Rust Bioinformatics Toolbox (rboss)

Rust Bioinformatics Toolbox, abbreviated as rboss, is a command-line tool designed to facilitate various operations on bioinformatics files. It provides a range of commands to manipulate sequence data files commonly used in bioinformatics, such as BAM, FASTA, and FASTQ formats.

Minimum Supported Rust Version (MSRV)

This project adheres to a Minimum Supported Rust Version (MSRV) policy. The Minimum Supported Rust Version (MSRV) is 1.70.0. We ensure that all code within the project is compatible with this version or newer to maintain stability and compatibility.

Features

• High Performance: Take advantage of Rust's performance for heavy computational tasks.
• Safety: Rust's strong type system and ownership model ensure safety across bioinformatics operations.
• Concurrency: Utilize Rust's modern concurrency tools for parallel data processing.

Installation

You can install rboss using Cargo, the Rust package manager. Ensure you have Rust and Cargo installed on your system, then run:

cargo install rboss

Getting Started

To begin using rboss, you may invoke it with the following syntax:

rboss [OPTIONS] [COMMAND]

rboss provides several commands to perform different operations:

Commands

• extract (aliases: e): Extract reads from a BAM file.

  Usage:

  rboss extract [OPTIONS] <BAM_FILE>
  

• index: Index a BAM file to speed up read access.

  Usage:

  rboss index <BAM_FILE>
  

• fa2fq: Convert a FASTA file to FASTQ format.

  Usage:

  rboss fa2fq <FASTA_FILE>
  

• fq2fa: Convert a FASTQ file to FASTA format.

  Usage:

  rboss fq2fa <FASTQ_FILE>
  

• rsoft: Create soft links to files with the same suffix in one directory recursively.

  Usage:

  rboss rsoft <TARGET_DIR> -s <SUFFIX>
  

• help: Print detailed help information for rboss or its subcommands.

  Usage:

  rboss help [COMMAND]
  

Options

• --generate <GENERATOR>: Generate shell completions for rboss for the specified shell. Possible values include bash, elvish, fish, powershell, and zsh.

• -v, --verbose: Increase verbosity. The more occurrences of this flag, the more detailed the output.

• -q, --quiet: Decrease verbosity. The more occurrences of this flag, the less detailed the output.

• -h, --help: Print help information for rboss and its subcommands.

• -V, --version: Print the version information for rboss.

Examples

Extracting reads from a BAM file based on reads.txt:

rboss extract reads.txt sample.bam

Indexing a BAM file:

rboss index sample.bam

Converting a FASTA file to FASTQ:

rboss fa2fq sample.fasta

Converting a FASTQ file to FASTA:

rboss fq2fa sample.fastq

Creating soft links for files with a .txt or .csv suffix:

rboss rsoft /path/to/directory -s txt csv

For further help on any specific command, you can use the help command:

rboss help extract

For the latest updates and more detailed documentation, please visit the official rboss repository.

Contributing

Contributions to rboss are welcome. If you have suggestions for improvements or have identified issues, please open an issue or a pull request in the repository.

Thank you for using rboss, the versatile Rust-powered toolbox for bioinformatics data manipulation!

License

rboss is distributed under the terms of both the MIT license and the Apache License (Version 2.0). See LICENSE-APACHE and LICENSE-MIT for details.

Community

Join us on Discord/Gitter/Forum to discuss rboss development, ask questions, and collaborate with other contributors.

Credits

rboss is being actively developed and maintained by bioinformatics enthusiasts and the Rust community. We thank all contributors for their efforts.