camlhmp 0.0.1

Classification through yAML Heuristic Mapping Protocol

camlhmp - Classification through yAML Heuristic Mapping Protocol (yeah, it's a stretch to make sure 🐪 is in the name!)

camlhmp

camlhmp is a tool for generating organism typing tools from YAML schemas. The idea came up from discussions with Tim Read about the need for a tool that would allow researchers to more easily define typing schemas for their organisms of interest. YAML seemed like a a nice format for this due to its simplicity and readability.

camlhmp is under active development, and any feedback is appreciated.

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 facilitates the management and analysis biological data, no matter the researchers experience level.

camlhmp does not supply any pre-defined typing schemas. Instead, it provides researchers with the tools necessary tools to create and maintain their own schemas. This I believe will ensure the schemas remain up to date with the latest developments in its respective field.

Additionally, this really aroses from a practical need to streamline my maintenance of multiple organism typing tools. Long-term maintenance of these tools is a challenge, and I think camlhmp will help me to keep them up-to-date and consistent.

Installation

camlhmp will be made available through PyPI and Bioconda. For now, you can install it from the GitHub repository with the following command:

conda create -n camlhmp python poetry
conda activate camlhmp
poetry add git+ssh://[e-mail]:rpetit3/camlhmp.git
camlhmp --help

YAML Schema Structure

The schema structure is designed to be simple and intuitive. Here is a basic skeleton of the expected schema structure:

%YAML 1.2
---
metadata:
  name: ""
  description: ""
  version: ""
  curators: []

engine:
  tool: ""

targets: []

aliases:
  - name: ""
    targets: []

profiles:
  - name: ""
    targets: []

From this schema we have a few sections:

• metadata: general information about the schema
• engine: computational requirements for sequence analysis
• targets: lists the sequence targets such as genes, proteins, or markers
• aliases: groups multiple targets under a common name for easier reference
• profiles: defines combinations of targets and aliases to form typing profiles

Within each section there are additional fields that will be descibed in the next sections.

metadata

The metadata section provides general information about the schema. This includes:

Field	Type	Description
name	string	The name of the schema
description	string	A brief description of the schema
version	string	The version of the schema
curators	list	A list of curators of the schema

engine

The engine section specifies the computational tools used for sequence analysis. Currently only one tool can be specified, and only blastn is supported.

Field	Type	Description
tool	string	The tool used to generate the data

targets

The targets section lists the specific sequence targets such as genes, proteins, or markers that the schema will analyze. These should be included in the associated sequence query data.

Field	Type	Description
targets	list	A list of targets to be analyzed

aliases

aliases are a convenient way to group multiple targets under a common name for easier reference.

Field	Type	Description
name	string	The name of the alias
targets	list	A list of targets that are part of the alias

profiles

The profiles section defines specific combinations of targets and aliases to form distinct typing profiles.

Field	Type	Description
name	string	The name of the profile
targets	list	A list of targets (can use aliases) that are part of the profile

Example Schema: Partial SCCmec Typing

Here is an example of a partial schema for SCCmec typing:

%YAML 1.2
---
# metadata: general information about the schema
metadata:
  name: "SCCmec Typing"                              # name of the schema
  description: "A partial schema for SCCmec typing"  # description of the schema
  version: "0.1"                                     # version of the schema
  curators:                                          # A list of curators of the schema
    - "Robert Petit"
# engine: specifies the computational tools and additional parameters used for sequence
#         analysis.
engine:
  tool: blastn # The tool used to generate the data
# targets: Lists the specific sequence targets such as genes, proteins, or markers that the
#          schema will analyze. These should be included in the associated sequence query data
targets:
  - "ccrA1"
  - "ccrA2"
  - "ccrA3"
  - "ccrB1"
  - "ccrB2"
  - "ccrB3"
  - "IS431"
  - "IS1272"
  - "mecA"
  - "mecI"
  - "mecR1"
# aliases: groups multiple targets under a common name for easier reference
aliases:
  - name: "ccr Type 1"           # name of the alias
    targets: ["ccrA1", "ccrB1"]  # list of targets that are part of the alias
  - name: "ccr Type 2"
    targets: ["ccrA2", "ccrB2"]
  - name: "ccr Type 3"
    targets: ["ccrA3", "ccrB3"]
  - name: "mec Class A"
    targets: ["IS431", "mecA", "mecR1", "mecI"]
  - name: "mec Class B"
    targets: ["IS431", "mecA", "mecR1", "IS1272"]
# profiles: define specific combinations of targets and aliases to form distinct typing profiles
profiles:
  - name: "I"          # name of the profile
    targets:           # list of targets (can use aliases) that are part of the profile
      - "ccr Type 1"
      - "mec Class B"
  - name: "II"
    targets:
      - "ccr Type 2"
      - "mec Class A"
  - name: "III"
    targets:
      - "ccr Type 3"
      - "mec Class A"
  - name: "IV"
    targets:
      - "ccr Type 2"
      - "mec Class B"

From this schema, camlhmp can generate a typing tool that can be used to analyze input assemblies. This is only a partial schema, as there are many more SCCmec types and subtypes. But using this schema it should be straight forward to add additional targets and profiles.

Citations

If you make use of this tool, please cite the following:

• BLAST
  Basic Local Alignment Search Tool
  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!