Metadata-Version: 1.1
Name: htsget
Version: 0.1.0a2
Summary: Python API and command line interface for the GA4GH streaming API.
Home-page: http://pypi.python.org/pypi/htsget
Author: Jerome Kelleher
Author-email: jerome.kelleher@well.ox.ac.uk
License: Apache Software License
Description: ======
        htsget
        ======
        
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            :target: https://travis-ci.org/jeromekelleher/htsget
        
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            :target: https://ci.appveyor.com/project/jeromekelleher/htsget/branch/master
        
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        .. image:: https://readthedocs.org/projects/htsget/badge/?version=latest
            :target: http://htsget.readthedocs.io/en/latest/?badge=latest
            :alt: Documentation Status
        
        ``htsget`` is a pure-Python API and command line interface for the GA4GH Streaming API. It
        provides a simple and reliable way to retrieve high-throughput sequencing data from
        servers supporting the protocol. Full documentation is available on
        `read the docs <https://htsget.readthedocs.io/en/stable/>`_.
        
        ************
        Installation
        ************
        
        To install ``htsget``, simply run::
        
            $ pip install htsget
        
        If you wish to install ``htsget`` into a your local Python installation, use::
        
            $ pip install htsget --user
        
        However, you will need to ensure that the local binary directory (usually something
        like ``$HOME/.local/bin``) is in your PATH.
        
        *********
        CLI Usage
        *********
        
        The ``htsget`` command line downloads data from a URL as follows::
        
            $ htsget http://htsnexus.rnd.dnanex.us/v1/reads/BroadHiSeqX_b37/NA12878 \
                --reference-name=2 --start=1000 --end=20000 -O NA12878_2.bam
        
        Full documentation on the command line options is available via ``htsget --help`` or
        `online <https://htsget.readthedocs.io/en/stable/cli.html>`_.
        
        *********
        API Usage
        *********
        
        The Python API provides a single function ``get``, which supports all of the
        arguments provided in the protocol. For example, we might have::
        
            import htsget
        
            with open("NA12878_2.bam", "wb") as output:
                htsget.get(
                    "http://htsnexus.rnd.dnanex.us/v1/reads/BroadHiSeqX_b37/NA12878", output,
                    reference_name="2", start=1000, end=20000)
        
         Full API documentation is available on
        `read the docs <https://htsget.readthedocs.io/en/stable/api.html>`_.
        
Keywords: BAM,CRAM,Streaming
Platform: UNKNOWN
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Development Status :: 3 - Alpha
Classifier: Environment :: Other Environment
Classifier: Intended Audience :: Science/Research
Classifier: Operating System :: POSIX
Classifier: Operating System :: Microsoft :: Windows
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
