orfdata 0.14.0__tar.gz → 0.16.0__tar.gz

{orfdata-0.14.0 → orfdata-0.16.0}/MANIFEST.in

@@ -6,3 +6,4 @@ recursive-include tests/data/storage *.sqlite
 recursive-include tests/data/pfizer_rna *.gz *.xlsx
 recursive-include tests/data/search_reference *.gz
 recursive-include tests/data/wang *.zip *.gz
+recursive-include tests/data/ingolia *.gz *.txt

{orfdata-0.14.0/orfdata.egg-info → orfdata-0.16.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orfdata
-Version: 0.14.0
+Version: 0.16.0
 Summary: Reference open reading frames and experimental translation evidence on annotated transcripts
 Author: OpenVax
 License-Expression: Apache-2.0
@@ -106,6 +106,8 @@ assays, and DataCache-managed downloads. Downloadable
 [yeast calibrated protein/RNA abundance](docs/copy-yeast.md) use the same
 species-scoped API, as do [native dog and mouse RNA counts](docs/pfizer-rna.md)
 and [matched human tissue RNA/protein measurements](docs/human-tissue.md).
+[Yeast RNA and ribosome occupancy](docs/ingolia-yeast.md) retain their source
+regions, including UTR and ncRNA labels.
 Gene RNA and canonical protein measurements do not establish
 noncanonical ORF abundance. The [native search references](docs/search-references.md)
 preserve complete deposited sequences, including unreported entries. The

{orfdata-0.14.0 → orfdata-0.16.0}/README.md

@@ -79,6 +79,8 @@ assays, and DataCache-managed downloads. Downloadable
 [yeast calibrated protein/RNA abundance](docs/copy-yeast.md) use the same
 species-scoped API, as do [native dog and mouse RNA counts](docs/pfizer-rna.md)
 and [matched human tissue RNA/protein measurements](docs/human-tissue.md).
+[Yeast RNA and ribosome occupancy](docs/ingolia-yeast.md) retain their source
+regions, including UTR and ncRNA labels.
 Gene RNA and canonical protein measurements do not establish
 noncanonical ORF abundance. The [native search references](docs/search-references.md)
 preserve complete deposited sequences, including unreported entries. The

{orfdata-0.14.0 → orfdata-0.16.0}/docs/coverage.md

@@ -9,7 +9,7 @@ data coverage, independently of what the API can represent.
 | Human | Wang: 29 specimens, gene/transcript FPKM and estimated copies/cell | Wang: 15,210 groups, iBAQ and estimated copies/cell; Pfizer: 10,352 groups, 37 channels, iBAQ/rIBAQ | Wang: adjacent cryosections; Pfizer: native RNA missing |
 | Mouse | Pfizer: 606 libraries, 56,051 gene targets, counts | Pfizer: 12,124 groups, 63 channels, iBAQ/rIBAQ | Unresolved library-to-pool correspondence |
 | Dog | Pfizer: 434 libraries, 30,941 gene targets, counts | Pfizer: 9,929 groups, 38 channels, iBAQ/rIBAQ | Unresolved library-to-pool correspondence |
-| Budding yeast | CoPY: four RNA libraries plus a source aggregate, FPKM and estimated copies/cell | CoPY: calibrated SRM and separately calibrated label-free estimates | Explicit source-cohort pairing; individual cross-assay replicate matches unknown |
+| Budding yeast | CoPY: four RNA libraries plus a source aggregate, FPKM and estimated copies/cell; Ingolia: four RNA libraries, counts and densities | CoPY: calibrated SRM and separately calibrated label-free estimates | CoPY: explicit source-cohort pairing; individual cross-assay replicate matches unknown |
 
 Gene targets include measured zeros; their presence in a matrix does not imply
 expression in every sample. Protein-group representatives do not establish
@@ -25,12 +25,16 @@ individual protein isoforms or noncanonical ORFs.
 The separate existence-evidence catalogue contains 7,264 human noncanonical
 ORFs, including 2,186 with reported MS support. It has no released mouse, dog or
 yeast experimental ncORF catalogue yet. Its ribosome evidence and pooled PSM
-counts are not sample-level ribosome occupancy or protein abundance. No species
-currently has a released quantitative Ribo-seq dataset in this registry.
+counts are not sample-level ribosome occupancy or protein abundance. The separate
+Ingolia yeast release contains four Ribo-seq libraries across 13,748 source
+regions, alongside four RNA libraries. Exact region coordinates and RNA/RPF
+aliquot pairing remain unresolved. Other species do not yet have released
+quantitative Ribo-seq datasets in this registry.
 
