ggetrs
| Crates.io | ggetrs |
| lib.rs | ggetrs |
| version | |
| source | src |
| created_at | 2022-11-01 22:12:40.691689 |
| updated_at | 2024-11-22 01:29:49.731455 |
| description | Efficient querying of biological databases from the command line |
| homepage | https://noamteyssier.github.io/ggetrs/ |
| repository | https://github.com/noamteyssier/ggetrs |
| max_upload_size | |
| id | 703094 |
| Cargo.toml error: | TOML parse error at line 17, column 1 | 17 | autolib = false | ^^^^^^^ unknown field `autolib`, expected one of `name`, `version`, `edition`, `authors`, `description`, `readme`, `license`, `repository`, `homepage`, `documentation`, `build`, `resolver`, `links`, `default-run`, `default_dash_run`, `rust-version`, `rust_dash_version`, `rust_version`, `license-file`, `license_dash_file`, `license_file`, `licenseFile`, `license_capital_file`, `forced-target`, `forced_dash_target`, `autobins`, `autotests`, `autoexamples`, `autobenches`, `publish`, `metadata`, `keywords`, `categories`, `exclude`, `include` |
| size | 0 |
Noam Teyssier (noamteyssier)
documentation
README
ggetrs
Introduction
What is ggetrs?
ggetrs is a free, open-source command-line tool that enables efficient querying
of genomic databases.
It consists of a collection of separate but interoperable modules, each designed
to facilitate one type of database querying in a single line of code.
This is a rust reimplentation of the original python-based program
gget and was rewritten to take advantage
of rust's powerful HTTP and asynchronous functionality for a faster user experience.
There are some minor syntactic changes between function calls from the original gget
and a description for each tool is provided on the modules page.
Installation
The command line tool is distributed via crates.io and can be installed via the rust package manager cargo.
cargo install ggetrs
Alternative installation instructions as well as the python module installation can be found on the install page.
Documentation
Command Line and Python
All usage and function documentation for the command line and python utilities can be found on the ggetrs homepage.
Rust
ggetrs is implemented as a rust library as well as a standalone binary so all
documentation for API calls and Data Structures can be found on
docs.rs.
Contributing
This project is intended to be open-source and contributions are very welcome!
If you are new to rust or open source in general but still want to contribute please don't hesitate to reach out! I would be more than happy to help guide you through building your first module.
All new additions must pass and follow current testing standards.
FAQ
What makes this different than gget?
ggetrs takes advantage of rust's powerful powerful asynchronous features
and lets you perform a large numbers of HTTP requests without increasing wait times.
Since it is a compiled program as well there is no start-up time between commands
and you can run your favorite tool in a for loop with no overhead.
However ggetrs stays true to the original gget mindset and tries to make usage
as simple as possible no matter the interface (from python to CLI).
Does this have functions that gget doesn't?
We're working on having both tools mirror functionality - but currently this includes the Chembl bioactivity database, more endpoints from the Ensembl API, and direct queries to NCBI and Uniprot.
Does gget have functions that ggetrs does not?
ggetrs will likely not support the ggetrs muscle and ggetrs alphafold
functionalities for the time being.
The reasoning being that these are wrappers around existing binaries
and not HTTP requests.
Do I need to know rust to use this tool?
This tool is written fully in rust - but allows for a python interface using pyo3. Currently not all tools have a python API - but they are planned to be implemented eventually.
All of the currently supported gget modules have their python API implemented.