bigtrack 0.2

A lightweight Python package for creating UCSC Track Hubs with ease.

bigtrack

A lightweight Python package for creating UCSC Track Hubs with ease.

Note: This package was primarily developed to generate track hubs for my previous publications. It has not been tested for production use.

Installation

Install by pip:

pip install bigtrack

Install the latest version from source:

git clone https://github.com/zhang-shilong/bigtrack
cd bigtrack/
pip install .

Usage

Quick start

import bigtrack

# make a hub
hub = bigtrack.Hub(
    hub="ExampleHub",
    shortLabel="ExampleHub",
    longLabel="ExampleHub",
    email="[e-mail]",
)

# make a genome
genome = bigtrack.Genome(
    genome="ExampleGenome",
    organism="Example Organism",
    scientificName="Example Organism",
    twoBitPath="/path/to/two/bit/file",
    chromSizes="/path/to/sizes/file",
    defaultPos="chr1:0-100000",
    orderKey=1,
    description="This is an example",
    htmlPath="/path/to/html/description",
)
hub.add_genome(genome)  # add the genome to hub

# make a group
group_map = bigtrack.Group(
    name="map",
    label="Mapping and Sequencing",
    priority=2,
)
genome.add_group(group_map)  # add the group to genome

# make a trackDb
trackDb_map = bigtrack.TrackDb(
    include="trackDb_map.txt",
)
genome.add_trackDb(trackDb_map)  # add the trackDb to genome

# make a track
track_ideogram = bigtrack.Track(
    track="cytoBandIdeo",
    shortLabel="Chromosome Band (Ideogram)",
    longLabel="Ideogram for Orientation",
    bigDataUrl="/path/to/track/file",
    type="bigBed 4 +",
    group="map",
)
trackDb_map.add_track(track_ideogram)  # add the track to trackDb

# finally, one function to generate the file structure
hub.generate()

Then, find your track hub under the ExampleHub/ directory.

Data structure

When hub.generate() runs, bigtrack writes a directory tree suitable for hosting as a UCSC Track Hub. The exact layout can be configured, but a typical generated structure looks like:

ExampleHub/
├─ hub.txt
├─ genomes.txt
├─ ExampleGenome/
│  ├─ groups.txt
│  ├─ trackDb.txt  # include all trackDbs
│  ├─ trackDb_map.txt
│  └─ trackDb_xxx.txt
└─ AnotherGenome/
   ├─ groups.txt
   ├─ trackDb.txt  # include all trackDbs
   ├─ trackDb_map.txt
   └─ trackDb_xxx.txt

You can host this directory on any web server (HTTP/HTTPS/FTP) and point UCSC Genome Browser at the hub.txt URL.

Hub components

bigtrack models the standard UCSC hub components as Python classes. Each object has reserved keywords — those are required for correct hub generation. Some fields have sensible defaults. Please note, required keys may not consistent with UCSC guidance.

Hub

Top-level hub object. Represents hub.txt.

Required keys: hub, shortLabel, longLabel, genomesFile (default: genomes.txt), email.

Genome

Represents a genome entry (appears in genomes.txt and holds per-genome resources).

Required keys: genome, trackDb (default: trackDb.txt), groups (default: groups.txt), organism, scientificName.

Group

A logical grouping for tracks used for UI organization.

Required keys: name, label, priority (default: 1), defaultIsClosed (default: 0).

TrackDb

A container class that holds tracks and writes a trackDb file.

Required keys: include.

Track

Basic (atomic) track object.

Required keys: track, parent (default: None), shortLabel, longLabel, type.

To enhance usage, track collections are also available:

CompositeTrack

A composite track groups multiple subtracks that share the same type. See UCSC docs for composite track settings.

Required keys: track, compositeTrack (default: on), parent (default: None), shortLabel, longLabel, type.

SampledCompositeTrack

A convenience helper that produces a sampled subset of a CompositeTrack automatically. Useful when you have many samples and want to produce a smaller subset for quick browsing.

bigtrack.SampledCompositeTrack(
    full_track: bigtrack.CompositeTrack,
    number: int,  # number of sampled child tracks from full_track
    random_seed: int = 0,
    suffix: str = "_subset",
    **kwargs,  # kwargs to override
)

SuperTrack

A superTrack provides a higher-level container that can contain multiple composite tracks or plain tracks. See UCSC docs for super track settings.

Required keys: track, superTrack (default: on), parent (default: None), shortLabel, longLabel.

MultiWig

A multiWig track enables the simultaneous display and comparison of multiple wiggle signal tracks. See UCSC docs for multiWig settings.

Required keys: track, parent (default: None), container (default: multiWig), type (default: bigWig), shortLabel, longLabel.

Example

See codes for T2T Macaque Hub.

Todo

• Add pre-flight checks while generating hubs
• Add automatic format conversion

Acknowledgement

Thanks to the Python package daler/trackhub.

Citation

1. Zhang, S., Xu, N., Fu, L. et al. Integrated analysis of the complete sequence of a macaque genome. Nature (2025). https://doi.org/10.1038/s41586-025-08596-w
2. Zhang, S. et al. A complete and near-perfect rhesus macaque reference genome: lessons from subtelomeric repeats and sequencing bias. bioRxiv (2025). https://doi.org/10.1101/2025.08.04.668424

License

This project is licensed under the MIT License — see the LICENSE file for details.