orfdata 0.18.0__tar.gz → 0.28.0__tar.gz

{orfdata-0.18.0 → orfdata-0.28.0}/MANIFEST.in

@@ -1,5 +1,5 @@
-include lint.sh test.sh deploy.sh
-recursive-include docs *.md
+include lint.sh test.sh deploy.sh docs.sh mkdocs.yml
+recursive-include docs *.md *.css
 recursive-include tests *.py *.json *.md *.tsv *.fasta
 recursive-include tests/data/copy *.xlsx *.gz *.soft *.xml *.pdf
 recursive-include tests/data/storage *.sqlite
@@ -7,3 +7,6 @@ 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
+recursive-include tests/data/openprot *.zip *.gz
+recursive-include tests/data/ncorf_mammals *.bed *.fa *.xlsx *.gz *.md
+recursive-include tests/data/riborf *.xlsx *.gz *.md

orfdata-0.28.0/PKG-INFO

@@ -0,0 +1,147 @@
+Metadata-Version: 2.4
+Name: orfdata
+Version: 0.28.0
+Summary: Reference proteomes with evidence-backed noncanonical ORFs on PyEnsembl genomes
+Author: OpenVax
+License-Expression: Apache-2.0
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Provides-Extra: pyensembl
+Requires-Dist: pyensembl>=2.27.2; extra == "pyensembl"
+Provides-Extra: build-data
+Requires-Dist: openpyxl>=3.1; extra == "build-data"
+Provides-Extra: data
+Requires-Dist: datacache<2,>=1.25.1; extra == "data"
+Provides-Extra: columnar
+Requires-Dist: pyarrow>=14; extra == "columnar"
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+Requires-Dist: build; extra == "dev"
+Requires-Dist: twine; extra == "dev"
+Requires-Dist: openpyxl>=3.1; extra == "dev"
+Requires-Dist: pyensembl>=2.27.2; extra == "dev"
+Requires-Dist: datacache<2,>=1.25.1; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: mkdocs<2,>=1.6; extra == "docs"
+Requires-Dist: mkdocs-material<10,>=9.5; extra == "docs"
+Dynamic: license-file
+
+[![Tests](https://github.com/openvax/orfdata/actions/workflows/tests.yml/badge.svg)](https://github.com/openvax/orfdata/actions/workflows/tests.yml)
+[![PyPI](https://img.shields.io/pypi/v/orfdata.svg)](https://pypi.org/project/orfdata/)
+
+# orfdata
+
+orfdata builds the protein reference for a species: the proteins annotated in
+a [PyEnsembl](https://github.com/openvax/pyensembl) genome, plus open reading
+frames (ORFs) that ribosome-profiling studies found translated outside those
+annotations. These include upstream and downstream ORFs, ORFs in other reading
+frames of a coding sequence, and ORFs on RNAs annotated as noncoding. Each added
+ORF stays bound to its PyEnsembl transcript, with its source, category and
+evidence.
+
+## Installation
+
+Use Python 3.9 or later. Install orfdata and one PyEnsembl annotation:
+
+```sh
+python -m pip install 'orfdata[pyensembl]'
+pyensembl install --release 115 --species human
+```
+
+## Example
+
+```python
+from pyensembl import EnsemblRelease
+from orfdata import Proteome
+
+genome = EnsemblRelease(115, species="human")
+proteome = Proteome.from_genome(genome).with_extra_orfs(evidence="ms")
+proteome.write_fasta("human-e115.fasta")
+print(proteome.summary()["kinds"], len(proteome.excluded))
+```
+
+```text
+{'annotated': 245535, 'extra_orf': 2181} 5
+```
+
+This takes every protein in the Ensembl 115 annotation and adds the 2,181
+bundled human ORFs that have supporting mass-spectrometry peptides and are
+encoded by an Ensembl 115 transcript. Each entry lists every transcript encoding
+it; the other 5 selected ORFs are listed in `proteome.excluded` with the
+reason. Use `evidence="ribosome"` for all 7,239 encoded ribosome-profiling ORFs,
+or a rule such as `RiboSeq(min_studies=2) & MS()` to set Ribo-seq and MS
+stringency separately (1,293 encoded ORFs).
+`proteome.save(path)` writes a checksummed snapshot that `Proteome.load` reads
+offline. From the command line:
+
+```sh
+orfdata proteome --species human --release 115 --output human-e115.fasta
