
needletail = "0.4"

为开发安装needletail本身

git clone https://github.com/onecodex/needletail
cargo test  # to run tests

Python

文档

对于实际示例，您可以参考test_python.py。

Python库只抛出一个类型的异常：NeedletailError。

有两种方法可以解析FASTA/FASTQ：如果您有一个字符串（parse_fastx_string(content: str)）或文件的路径（parse_fastx_file(path: str)）。如果文件未找到或内容无效，这些函数将抛出异常，并返回一个迭代器。

from needletail import parse_fastx_file, NeedletailError, reverse_complement, normalize_seq

try:
    for record in parse_fastx_file("myfile.fastq"):
        print(record.id)
        print(record.seq)
        print(record.qual)
except NeedletailError:
    print("Invalid Fastq file")

记录具有以下形状

class Record:
    id: str
    seq: str
    qual: Optional[str]

    def is_fasta(self) -> bool
    def is_fastq(self) -> bool
    def normalize(self, iupac: bool)

请注意，normalize（请参阅https://docs.rs/needletail/0.4.1/needletail/sequence/fn.normalize.html了解其功能）会修改self.seq。它还可以作为normalize_seq(seq: str, iupac: bool)函数使用，此函数会返回标准化序列。

最后，还有一个reverse_complement(seq: str)函数，它将执行其名称所描述的操作。如果你传递一些无效字符，它不会引发错误。

构建

在Mac OS X/Unix系统上工作Python库（需要Python 3）

pip install maturin

# finally, install the library in the local virtualenv
maturin develop --cargo-extra-args="--features=python"

构建二进制轮盘并推送到PyPI

# The Mac build requires switching through a few different python versions
maturin build --features python --release --strip

# The linux build is automated through cross-compiling in a docker image
docker run --rm -v $(pwd):/io ghcr.io/pyo3/maturin:main build --features=python --release --strip -f
twine upload target/wheels/*

获取帮助

请将问题作为GitHub问题提出。我们计划很快添加更多文档，但在此期间，“doc”注释包含在源代码中。

贡献

请这样做！我们很高兴讨论可能的添加和/或接受拉取请求。

致谢

从0.4版本开始，解析器算法来自seq_io。虽然它已经略有修改，但主要来自该库。原始文件的链接可在src/parser/fast{a,q}.rs中找到。