Metadata-Version: 1.1
Name: plastid
Version: 0.4.0
Summary: Convert genomic datatypes into Pythonic objects useful to the SciPy stack
Home-page: https://github.com/joshuagryphon/plastid
Author: Joshua Griffin Dunn
Author-email: Joshua Griffin Dunn
License: BSD 3-Clause
Download-URL: https://pypi.python.org/pypi/plastid/
Description: Welcome to `plastid`!
        =====================
        
        For documentation, see `our home page <http://plastid.readthedocs.org/en/latest/>`_
        on `ReadtheDocs.org <http://readthedocs.org>`_.
        
        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 that create a simple,
             intuitive interfaces to genomic features,
             read alignments, and quantitative data. These objects readily
             interface with existing scientific tools, like the SciPy stack,
             to facilitate interactive or exploratory data analysis.
        
          #. 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.org/en/latest/>`_
             on `ReadtheDocs.org <http://readthedocs.org>`_.
        
        
        Installation
        ------------
        We're in development, so this takes a few extra steps:
        
            1. Make sure you have numpy and cython installed::
        
                pip install numpy cython
        
            2. Clone this repo::
                
                git clone https://github.com/joshuagryphon/plastid.git
        
            3. Install dependencies::
        
                cd plastid && pip install -r requirements.txt
        
            4. Build extensions::
        
                python setup.py build_ext --inplace
        
            5. Install beta::
        
                python setup.py develop --user
        
Keywords: ribosome profiling riboseq rna-seq sequencing genomics biology
Platform: OS Independent
Classifier: Development Status :: 4 - Beta
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development :: Libraries
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: POSIX
Classifier: Natural Language :: English
