bigLolly example

You can read more about preparing the files necessary for a bigLolly track on UCSC’s bigLolly help page. The following code uses the example files provided by UCSC. This track type uses non-standard names for some parameters. These paramters can be added as a dictionary and setting trackhub.settings.VALIDATE = False.

This code is automatically run and the built trackhub is uploaded to the trackhub-demo repository. You can view the live hub using this link.

import trackhub

trackhub.settings.VALIDATE = False
hub, genome, genomes_file, trackdb = trackhub.default_hub(
    hub_name="bigLolly",
    short_label="bigLolly",
    long_label="bigLolly",
    genome="hg38",
    defaultPos="chr21:25891755-25891870",
    email="eva.jason@nih.gov",
)

add_kwargs = {"yAxisLabel.1": "0 on 30,30,190 0", "yAxisLabel.1": "5 on 30,30,190 5"}

track = trackhub.Track(
    tracktype="bigLolly",
    bigDataUrl="http://genome.ucsc.edu/goldenPath/help/examples/bigLollyExample3.bb",
    name="bigLolly",
    lollySizeField="lollySize",
    visibility="full",
    noStems="on",
    lollyMaxSize=10,
    **add_kwargs
)
trackdb.add_tracks(track)

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