jperkel / gb_read

An example GenBank file reader in Rust

GB_READ: A Rust GenBank file reader

Update: 26 Nov 2020: Thanks to a suggestion from Avi Srivastava, gb_read now uses the clap crate for command-line processing. As a result, the syntax for specifying an alternate file on the command line has changed. See step 4 below for details.

This project was created to accompany a Nature Toolbox article (published 1 Dec 2020) on the use of Rust in science. It uses the gb-io crate for parsing a GenBank-formatted file, counting the genes, and translating them.

To use:

1. If you have not installed the Rust programming language, do so here.
2. Clone this GitHub repository. Click the green "Code" button above the file listing and select "Open with GitHub Desktop". Or, from the command line, execute git clone https://github.com/jperkel/gb_read.git.
3. Build the application, using Rust's build tool/package manager, Cargo. From the command line, execute cargo run. (If you do not have gb-io and other required libraries (or 'crates') installed, this step will do so for you.)
4. By default, the program will parse the included file nc_005816.gb. However, the user can specify another filename at the command line, eg: cargo run pbr322cargo run -- -i pbr322.gb. (pbr322.gb and two additional example files, puc19.gb and circdna.gb, are included in this repository.)
5. By default, the program uses a three-letter amino acid code (e.g., Met for methionine). Use -o to use a one-character code instead, e.g., cargo run -- -o -i pbr322.gb.
6. To create and view auto-generated documentation for this project, execute cargo doc --open.
7. To run the program's test suite, execute cargo test.

The R Markdown notebook, Growth_of_cratesio.Rmd, recreates the "Rust rising" graphic included in the article.

gb_read's Issues

Probably worth adding tarpaulin + coveralls

Hi @jperkel ,

The repo look great ! I
I just have a minor suggestion to improve & maintain the robustness of the code.
Through github actions and tarpaulin you can also track what percentage of your source code is covered through unit tests, coveralls also provides a nice web interface to track it.
Just as an example check this out for one of my repo, the code to add can be found here.

test

tagging @jperkel ...