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)