Python API and command line interface for the GA4GH streaming API.
Project description
======
htsget
======
.. image:: https://img.shields.io/travis/jeromekelleher/htsget/master.svg
:target: https://travis-ci.org/jeromekelleher/htsget
.. image:: https://ci.appveyor.com/api/projects/status/n68yw9qklvdham82/branch/master?svg=true
:target: https://ci.appveyor.com/project/jeromekelleher/htsget/branch/master
.. image:: https://img.shields.io/codecov/c/github/jeromekelleher/htsget.svg
:target: https://codecov.io/gh/jeromekelleher/htsget
.. 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>`_.
htsget
======
.. image:: https://img.shields.io/travis/jeromekelleher/htsget/master.svg
:target: https://travis-ci.org/jeromekelleher/htsget
.. image:: https://ci.appveyor.com/api/projects/status/n68yw9qklvdham82/branch/master?svg=true
:target: https://ci.appveyor.com/project/jeromekelleher/htsget/branch/master
.. image:: https://img.shields.io/codecov/c/github/jeromekelleher/htsget.svg
:target: https://codecov.io/gh/jeromekelleher/htsget
.. 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>`_.
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