osteosarc

Python library and command-line tool for the public osteosarc.com dataset: one patient's osteosarcoma sequencing, variant calls, cancer vaccines and clinical history.

• Explore it: every sample and what was sequenced, every file in the bucket, the variant catalogue with its vaccines, and the clinical timeline.
• Make test data from it: pull the reads around a few variants out of a remote BAM into a small local one, without downloading the BAM.

Documentation · Command line · Python API · Changelog

Install

python -m pip install osteosarc

Needs Python 3.9+ on Linux or macOS, and SAMtools on your PATH to fetch reads.

Explore

osteosarc sync                # once: about 57 MB of the website's metadata
osteosarc                     # the snapshot in use, and every command
osteosarc samples             # samples and what was sequenced
osteosarc samples T1_tumor    # one sample's files, and commands to get them
osteosarc files               # what's in the bucket, by kind and folder
osteosarc variants --gene MAP2
osteosarc timeline            # treatments, procedures, scans and MRD

Every command prints text for people, or JSON with --json. In Python or a notebook, everything shows a readable preview; osteosarc repl opens Python with the data loaded:

from osteosarc import Dataset

data = Dataset.sync()   # later: Dataset.open(), offline
data                    # what's here, and how to get it
data.samples["T1_tumor"]

Make test data

The reads around a variant in each of a sample's RNA-seq BAMs, saved in a folder:

osteosarc reads T0_tumor --assay rna-seq --variant DYNC1H1-chr14-101980529 --padding 100 --to tests/data

Or in Python, for one BAM:

source = data.file("rna-seq/reprocessed/BG003082/BG003082.Aligned.sortedByCoord.out.md.bam")
dync1h1 = data.variants(gene="DYNC1H1", status="ready")
reads = data.extract_reads(source, variants=dync1h1, padding=100, to="tests/data")
print(reads.path)

Only the reads near the variants are fetched, into a small indexed BAM; asking again reuses it, even offline. For a bundle anyone can rebuild, with a balanced set of reads at each variant and every record pinned, use osteosarc test-data make; a test then reads a member with osteosarc.bundle_file(bundle, member). The OpenVax libraries share one such bundle, openvax-v2.

The website changes over time, so its metadata is saved as dated snapshots: osteosarc snapshots lists them, and --snapshot 2026-09 picks the newest from that month. Osteosarc also fixes known errors in the website's data; osteosarc --no-corrections shows the published values.

Guides

Data, license and citation

Code is Apache-2.0. The dataset is listed as CC0-1.0 in the AWS Open Data Registry. Cite the dataset and your access date when using it.

Development

python -m pip install -e '.[test]'
ruff check osteosarc tests scripts
python -m pytest -q

See testing for documentation builds and live-example checks.