osteosarc 0.1.0__tar.gz

osteosarc-0.1.0/LICENSE

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osteosarc-0.1.0/MANIFEST.in

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+include LICENSE
+include mkdocs.yml
+recursive-include docs *.md
+recursive-include tests *.py *.json *.tsv *.csv *.html
+recursive-include scripts *.py

osteosarc-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: osteosarc
+Version: 0.1.0
+Summary: Reproducible access to the public osteosarc.com dataset
+Author-email: Alex Rubinsteyn <alex.rubinsteyn@gmail.com>
+License-Expression: Apache-2.0
+Project-URL: Documentation, https://iskandr.github.io/osteosarc/
+Project-URL: Source, https://github.com/iskandr/osteosarc
+Project-URL: Issues, https://github.com/iskandr/osteosarc/issues
+Project-URL: Dataset, https://osteosarc.com/data/
+Keywords: osteosarcoma,genomics,neoantigen,bioinformatics,openvax
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: MacOS
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: beautifulsoup4>=4.12
+Provides-Extra: reads
+Requires-Dist: pysam>=0.22; extra == "reads"
+Provides-Extra: test
+Requires-Dist: pytest>=8; extra == "test"
+Requires-Dist: pysam>=0.22; extra == "test"
+Requires-Dist: ruff>=0.9; extra == "test"
+Requires-Dist: build>=1; extra == "test"
+Provides-Extra: docs
+Requires-Dist: mkdocs<2,>=1.6; extra == "docs"
+Dynamic: license-file
+
+# osteosarc
+
+A shared Python API for the public [osteosarc.com](https://osteosarc.com/data/)
+dataset: discover files, cache verified downloads, parse source tables, select
+variants and vaccines, and extract indexed sequencing reads.
+
+The initial implementation consolidates the acquisition patterns found in
+Varcode, Isovar, Topiary, and Vaxrank. Those repositories have not yet been
+migrated. See the [comparison and migration guide](https://iskandr.github.io/osteosarc/migration/).
+
+[Documentation and short examples](https://iskandr.github.io/osteosarc/) ·
+[Consumer migration recipes](https://iskandr.github.io/osteosarc/consumers/)
+
+## Install
+
+Python 3.10+, Linux or macOS, and `curl` are required. Indexed read extraction
+also requires `samtools` on PATH and the `reads` extra.
+
+```sh
+python -m pip install 'osteosarc[reads]'
+```
+
+For development, clone the repository and use `python -m pip install -e '.[test]'`.
+
+## One dataset, one cache
+
+```python
+from osteosarc import Cache, Dataset
+
+cache = Cache()  # the shared OpenVax cache (see below)
+data = Dataset.sync("2026-09-18", cache=cache)  # explicit metadata download
+
+# Later: verifies the saved snapshot and opens it without network access.
+data = Dataset.open("2026-09-18", cache=cache)
+```
+
+`sync` acquires about 57 MB of metadata, including the full dated bucket index
+and the timeline sources.
+It does not download BAMs, FASTQs, or other large data files. Importing the
+package also does no downloading.
+
+Files are stored in the **shared OpenVax cache**, the same layout vaxrank's
+downloader uses, so identical bytes are stored once across OpenVax tools:
+`<root>/objects/sha256/<sha256><original suffixes>` (for example
+`…9c2e.genes.results`). osteosarc keeps its receipts, snapshots, bindings and
+extracted reads under `<root>/osteosarc/`. The root is `OPENVAX_DATA_CACHE`,
+otherwise the platform cache directory for `openvax` (`~/Library/Caches/openvax`
+on macOS, `$XDG_CACHE_HOME/openvax` or `~/.cache/openvax` on Linux).
+`OSTEOSARC_CACHE` or `Cache(root)` selects an isolated cache instead.
+
+Snapshots pin source URLs and SHA256 receipts. Downloads use atomic publication,
+per-URL locks, bounded retries, and checksum verification on reuse. Interrupted
+downloads restart; byte-range resume of whole objects is not implemented.
