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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.

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.

Quick Start

To quickly get started with camlhmp, you can install it through Bioconda and run the command-line interface:

# Install camlhmp through Bioconda
conda create -n camlhmp -c conda-forge -c bioconda camlhmp
conda activate camlhmp
camlhmp --help

# Example usage of camlhmp-blast-alleles
# Acquire test data
wget https://raw.githubusercontent.com/rpetit3/camlhmp/refs/heads/main/tests/data/blast/alleles/spn-pbptype.yaml
wget https://raw.githubusercontent.com/rpetit3/camlhmp/refs/heads/main/tests/data/blast/alleles/spn-pbptype.fasta
wget https://github.com/rpetit3/camlhmp/raw/refs/heads/main/tests/data/blast/alleles/SRR2912551.fna.gz

# Run camlhmp-blast-alleles
camlhmp-blast-alleles \
    --yaml spn-pbptype.yaml \
    --targets spn-pbptype.fasta \
    --input SRR2912551.fna.gz

Running camlhmp-blast-alleless with following parameters:
    --input SRR2912551.fna.gz
    --yaml spn-pbptype.yaml
    --targets spn-pbptype.fasta
    --outdir ./
    --prefix camlhmp
    --min-pident 95
    --min-coverage 95

Starting camlhmp for S. pneumoniae PBP typing...
Running tblastn...
Processing hits...
Final Results...
                               S. pneumoniae PBP typing
┏━━━┳━━━┳━━━┳━━━┳━━━┳━━━┳━━━┳━━━┳━━━┳━━━━┳━━━┳━━━━┳━━━┳━━━━┳━━━┳━━━━┳━━━┳━━━━┳━━━┳━━━━┓
┃ … ┃ … ┃ … ┃ … ┃ … ┃ … ┃ … ┃ … ┃ … ┃ 1… ┃ … ┃ 2… ┃ … ┃ 2… ┃ … ┃ 2… ┃ … ┃ 2… ┃ … ┃ 2… ┃
┡━━━╇━━━╇━━━╇━━━╇━━━╇━━━╇━━━╇━━━╇━━━╇━━━━╇━━━╇━━━━╇━━━╇━━━━╇━━━╇━━━━╇━━━╇━━━━╇━━━╇━━━━┩
│ … │ … │ … │ … │ … │ … │ … │ … │ … │    │ 0 │ 1… │ … │ 5… │   │ 2  │ … │ 1… │ … │    │
└───┴───┴───┴───┴───┴───┴───┴───┴───┴────┴───┴────┴───┴────┴───┴────┴───┴────┴───┴────┘
Writing outputs...
Final predicted type written to ./camlhmp.tsv
tblastn results written to ./camlhmp.tblastn.tsv

For more example commands and outputs, see the documentation for each command:

Documentation Overview

Installation
Information for installing camlhmp on your system

Available Tools
A list of available typing tools utilizing camlhmp

Schema Definition
Details about defining schemas for use with camlhmp

CLI Reference
Details about available CLI commands from camlhmp

API Reference
Details about using the camlhmp package in your own code

About
Information about the development and funding of camlhmp

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).

Wyoming Public Health Division Center for Applied Pathogen Epidemiology and Outbreak Control

Citing camlhmp

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