# plastid

**Repository Path**: biozzc/plastid

## Basic Information

- **Project Name**: plastid
- **Description**: Position-wise analysis of sequencing and genomics data
- **Primary Language**: Unknown
- **License**: BSD-3-Clause
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2021-09-15
- **Last Updated**: 2024-05-30

## Categories & Tags

**Categories**: Uncategorized

**Tags**: Ribo-seq

## README

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/h17go7tnas4hpby/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``'s 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 anlysis. 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/>`_ on `ReadtheDocs
   <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 necesary dependencies for ``plastid`` in an
isolated environment.

PyPI
....

``plastid`` can be installed directly from PyPI, but requires numpy, pysam,
and cython to be installed first i.e.::

    $ 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


Links & help
------------

- `Documentation <http://plastid.readthedocs.io>`_

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

- Subscribe to our mailing list by emailing ``listserv@listserv.ucsf.edu``
  with the message *subscribe plastidinfo firstname lastname* and an empty
  subject line

- `Test dataset <https://www.dropbox.com/s/h17go7tnas4hpby/plastid_test_data.tar.bz2?dl=0>`_,
  for development or validation of installations

- `Bioconda <bioconda.github.io>`_