MAFChunk is a Rust-based command-line tool designed to process MAF (Multiple Alignment Format) files, specifically to split alignment blocks into smaller, specified lengths. This functionality is particularly useful for handling chromosome-length blocks that are output by tools like wgatools pseudomaf, which generates MAF files relative to a reference sequence.
- Split MAF Blocks: Splits each alignment block in the MAF file into chunks of a user-defined length.
- Preserve Alignment Information: While splitting the blocks, it ensures that the essential alignment information (such as the source, start, size, strand, and sequence) is accurately maintained and represented in the resulting chunks.
- Rust Programming Language: The tool is written in Rust, so you will need the Rust compiler to compile the source code. You can install Rust through rustup.
To install MAFChunk, follow these steps:
- Clone the repository or download the source code to your local machine.
- Navigate to the directory containing the
Cargo.tomlfile. - Compile the project using Cargo, Rust's package manager and build system, by running the command
cargo build --release. - The executable will be located in
target/release/directory.
To use MAFChunk, you need to provide it with an input MAF file and the desired split length. The command-line syntax is as follows:
mafchunk <input_file.maf> <split_length>
<input_file.maf>: The path to the input MAF file you wish to process.<split_length>: The desired length of each chunk. This must be an integer value.
Example:
./mafchunk example.maf 1000
This command will process example.maf, splitting its blocks into chunks of 1000 base pairs each.
MAFChunk writes its output directly to the standard output (stdout). You can redirect this output to a file using shell redirection:
./mafchunk example.maf 1000 > output.maf
MAFChunk is released under the MIT License. See the LICENSE file for more details.