Installation

For most users, you'll want to install this as a text editor extension. Each editor has its own installation instructions to follow. If you're looking to use tree-sitter-fastq as a library through Tree-sitter's supported language bindings, see Library installation, below.

Tree-sitter parsers are dynamic libraries compiled from C code, so you'll need a C compiler available on your system. Common choices include:

The parser is generated with tree-sitter version 0.26, which has a minimum parser application binary interface (ABI) of 13 and max parser ABI of 15.

Editor extensions

The following editors are supported:

• Helix
• Zed / Gram

Tree-sitter parsers are supported by the following editors, but installation is not supported at this time:

• Visual Studio Code / VSCodium / Other forks ¹
• Sublime Text ²
• Neovim ³
• Lapce ⁴
• Emacs ⁵

Helix

We need to add a fastq language and grammar to Helix's languages.toml configuration file.

[[language]] # (1)!
name = "fastq"
scope = "source.fastq"
file-types = ["fastq", "fq"]
roots = []

[[grammar]] # (2)!
name = "fastq"
source = { git = "https://gitlab.com/jrhawley/tree-sitter-fastq", rev = "..." } # (3)!

[[language]] # (1)!
name = "fastq"
scope = "source.fastq"
file-types = ["fastq", "fq"]
roots = []

[[grammar]] # (2)!
name = "fastq"
source = { git = "https://gitlab.com/jrhawley/tree-sitter-fastq", rev = "..." } # (3)!

[[language]] # (1)!
name = "fastq"
scope = "source.fastq"
file-types = ["fastq", "fq"]
roots = []

[[grammar]] # (2)!
name = "fastq"
source = { git = "https://gitlab.com/jrhawley/tree-sitter-fastq", rev = "..." } # (3)!

Then fetch and build the grammars to install it into Helix's runtime directory.

hx --grammar fetch
hx --grammar build

hx --health fastq

Configured language servers: None
Configured debug adapter: None
Configured formatter: None
Tree-sitter parser: ✓ # (1)!
Highlight queries: ✓  # (2)!
Textobject queries: ✘
Indent queries: ✘

hx --health fastq

Configured language servers: None
Configured debug adapter: None
Configured formatter: None
Tree-sitter parser: ✓ # (1)!
Highlight queries: ✓  # (2)!
Textobject queries: ✘
Indent queries: ✘

hx --health fastq

Configured language servers: None
Configured debug adapter: None
Configured formatter: None
Tree-sitter parser: ✓ # (1)!
Highlight queries: ✓  # (2)!
Textobject queries: ✘
Indent queries: ✘

See Helix's language configuration docs for additional details.

Zed / Gram

Zed and Gram both support the tree-sitter-fastq parser through the gram-zed-fastx extension. Open the "Extensions" page in Zed / Gram, click "Install from URL" and provide https://gitlab.com/jrhawley/gram-zed-fastx. This will compile the extension in the background.

A Rust toolchain must be installed on your system to compile this parser into a WebAssembly object, which Zed and Gram use to package their extensions. See Rust's documentation for directions how to install a Rust toolchain. Ensure the wasm32-wasip2 target is available in your toolchain by running:

rustup toolchain add wasm32-wasip2

The extension will be listed on the "Extensions" page if successfully installed.

Library installation

Tree-sitter has multiple official language bindings that allow Tree-sitter parsers to be used from other programming languages. Below are some examples of how to load tree-sitter-fastq parsers in those languages.

Rust

Add tree-sitter and tree-sitter-fastq to your project's Cargo.toml manifest.

[dependencies]
tree-sitter = "0.26.8"
tree-sitter-fastq = { git = "https://gitlab.com/jrhawley/tree-sitter-fastq" }

Then, in your code you can add the parser.

use tree_sitter::{InputEdit, Language, Parser, Point};

let mut parser = Parser::new();
parser.set_language(&tree_sitter_fastq::LANGUAGE.into()).expect("Error loading FASTQ grammar");

let source_code = r#">chr1
ACTAGTAGTCTA"#;
let mut tree = parser.parse(source_code, None).unwrap();
let root_node = tree.root_node();

assert_eq!(root_node.kind(), "source_file");
assert_eq!(root_node.start_position().column, 0);
assert_eq!(root_node.end_position().column, 12);

See tree-sitter for details.

Python

pip install tree-sitter
pip install git+https://gitlab.com/jrhawley/tree-sitter-fastq.git

conda install -c conda-forge tree_sitter
python -m pip install git+https://gitlab.com/jrhawley/tree-sitter-fastq.git

Then, in your code you can add the parser.

import tree_sitter_fastq as tsfastq
from tree_sitter import Language, Parser

FQ_LANGUAGE = Language(tsfastq.language())
parser = Parser(FQ_LANGUAGE)

source_code = """>chr1
ACTAGTAGTCTA"""
tree = parser.parse(bytes(source_code, "utf8"))
root_node = tree.root_node

assert root_node.type == "source_file"
assert root_node.start_point == (0, 0)
assert root_node.end_point == (1, 12)

See py-tree-sitter for details.