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camlhmp

🐪 camlhmp 🐪 - Classification through yAML Heuristic Mapping Protocol

camlhmp is a tool for generating organism typing tools from YAML schemas. Through discussions with Tim Read, we identified a need for a straightforward method to define and manage typing schemas for organisms of interest. YAML was chosen for its simplicity and readability.

Full documentation for camlhmp can be found at https://rpetit3.github.io/camlhmp/.

Purpose

The primary purpose of camlhmp is to provide a framework that enables researchers to independently define typing schemas for their organisms of interest using YAML. This approach facilitates the management and analysis biological data for researchers at any level of experience.

camlhmp does not supply pre-defined typing schemas. Instead, it equips researchers with the necessary tools to create and maintain their own schemas, ensuring these schemas can easily remain up to date with the latest scientific developments.

Finally, the development of camlhmp was driven by a practical need to streamline maintenance of multiple organism typing tools. Managing these tools separately is time-consuming and challenging. camlhmp simplifies this by providing a single framework for each tool.

Installation

camlhmp is available through PyPI and Bioconda. While you can install it through PyPi, it is recommended to install it through BioConda so that non-Python dependencies are also installed.

conda create -n camlhmp -c conda-forge -c bioconda camlhmp
conda activate camlhmp
camlhmp

Citing camlhmp

If you make use of camlhmp in your analysis, please cite the following:

• camlhmp
  Petit III RA, Read TD camlhmp: Classification through yAML Heuristic Mapping Protocol (GitHub)

• BLAST+
  Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL BLAST+: architecture and applications. BMC Bioinformatics 10, 421 (2009)

Naming

If I'm being honest, I really wanted to name a tool with "camel" in it because they are my wife's favorite animal🐪 and they also remind me of my friends in Oman!

Once it was decided YAML was going to be the format for defining schemas, I quickly stumbled on "Classification through YAML" and quickly found out I wasn't the only once who thought of "CAML". But, no matter, it was decided it would be something with "CAML", then Tim Read came with the save and suggested "Heuristic Mapping Protocol". So, here we are - camlhmp!

License

I'm not a lawyer and MIT has always been my go-to license. So, MIT it is!

Funding

Support for this project came (in part) from the Wyoming Public Health Division, and the Center for Applied Pathogen Epidemiology and Outbreak Control (CAPE).