.. _assembly-example:

Assembly example
----------------
The following example shows how to generate an `Assembly Hub
<http://genomewiki.ucsc.edu/index.php/Assembly_Hubs>`_, which is a way of
supporting an assembly that is not already supported on UCSC.


It requires a ``.2bit`` file, which is created from a FASTA file using UCSC's
``faToTwoBit`` tool. If you have `bioconda <https://bioconda.github.io>`_ set
up, you can get this with ``conda install ucsc-fatotwobit``, or download it
from http://hgdownload.cse.ucsc.edu/admin/exe/.

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/hgHubConnect?hgHub_do_redirect=on&hgHubConnect.remakeTrackHub=on&hgHub_do_firstDb=1&hubUrl=https://raw.githubusercontent.com/daler/trackhub-demo/master/example_assembly_hub/assembly_hub.hub.txt>`_.

.. code-block:: python

    import trackhub
    import re
    import sys
    import os
    import glob

    # In contrast to the example in the README, we do not use the
    # `trackhub.default_hub` function but instead build up the hub from its
    # component pieces.
    hub = trackhub.Hub(
        "assembly_hub",
        short_label="assembly_hub",
        long_label="an example of an assembly hub",
        email="none@example.com")

    # The major difference from a regular track hub is this object, which needs
    # to be added to the genomes_file object:
    genome = trackhub.Assembly(
        genome="newOrg1",
        twobit_file=os.path.join(trackhub.helpers.data_dir(), "newOrg1.2bit"),
        organism="Big Foot",
        defaultPos="chr1:0-1000000",
        scientificName="Biggus Footus",
        description="BigFoot V4",
        html_string="BIGFOOT V4 INFO\n",
        orderKey=4800
    )

    genomes_file = trackhub.GenomesFile()
    hub.add_genomes_file(genomes_file)

    # we also need to create a trackDb and add it to the genome
    trackdb = trackhub.TrackDb()
    genome.add_trackdb(trackdb)

    # add the genome to the genomes file here:
    genomes_file.add_genome(genome)

    # Find all bigwigs for this genome in the example data directory, and make
    # tracks for them
    for bw in glob.glob(os.path.join(trackhub.helpers.data_dir(), "*no1*.bw")):
        name, _, _ = os.path.basename(bw).split(".")
        track = trackhub.Track(
            name=trackhub.helpers.sanitize(name),
            source=bw,
            tracktype='bigWig',
            autoScale='on')
        trackdb.add_tracks(track)

    # Same with bigBeds
    for bb in glob.glob(os.path.join(trackhub.helpers.data_dir(), "*no1*.bigBed")):
        name, _ = os.path.basename(bb).split(".")
        track = trackhub.Track(
            name=trackhub.helpers.sanitize(name),
            source=bb,
            tracktype='bigBed')
        trackdb.add_tracks(track)

    # Assembly hubs also need to have a Group specified. Here's how to do that:
    example_group = trackhub.groups.GroupDefinition(
        "example_tracks",
        label="Example Tracks",
        priority=1,
        default_is_closed=False)

    groups_file = trackhub.groups.GroupsFile([example_group])
    genome.add_groups(groups_file)

    # We can now add the "group" parameter to all the children of the trackDb
    for track in trackdb.children:
        track.add_params(group="example_tracks")

    trackhub.upload.upload_hub(hub=hub, host='localhost',
        remote_dir='example_hubs/example_assembly_hub')