Welcome to plastid!

For documentation, see our home page <http://plastid.readthedocs.io/en/latest/> on ReadtheDocs <http://readthedocs.io>.

To run the tests, download the test dataset <https://www.dropbox.com/s/np3wlfvp6gx8tb8/2022-05-04.plastid-test-data.tar.bz2?dl=0>_ and unpack it into plastid/test.

Introduction

plastid is a Python library for genomic analysis -- in particular, high-throughput sequencing data -- with an emphasis on simplicity for users. It was written by Joshua Dunn in Jonathan Weissman's lab <http://weissmanlab.ucsf.edu> at UCSF <http://ucsf.edu>, initially for analysis of ribosome profiling and RNA-seq data. Versions of it have been used in several publications.

plastid intended audience includes computational and traditional biologists, software developers, and even those who are new to sequencing analysis. It is released under the BSD 3-Clause license.

This package provides:

. A set of scripts that implement common sequencing analyses

. A set of classes for exploratory data analysis. These provide simple

and consistent interfaces for manipulating genomic features, read alignments, and quantitative data; and readily interface with existing scientific tools, like the SciPy stack.

. Script writing tools that make it easy to use the objects implemented in

plastid.

. Extensive documentation, both in source code and at `our home page

http://plastid.readthedocs.io/en/latest/_ onReadtheDocs http://readthedocs.io`_.

Installation

Bioconda ........

.. image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square :target: http://bioconda.github.io/recipes/plastid/README.html :alt: install with bioconda

Bioconda is a channel for the conda package manager with a focus on bioinformatics software. Once you have Bioconda installed, installing plastid is as easy as running::

$ conda create -n plastid plastid
$ source activate plastid

This will install all of the necessary dependencies for plastid in an isolated environment.

PyPI ....

plastid can be installed directly from PyPI

$ pip install numpy pysam cython
$ pip install plastid

If you get any runtime warnings about numpy versions having changed, or about a missing module in Pysam, or about some object being the wrong size, try regenerating the included C source files from the original Cython code. To do this type::

$ pip install --upgrade  --install-option='--recythonize' plastid

Running the tests

• NOTE: to run the entire test suite you'll first need to download our test dataset_ and unpack it into plastid/test/data.

We use nose as our test runner, and test under different versions of Python using tox. To completely control the environment (e.g. compilers et c), we recommend running the tests inside the Docker container, which contains large data files needed for the tests that aren't packaged with plastid by default:

.. code-block:: shell

build & run the Docker image from within the project folder

$ docker build --pull -t plastid . $ docker run -it --rm plastid

inside the container, run the tests over all default configurations

root@plastid $ tox

Our tox config lets developers run subsets of tests rather than the full suite. All positional arguments are passed through to nosetests

.. code-block:: shell

run all tests within the plastid.test.unit subpackage

root@plastid $ tox plastid.test.unit

run tests in two files

root@plastid $ tox plastid.test.unit.genomics.readers.test_bed plastid.test.unit.util.io.test_binary

By default, tox recompiles all C extensions before running the tests. This can be slow. To avoid doing that, set the environment variable PLASTID_NOREBUILD to true:

.. code-block:: shell

run unit tests without rebuilding the C extensions

root@plastid $ env PLASTID_NOREBUILD=true tox plastid.test.unit

Finally, if you only want to test in some, not all environments, you can do so with typical tox syntax:

.. code-block:: shell

list available test environments

root@plastid $ tox -l py36-pinned py36-latest py39-latest

run only in 2 selected environments

root@plastid $ tox -e py36-pinned,py39-latest plastid.test.unit

Links & help

• Documentation <http://plastid.readthedocs.io>_

• Our github repo <https://github.com/joshuagryphon/plastid>_