 See the short guides for [matched human tissues](human-tissue.md),
 [protein measurements](pfizer-protein.md),
-[native dog/mouse RNA](pfizer-rna.md), [yeast RNA/protein calibration](copy-yeast.md)
+[native dog/mouse RNA](pfizer-rna.md), [yeast RNA/protein calibration](copy-yeast.md),
+[yeast RNA/ribosome occupancy](ingolia-yeast.md)
 and [complete search sequences](search-references.md). The
 [roadmap](https://github.com/openvax/orfdata/issues/3) tracks further human
 comparators, quantitative Ribo-seq, ncORF evidence and additional species.

{orfdata-0.14.0 → orfdata-0.16.0}/docs/human-tissue.md

@@ -37,6 +37,18 @@ for value in dataset.measurements(target=gene, sample_id="V122"):
     print(value.quantity, value.value, value.unit, value.status)
 ```
 
+Select the same gene on both sides for a specimen's native gene-level comparison:
+
+```python
+match, = dataset.matched_measurements(
+    allowed_bases=["adjacent_donor_tissue"],
+    pair_ids=["rna_genes:protein_genes:V122"],
+    left_target=gene, right_target=gene,
+    left_filters={"unit": "FPKM"}, right_filters={"unit": "iBAQ"},
+)
+print(match.left[0].value, match.right[0].value)  # 51.09, 112559620.9
+```
+
 With Ensembl 83 already installed in PyEnsembl, the same target can be built with
 `ScopedTarget.from_pyensembl(gene_object, kind="gene", namespace="ensembl",
 context=reference)`. The context pins the historical GRCh38.p5 assembly accession,

orfdata-0.16.0/docs/ingolia-yeast.md

@@ -0,0 +1,64 @@
+# Yeast RNA and ribosome occupancy
+
+`ingolia-yeast-rna-ribo` contains the processed RNA and ribosome-footprint
+measurements from [Ingolia et al. (2009)](https://doi.org/10.1126/science.1168978),
+[GSE13750](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13750).
+It uses the same dataset API as human, mouse and dog.
+
+```sh
+pip install 'orfdata[data]'
+orfdata datasets info ingolia-yeast-rna-ribo
+orfdata datasets download ingolia-yeast-rna-ribo
+```
+
+The download is about 24 MB compressed, 210 MB installed. It contains 329,952
+observations: counts, reads/kb and RPKM for 13,748 source regions in eight
+libraries. Four libraries measure RNA and four measure ribosome footprints,
+in rich medium or after 20 minutes of amino-acid starvation. Source sample
+titles identify the modality, condition and nominal replicate. In particular,
+GSM346114 is `Footprints-rich-2` despite its `fp_rich1` filename.
+
+```python
+from orfdata import DatasetRegistry, ScopedTarget
+
+dataset = DatasetRegistry().open("ingolia-yeast-rna-ribo")
+reference, = dataset.manifest.references
+target = ScopedTarget(reference, "region", "HRA1", "Ingolia2009:feature")
+for measurement in dataset.measurements(target=target, unit="RPKM"):
+    print(measurement.sample_id, measurement.quantity, measurement.value)
+```
+
+Queries work offline after download. `quantity="rna_abundance"` or
+`quantity="ribosome_occupancy"` selects one modality. `unit="counts"` returns
+the original aligned read counts. The other two native series have
+`origin="derived"` and link to their count observation. Source formulas,
+feature lengths and total CDS-aligned reads remain attached; the reported
+rounded values are preserved. Zeros remain measured zeros. GSM346118 has no
+zero-count rows; ORFdata does not add or remove a pseudocount.
+
+## What these regions establish
+
+The source includes 3,523 5′ UTRs, 4,592 3′ UTRs, 225 intron windows and 5,408
+other feature labels, including coding, ncRNA and mitochondrial labels.
+Ribosome occupancy over a UTR does not identify a particular uORF. These targets
+therefore retain `kind="region"`; they do not expand the experimental ORF
