.. _hic_example:

Hi-C example
------------
You can read more about preparing the files necessary for a Hi-C track
on `UCSC's hic help page
<https://genome.ucsc.edu/goldenPath/help/hic.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_hic_hub/hic.hub.txt>`_.

.. code-block:: python

     import trackhub
     hub, genomes_file, genome, trackdb = trackhub.default_hub(
          hub_name = 'hic',
          defaultPos= 'chr21:32000000-35000000',
          short_label = 'hic',
          long_label = 'hic',
          genome = 'hg19',
          email = 'eva.jason@nih.gov')

     track = trackhub.Track(
          name = 'examplehicTrack',
          tracktype = 'hic',
          visibility = 'dense',
          url = 'http://hgdownload.soe.ucsc.edu/gbdb/hg19/bbi/hic/GSE63525_GM12878_insitu_primary+replicate_combined.hic',
          longLabel = 'This hic file shows in situ Hi-C data from Rao et al. (2014) on the GM12878 cell line')

     trackdb.add_tracks(track)
     trackhub.upload.upload_hub(hub = hub, host = 'localhost', remote_dir = 'example_hubs/example_hic_hub')