+`Dataset.download` binds its first acquired receipt to that snapshot, so
+refreshing a URL elsewhere cannot change previously acquired data. Use a new
+name with `Dataset.sync(..., refresh=True)` to acquire fresh metadata. Existing
+snapshot names cannot be overwritten. `Cache.fetch(url, refresh=True)` can
+refresh standalone downloads while keeping old content available.
+
+## Find samples and sequencing products
+
+```python
+data = Dataset.open("2026-09-18", offline=False)  # permit explicit acquisition
+
+rna = data.assets.select(kind="alignment", assay="rna-seq", timepoint="T2")
+ont = data.assets.select(kind="alignment", platform="ont")
+vcfs = data.assets.select(kind="variants", format="vcf")
+pvac = data.assets.select(prefix="neoantigen_prediction/pvactools/", format="tsv")
+hla = data.assets.select(contains="hla", format="tsv")
+raw_reads = data.assets.select(kind="reads", timepoint="T1")
+
+sample_claims = data.samples          # table with source and asset IDs
+timepoint_claims = data.timepoints    # published date precision is preserved
+
+for asset in rna:
+    print(asset.id, asset.key, asset.size, asset.conflicts)
+```
+
+An **asset is a processing product**, not an independent biological replicate.
+An ID hashes the complete URL, so identical filenames in different directories
+remain distinct. Sample claims come from the BAM viewer, consolidated public
+metadata, VAF export, and data-page tables. Conflicting or absent values do not
+match a metadata filter by default. Inspect `asset.claims`, `asset.conflicts`,
+or `asset.values("timepoint")`; use `include_conflicts=True` to match any claim.
+The catalog-wide viewer assembly label is never used to authorize read queries.
+
+Assays are `rna-seq`, `scrna-seq`, `cite-seq`, `wgs`, and `wes`; known platforms
+are `ont`, `pacbio`, and `illumina`. Platform is left unknown when it is not
+explicit in the source. For paths with no published mapping, timepoint and a
+few recognizable library IDs are retained as **inferences**, accessible with
+`include_inferred=True`. Pooled blood libraries remain library-level records.
+
+Every bucket object remains discoverable, including unclassified files.
+The website listing has its own generation date and is not guaranteed current.
+To discover newer files explicitly:
+
+```python
+from osteosarc import list_bucket
+
+listing = list_bucket(cache, "ONT/", refresh=True)
+# listing["files"]: complete key/size/mtime rows; listing["receipts"]: every page
+```
+
+Live listings are returned separately; they do not silently mutate a snapshot.
+Missing or repeated continuation tokens and incomplete pagination raise errors.
+
+## Variant sets, annotations, and vaccines
+
+```python
+site = data.variants()                  # every site entry, including unresolved
+all_exported = data.variants("all")     # also includes count-export entries
+vaccine_targets = data.variants("vaccine")  # site-reported vaccine count > 0
+mrna = data.variants(vaccine="mRNA")     # vaccine-overlap JSON membership
+ready = site.select(status="ready")
+dynein = site.select(gene="DYNC1H1")     # may contain multiple alleles
+detected = data.variants(pipeline="oncoanalyser")
+
+print(data.vaccine_names, data.pipeline_names)
+annotations = data.annotations         # original variant annotation records
+peptides = data.vaccine_peptides("mRNA")
+elispot = data.vaccines                 # original tested/status/response fields
+
+# A different source's membership assertion, explicitly requested:
+source_membership = data.variants(vaccine="JLF V3", vaccine_source="source_variants")
+```
+
+The variant index, vaccine-overlap JSON, and source variant JSON can disagree.
+`Variant.vaccines` contains overlap-JSON membership joined only at an unambiguous
+gene/locus; `annotations["source_vaccines"]` preserves source-JSON flags.
+Disagreements and ambiguous joins remain in annotations. Counts from the site
+table, peptide inclusion, pipeline detection, and ELISPOT measurements are kept
+separately. A blank or untested measurement is not converted to a negative one.
+
+Variants retain the published assembly and original VCF-style anchored allele.
+`ready` means a unique literal allele with internally consistent coordinates;
+it does **not** mean independently validated, somatic, normalized, or clinically
+confirmed. Incomplete entries have a status such as `missing_literal_allele`,
+`non_literal_allele`, or `ambiguous_literal_allele`. No allele is fabricated from
+a gene symbol or protein label, and no coordinates are silently lifted over.
