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https://github.com/joshuagryphon/plastid

Position-wise analysis of sequencing and genomics data
https://github.com/joshuagryphon/plastid

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Position-wise analysis of sequencing and genomics data

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README 

        
Welcome to `plastid`!

=====================



For documentation, see `our home page

`_ on `ReadtheDocs

`_.



To run the tests, download the `test dataset

`_

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

`_ at `UCSF `_,  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

   `_ on `ReadtheDocs

   `_.



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 `_



- `Our github repo `_