+catalogue or establish stable protein abundance, copies/cell or translation flux.
+
+The yeast reference has taxon 4932 and the source annotation date, SGD
+2008-06-22. Exact genomic windows and assembly remain unresolved, including
+the UTR definitions attributed to Nagalakshmi et al. (2008). The biological
+strain BY4741 is sample metadata. Current PyEnsembl coordinates cannot be
+substituted for these historical windows without a validated mapping.
+
+The paper reports RNA and footprints from the same samples, but the exact
+GSM-to-GSM aliquot crosswalk is unresolved. The release retains eight separate
+libraries and creates no assay pairs or translation-efficiency ratios. It also
+does not pair these cultures with the separate [CoPY protein study](copy-yeast.md).
+[Issue #11](https://github.com/openvax/orfdata/issues/11) tracks these source gaps.
+
+To rebuild, install `orfdata[data,build-data]` and run
+`orfdata datasets build ingolia-yeast-rna-ribo`, or
+`DatasetRegistry().build("ingolia-yeast-rna-ribo")`. All 17 source inputs have
+pinned URLs, sizes and checksums. Verified local inputs can be supplied through
+`--source-path ASSET=PATH` or `source_paths={...}`. Query a local build using
+`DatasetRegistry().open_build(...)` or `orfdata datasets query ... --built`.

{orfdata-0.14.0 → orfdata-0.16.0}/docs/measurements.md

@@ -8,8 +8,9 @@ it is not a separate measurement of each ORF in that gene.
 
 Install `orfdata[data]` to manage datasets. The registry includes downloadable
 [Pfizer/Oziolor human, mouse and dog protein summaries](pfizer-protein.md);
-[native dog/mouse RNA](pfizer-rna.md), [matched human tissues](human-tissue.md)
-and [yeast RNA/protein calibration](copy-yeast.md) use the same objects.
+[native dog/mouse RNA](pfizer-rna.md), [matched human tissues](human-tissue.md),
+[yeast RNA/protein calibration](copy-yeast.md) and
+[yeast RNA/ribosome occupancy](ingolia-yeast.md) use the same objects.
 See [released coverage and gaps](coverage.md);
 the [data roadmap](https://github.com/openvax/orfdata/issues/3) tracks further
 imports. The bundled human ORF evidence catalogue remains available offline.

{orfdata-0.14.0 → orfdata-0.16.0}/docs/pairing.md

@@ -38,6 +38,25 @@ The CLI streams the same table rows:
 orfdata datasets pairs DATASET --version RELEASE --basis same_material
 ```
 
+Select exact targets with `left_target=...` and `right_target=...`, using the
+same `ScopedTarget` objects as ordinary measurement queries, including targets
+constructed from PyEnsembl genes. `reference` identifies the left context;
+a left target supplies that scope when omitted. Each right target keeps its own
+native reference. Incompatible species or reference selections fail explicitly.
+
+`left_filters` and `right_filters` select native `quantity`, `status`, `unit`,
+`scale` and `log_base`. They do not override assay identities. Pairing strength
+and target attribution are unchanged; filtered-out values leave empty sides,
+not measured zeros. `pair_ids` and `relation_ids` select original source IDs.
+Relationships can also be inspected with `dataset.relations(left_target=gene)`
+or `dataset.pairings(pair_ids=[...], reference=reference)` without scanning
+unrelated Python objects. See the [human example](human-tissue.md).
+
+CLI equivalents use `--left-unit`, `--right-unit` and the other prefixed native
+filters. A target requires all four of `--left-target`, `--left-kind`,
+`--left-namespace` and `--left-reference` (or the corresponding `--right-...`
+arguments). ID selectors remain `--pair-id` and `--relation-id`.
+
 ## Which targets are being compared?
 
 `TargetRelation` links exact, reference-scoped targets with mapping evidence