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Quickstart

Installation

Install from PyPI using

$ pip install htsget

See the :ref:`sec-installation` section for more details.

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 the :ref:`sec-cli` section.

API Usage

The Python API provides a single function :func:`.get` which supports all of the arguments provided in the protocol. For example, to duplicate the example above, we can use the following code:

import htsget

url = "http://htsnexus.rnd.dnanex.us/v1/reads/BroadHiSeqX_b37/NA12878"
with open("NA12878_2.bam", "wb") as output:
    htsget.get(url, output, reference_name="2", start=1000, end=20000)

See the :ref:`sec-api` section for full details.