.. _vcfTabix:

vcfTabix example
----------------
You can read more about preparing the files necessary for a vcfTabix track
on `UCSC's bigInteract help page
<https://genome.ucsc.edu/goldenPath/help/vcf.html>`_. The following code
uses the example files provided by UCSC.

This code is automatically run and the built trackhub is uploaded to the
`trackhub-demo <https://github.com/daler/trackhub-demo>`_ repository. You can
view the live hub using `this link <http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hubUrl=https://raw.githubusercontent.com/daler/trackhub-demo/master/example_vcfTabix_hub/vcfTabix.hub.txt&position=chr21:33034804-33037719>`_.

.. code-block:: python

    import trackhub

    hub, genome, genomes_file, trackdb = trackhub.default_hub(
        hub_name="vcfTabix",
        short_label="vcfTabix",
        long_label="vcfTabix",
        genome="hg19",
        defaultPos="chr21:33034804-33037719",
        email="eva.jason@nih.gov",
    )

    track = trackhub.Track(
        tracktype="vcfTabix",
        name="VCF_Example_One",
        chromosomes="chr21",
        visibility="pack",
        url="http://genome.ucsc.edu/goldenPath/help/examples/vcfExample.vcf.gz",
    )
    trackdb.add_tracks(track)

    trackhub.upload.upload_hub(
        hub=hub, host="localhost", remote_dir="example_hubs/example_vcfTabix_hub"
    )