Metadata-Version: 1.1
Name: plastid
Version: 0.4.2
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 simple, intuitive interfaces to complex
             genomic features, read alignments, and quantitative data. These objects
             readily interface with existing scientific tools, like the SciPy stack,
             to facilitate interactive / 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
        ------------
        ``plastid`` can be installed directly from PyPI.
        
            1. First make sure you have numpy and pysam installed::
        
                pip install numpy pysam
        
            2. Then::
                
                pip install plastid
        
            3. If when running you get any warnings about numpy versions having changed,
               regenerate the c files to match your numpy headers by typing:
        
               pip install cython
               pip install plastid --recythonize
        
        
        Links & help
        ------------
        
          - `Documentation <http://plastid.readthedocs.org>`_
        
          - `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 developers or validating installs
        
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