+
+## Timelines, specimens, and the terminal explorer
+
+```python
+print(data.timeline.render(since="2024-05", until="2024-09", width=100))
+print(data.timeline.around("2025-01-28", days=5).listing())
+t2 = next(r for r in data.specimens if r["sample_id"] == "T2_tumor")
+print(t2["date"], t2["site"], len(t2["assets"]), t2["corrections"])
+mrd = data.measurements.select(source="mrd")
+```
+
+The timeline brings together every dated public source: treatments and doses,
+procedures, imaging (events and DICOM studies), pathology, omics, time points,
+specimens, MRD, flow-cytometry draws, and lab and cytometry dates. Run
+`osteosarc explore baseline` to browse it interactively, or
+`osteosarc timeline baseline --since 2024-05` for a chart. See
+[timelines](https://iskandr.github.io/osteosarc/timeline/) and the [guided tour](https://iskandr.github.io/osteosarc/tour/).
+
+## Corrections are central, optional, and drift-aware
+
+All hand-written interpretation of the sources lives in `osteosarc/curation.py`.
+Verified corrections are applied by default, for example the GRCh37 Tempus
+counts, five relocated Tempus alleles, MAP2's observed allele, stale viewer
+labels, and specimen dates and sites. Each touched object names its
+corrections, and `Dataset.open(name, corrections=False)` gives the published
+sources unchanged. Every load re-checks each correction against the sources, so
+an upstream change makes it `stale` and unapplied rather than silently wrong.
+
+```python
+for row in data.corrections:
+    print(row["status"], row["id"])
+print(list(data.unrecognized))       # labels outside the vocabulary
+```
+
+`osteosarc curation baseline --strict` exits nonzero on drift. See
+[corrections and drift](https://iskandr.github.io/osteosarc/curation/).
+
+## Download and parse
+
+```python
+counts = data.table("vafs")
+counts_for_gene = counts.select(gene="SMC5")  # raw values, including "0" and "NA"
+dna_fusions = data.table("dna_fusions")
+rna_fusions = data.table("rna_fusions")
+snvs = data.table("snv_top")
+
+report = pvac[0]
+path = data.download(report)     # explicit full-object download
+table = data.parse(report)       # same cache; original column names/strings
+frame = table.to_dataframe()     # optional pandas, no automatic numeric coercion
+
+with data.open_variants(vcfs[0]) as calls:  # optional pysam
+    for call in calls:
+        print(call.contig, call.pos, call.ref, call.alts)
+```
+
+Built-in parsers cover TSV, CSV, JSON, and FASTA. `open_variants` preserves
+VCF/BCF headers, INFO/FORMAT fields, sample genotypes, multiallelic records, and
+symbolic alleles through pysam. Other objects (GTFs, matrices, RDS, imaging,
+etc.) can be downloaded for their format-specific tools. Parsing a large text
+table or FASTA currently materializes it in memory; use its downloaded path
+with a streaming reader for very large files.
+
+## Indexed read extraction
+
+```python
+from osteosarc import ReadFilter, Region
+
+# Explicit source product; prefix/substring selectors can return several BAMs.
+source = data.asset(
+    "rna-seq/reprocessed/BG003082/BG003082.Aligned.sortedByCoord.out.md.bam"
+)
+variant = data.variants()["DYNC1H1-chr14-101980529"]
+subset = data.extract_reads(source, [variant.region(padding=100)])
+
+# Region coordinates in Python are always zero-based and half-open.
+region = Region("chr14", 101980528, 101980530, "GRCh38")
+filtered = data.extract_reads(
+    source, [region], filters=ReadFilter(min_mapq=20, exclude_flags=0x100 | 0x400)
+)
+with subset.open() as bam:
+    for read in bam.fetch("chr14", 101980528, 101980530):
+        print(read.query_name, read.cigarstring)
+```
+
+The extractor inspects reference lengths before querying, resolves contig
+aliases, and refuses assembly conflicts, out-of-bounds intervals, ambiguous
+contigs, and missing indexes. GRCh37 mitochondrial queries additionally require
+the exact `reference_length` because hg19 and hs37d5 differ there. CRAM requires
+a local indexed reference FASTA. Sparse/custom reference headers that cannot
+establish the assembly are rejected.
