pdm_utils package

Overview

The pdm_utils source code is structured within a general hierarchical strategy in mind:

• Submodules in the ‘constants’ subpackage define global variables for the entire package, and they do not import any other pdm_utils or third-party modules.

• Submodules in the ‘classes’ subpackage only import from the ‘constants’ subpackage, the ‘basic’ submodule in the ‘functions’ subpackage, or third-party modules. In general, each submodule defines one class.

• Submodules in the ‘functions’ subpackage (other than the ‘basic’ submodule) contain functions that are either stand-alone, that rely on third-party packages, or that manipulate pdm_utils objects.

• Submodules in the ‘pipelines’ subpackage contain programs that can be executed as command line tools that are meant to run from start to completion, and that can import all other submodules in the other subpackages. The most common entry point for these pipelines is the main() function. These submodules are functionalized such that custom Python tools can create alternative pipeline entry points or utilize individual functions.

• The ‘run’ module’ controls the command line toolkit. It is not intended to be called from other tools.

Subpackages

• constants
• classes
• functions
• pipelines

Submodules

• run

Bio-centric object relational mapping

A subset of pdm_utils classes represents the ‘back-end’ bio-centric ORM that can be used to exchange data between different data sources and perform biology-related tasks with the data:

• Bio-centric ORM

Tutorial

Refer to the brief introductory library tutorial to coding with the pdm_utils library.