plastid package

Welcome to plastid!

This package contains various utilities for analyzing high-throughput sequencing data, with an emphasis on simplicity for users. To this end, this package provides:

  1. A set of command-line scripts that implement common sequencing workflows (see plastid.bin).

  2. Readers that abstract data from various file formats into a minimal set of object types. These object types define APIs that easily interface with existing scientific tools, such as the SciPy stack (see plastid.genomics and plastid.readers)

  3. Tools to facilitate writing command-line scripts (see plastid.util.scriptlib)

Package overview

plastid is divided into the following subpackages:

Package

Contents

plastid.bin

Command-line scripts

plastid.genomics

Classes and functions to manipulate genome annotations, alignments, and quantitative data

plastid.plotting

Tools for plotting

plastid.readers

Parsers for various file formats

plastid.util

Utilities (e.g. function decorators, exceptions, argument parsers)

plastid.test

Unit and functional tests (requires download of test datasets)

Subpackages