Metadata-Version: 1.1
Name: plastid
Version: 0.3.0
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`!
        ====================
        
        We're in beta!
        --------------
        Welcome! ``plastid`` is still in beta. This means that the package
        is functional, but we're adding speed/memory optimizations, and considering
        moving some things around inside the package so that they either make more
        sense or take lest time to get to. We welcome your feedback
        in this process, should you have any.
        
        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
             interace 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 readthedocs
        
        
        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: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development :: Libraries
Classifier: Intended Audience :: Intended Audience :: Science/Research
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: POSIX
Classifier: Natural Language :: English
