tracknado 0.3.1

CLI library to generate UCSC trackhubs from sequencing data

TrackNado 🌪️

TrackNado is a powerful Python library and CLI tool designed to rapidly generate complex UCSC Genome Browser track hubs. It handles the "heavy lifting" of metadata extraction, multi-dimensional groupings, and automated file conversion, letting you focus on the science.

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🚀 Key Features

• Fluent Python API: A declarative HubBuilder for intuitive and reproducible hub construction.
• Automated Conversion: Built-in, container-backed conversion for BED → bigBed and GTF/GFF → bigGenePred (with codon display).
• Custom Genomes (Assembly Hubs): Deep support for private assemblies with .2bit integration.
• Multi-Dimensional Grouping: Seamlessly create SuperTracks, CompositeTracks (matrix display), and OverlayTracks.
• Universal Metadata: Extract metadata from filenames, parent directories, or external CSV/TSV tables.
• Smart Merging: Combine multiple projects into a single unified hub via sidecar JSON configurations.
• Type Safety: Fully validated by Pydantic and Pandera.

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📦 Installation

pip install tracknado

TrackNado will automatically attempt to use UCSC tools from your $PATH. If not found, it can automatically pull and run them via Docker or Apptainer.

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🛠️ Quick Start (CLI)

The CLI is powered by Typer and provides a modern, colorized experience with rich help strings.

1. Generate a Metadata Template

tracknado create --template tracks.csv

2. Create a Hub

tracknado create \
  --metadata tracks.csv \
  --output ./my_hub \
  --genome-name hg38 \
  --subgroup-by cell_type \
  --subgroup-by assay \
  --convert \
  --chrom-sizes hg38.chrom.sizes

3. Create a Custom Assembly Hub

tracknado create \
  -i tracks/*.bw \
  --output ./custom_hub \
  --custom-genome \
  --twobit reference.2bit \
  --organism "MySpecies"

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🐍 Quick Start (Python API)

TrackNado’s fluent API makes complex hubs readable and maintainable.

import tracknado as tn

# Build a multi-dimensional hub with one statement
builder = (
    tn.HubBuilder()
    .add_tracks(['data/peaks.bed', 'data/signal.bw'])
    .with_metadata_extractor(tn.from_seqnado_path)
    .group_by('assay', as_supertrack=True)  # Signal vs Peaks folders
    .group_by('cell_type', 'condition')     # Matrix display
    .color_by('condition', palette='hls')
    .with_convert_files()
    .with_chrom_sizes("hg38.chrom.sizes")
)

# Build and Stage
hub = builder.build(
    name="Scientific_Project",
    genome="hg38",
    outdir="hub_out/",
    hub_email="[e-mail]",
    description_html="docs/project_summary.html"
)

hub.stage_hub()

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🔍 Validation

Never host a broken hub again. TrackNado includes a built-in structural validator and support for the official UCSC hubCheck.

tracknado validate my_hub/

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📖 Learn More

For full documentation, example metadata tables, and API references, visit: 👉 Documentation Portal

📄 License

TrackNado is released under the GNU General Public License v3.