bam example

You can read more about preparing the files necessary for a bam track on UCSC’s bam help page. 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 repository. You can view the live hub using this link.

import trackhub

hub, genomes_file, genome, trackdb = trackhub.default_hub(
    hub_name="bam",
    short_label="bam",
    long_label="bam",
    genome="hg18",
    defaultPos="chr21:33038946-33039092",
    email="eva.jason@nih.gov",
)

track = trackhub.Track(
    tracktype="bam",
    name="bam",
    description="bam ex. 1: 1000 genomes read alignments (individual na12878)",
    pairEndsByName=".",
    pairSearchRange="10000",
    chromosomes="chr21",
    maxWindowToDraw="200000",
    visibility="pack",
    bigDataUrl="http://genome.ucsc.edu/goldenPath/help/examples/bamExample.bam",
)
trackdb.add_tracks(track)
trackhub.upload.upload_hub(
    hub=hub, host="localhost", remote_dir="example_hubs/example_bam_hub"
)