+
+SAMtools reads the indexed union of all intervals. Overlapping query intervals
+do not cause repeated emission; genuine repeated source records are preserved.
+Defaults retain secondary, supplementary, duplicate-marked, and low-MAPQ reads,
+including original qualities, barcodes, UMIs, and other tags. Optional filters
+are recorded in the request. `ReadFilter(barcodes=("...",))` selects the `CB`
+tag (customizable via `barcode_tag`). `fetch_pairs=True` additionally retrieves
+paired mates, but is not recovery of every supplementary record for a template.
+
+The result contains an indexed BAM, source header, BED intervals, checksum
+receipt, source/index identities, tool versions, and record count. It is cached
+by the complete request. Remote identity is checked before and after new
+extractions; cached results are verified offline without contacting the source.
+No full-alignment scan is used as a fallback.
+
+Local BAMs use the same implementation:
+
+```python
+from osteosarc import extract_reads, subset_templates
+
+local = str(subset.path)  # any local indexed BAM; here, the subset from above
+regional = extract_reads(local, [region], cache=cache)
+fixture = subset_templates(regional, count=48, seed="regression-v1", cache=cache)
+```
+
+Template sampling is a separate operation, keyed by `(read group, query name)`.
+It retains all available regional records for selected templates and marks the
+receipt as a sampled fixture unsuitable for estimating VAF.
+
+## Downstream libraries and CLI
+
+```python
+# Optional varcode / pyensembl adapter; the caller provides its reference.
+from pyensembl import EnsemblRelease
+variants = ready.to_varcode(genome=EnsemblRelease(95))
+# Pass variants and subset.path to Isovar, then its products to Topiary/Vaxrank.
+```
+
+Osteosarc does not choose an Ensembl release, install a genome, calculate effects,
+assemble RNA, score epitopes, infer somatic truth, or design a vaccine.
+
+```sh
+osteosarc --cache .cache/osteosarc sync baseline
+osteosarc --cache .cache/osteosarc assets baseline --assay rna-seq --timepoint T2
+osteosarc --cache .cache/osteosarc variants baseline --set vaccine --status ready
+osteosarc --cache .cache/osteosarc variants baseline --vaccine 'JLF V3'
+osteosarc --cache .cache/osteosarc table baseline dna_fusions
+osteosarc --cache .cache/osteosarc reads baseline 'rna-seq/reprocessed/BG003082/BG003082.Aligned.sortedByCoord.out.md.bam' chr14:101980529-101980530 --assembly GRCh38
+osteosarc --cache .cache/osteosarc discover 'neoantigen_prediction/pvactools/'
+osteosarc --cache .cache/osteosarc timeline baseline --since 2024-05 --until 2024-09
+osteosarc --cache .cache/osteosarc specimens baseline T1_tumor
+osteosarc --cache .cache/osteosarc curation baseline --strict
+osteosarc --cache .cache/osteosarc --no-corrections variants baseline --gene MAP2
+```
+
+CLI regions are **one-based inclusive**, matching SAMtools. Add the global
+`--offline` flag to prohibit acquisition. `sync --source-revision <commit>` pins
+every GitLab source-repository resource (variant JSON, BAM metadata, and the
+timeline and specimen sources) to a full commit; site-served files are not
+versioned by the site.
+
+## Development and provenance
+
+```sh
+python -m pip install -e '.[test]'
+ruff check osteosarc tests scripts
+python -m pytest -q
+python -m build --no-isolation
+```
+
+Tests are offline and use small public metadata excerpts plus synthetic indexed
+BAMs. See [validation](https://iskandr.github.io/osteosarc/validation/) for the bounded live check and
+[API contracts](https://iskandr.github.io/osteosarc/design/) for the design rationale.
+
+Code is Apache-2.0. The public dataset is separately listed as CC0-1.0 in the
+[AWS Open Data Registry](https://registry.opendata.aws/sid-osteosarc/). Cite the
+dataset and the access date when using its data.