autoBIGS.engine/README.md

# autoMLST.Engine

A python library implementing common BIGSdb MLST schemes and databases. Implementation follows the RESTful API outlined by the official [BIGSdb documentation](https://bigsdb.readthedocs.io/en/latest/rest.html) up to `V1.50.0`.

## Features

Briefly, this library can:
- Import multiple `FASTA` files
- Fetch the available BIGSdb databases that is currently live and available
- Fetch the available BIGSdb database schemas for a given MLST database
- Retrieve exact/non-exact MLST allele variant IDs based off a sequence
- Retrieve MLST sequence type IDs based off a sequence
- Output all results to a single CSV

Furthermore, this library is highly asynchronous where any potentially blocking operation, ranging from parsing FASTAs to performing HTTP requests are at least asynchronous, if not fully multithreaded.

## Usage

This library can be installed through pip. Learn how to [setup and install pip first](https://pip.pypa.io/en/stable/installation/).

Then, it's as easy as running `pip install automlst-engine` in any terminal that has pip in it's path (any terminal where `pip --version` returns a valid version and install path).

### CLI usage

This is a independent python library and thus does not have any form of direct user interface. One way of using it could be to create your own Python script that makes calls to this libraries functions. Alternatively, you may use `automlst-cli`, a `Python` package that implements a CLI for calling this library.
Elaborated on the README.md and added references to it in pyproject.toml 2025-01-17 15:08:47 +00:00			`# autoMLST.Engine`
Copied over most code from another of my projects 2025-01-08 15:14:06 +00:00
Elaborated on the README.md and added references to it in pyproject.toml 2025-01-17 15:08:47 +00:00			A python library implementing common BIGSdb MLST schemes and databases. Implementation follows the RESTful API outlined by the official [BIGSdb documentation](https://bigsdb.readthedocs.io/en/latest/rest.html) up to `V1.50.0`.
Updated README.md 2025-01-09 16:08:44 +00:00
Elaborated on the README.md and added references to it in pyproject.toml 2025-01-17 15:08:47 +00:00			`## Features`
Updated README.md 2025-01-09 16:08:44 +00:00
Elaborated on the README.md and added references to it in pyproject.toml 2025-01-17 15:08:47 +00:00			`Briefly, this library can:`
			- Import multiple `FASTA` files
			`- Fetch the available BIGSdb databases that is currently live and available`
			`- Fetch the available BIGSdb database schemas for a given MLST database`
			`- Retrieve exact/non-exact MLST allele variant IDs based off a sequence`
			`- Retrieve MLST sequence type IDs based off a sequence`
			`- Output all results to a single CSV`
Updated README.md 2025-01-09 16:08:44 +00:00
Elaborated on the README.md and added references to it in pyproject.toml 2025-01-17 15:08:47 +00:00			`Furthermore, this library is highly asynchronous where any potentially blocking operation, ranging from parsing FASTAs to performing HTTP requests are at least asynchronous, if not fully multithreaded.`
Updated README.md 2025-01-09 16:08:44 +00:00
Elaborated on the README.md and added references to it in pyproject.toml 2025-01-17 15:08:47 +00:00			`## Usage`

			`This library can be installed through pip. Learn how to [setup and install pip first](https://pip.pypa.io/en/stable/installation/).`

			Then, it's as easy as running `pip install automlst-engine` in any terminal that has pip in it's path (any terminal where `pip --version` returns a valid version and install path).

			`### CLI usage`

			This is a independent python library and thus does not have any form of direct user interface. One way of using it could be to create your own Python script that makes calls to this libraries functions. Alternatively, you may use `automlst-cli`, a `Python` package that implements a CLI for calling this library.