🐪 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/.
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.
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
camlhmpIf 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)
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!
I'm not a lawyer and MIT has always been my go-to license. So, MIT it is!
Support for this project came (in part) from the Wyoming Public Health Division, and the Center for Applied Pathogen Epidemiology and Outbreak Control (CAPE).