+```
+
+A translated ORF or a detected peptide does not by itself establish a stable,
+functional protein. Most MS support in the bundled human catalogue comes from
+immunopeptidomics: peptides eluted from HLA molecules.
+
+## Species
+
+The bundled noncanonical ORF catalogue is human GRCh38. Mouse has 48,805:
+Ribo-seq ORFs of Chang et al. 2025 and Yang et al. 2024, and 2,976 MS-supported
+ones from OpenProt 2.2;
+`pip install "orfdata[data,build-data]"` then `orfdata setup --species mouse`
+builds all three from their sources' own files. After `orfdata chains download` (add
+`--accept-terms` for UCSC's non-commercial mouse chains), older assemblies
+(GRCh37, NCBI36, GRCm38, NCBIM37) and T2T-CHM13 use these catalogues lifted
+to them; `orfdata genomes install t2t-chm13` installs a CHM13 annotation. Dog and yeast proteomes contain their
+PyEnsembl-annotated proteins. `load_catalog(species=...)` and
+`with_extra_orfs()` pick the catalogue for a species and raise when none is
+available or built.
+Human evidence is never transferred to another species. Viral proteomes can be added with
+`with_viral(...)`, but only to a proteome for one of the virus's recorded hosts.
+orfdata also provides [RNA, ribosome and protein measurements](https://openvax.github.io/orfdata/measurements/)
+for human, mouse, dog and yeast.
+
+## Measurement datasets
+
+RNA, ribosome and protein measurements are separate, downloadable datasets with
+the same species-scoped API. Install the `data` extra, then download and query
+one:
+
+```sh
+pip install 'orfdata[data]'
+orfdata datasets list
+orfdata datasets download ingolia-yeast-rna-ribo
+```
+
+| Guide | Species | Measurements |
+| --- | --- | --- |
+| [Protein abundance](https://openvax.github.io/orfdata/pfizer-protein/) | Human, mouse, dog | TMT protein groups (Oziolor et al.) |
+| [RNA abundance](https://openvax.github.io/orfdata/pfizer-rna/) | Dog, mouse | Native gene counts (Oziolor et al.) |
+| [Matched human tissues](https://openvax.github.io/orfdata/human-tissue/) | Human | RNA and protein from adjacent cryosections (Wang et al.) |
+| [Yeast protein and RNA](https://openvax.github.io/orfdata/copy-yeast/) | Budding yeast | Calibrated protein and RNA abundance (CoPY) |
+| [Yeast RNA and ribosome occupancy](https://openvax.github.io/orfdata/ingolia-yeast/) | Budding yeast | Source regions, including UTR and ncRNA labels (Ingolia et al.) |
+
+Gene RNA and canonical protein measurements do not establish noncanonical ORF
+abundance. See [released data and gaps](https://openvax.github.io/orfdata/coverage/).
+
+## Documentation
+
+The [documentation](https://openvax.github.io/orfdata/) covers:
+
+| Task | Guide |
+| --- | --- |
+| Build a proteome: evidence levels, exclusions, contigs, viral proteins | [Build a reference proteome](https://openvax.github.io/orfdata/proteome/) |
+| ORF classes, evidence definitions, Varcode and Isovar integration | [ORFs and evidence](https://openvax.github.io/orfdata/reference/) |
+| Species and reference identity, mitochondrial genetic codes | [Species, references and genetic codes](https://openvax.github.io/orfdata/species/) |
+| Versioned ORF catalogues managed through DataCache | [Optional ORF catalogues](https://openvax.github.io/orfdata/catalogs/) |
+| Quantitative datasets and what has been released | [Measurements](https://openvax.github.io/orfdata/measurements/), [released data and gaps](https://openvax.github.io/orfdata/coverage/) |
+
+The [data roadmap](https://github.com/openvax/orfdata/issues/3) tracks further
+species and sources. Every PR includes a version bump, lint and tests;
+maintainers publish with `./deploy.sh` from clean `main`.
+
+## License
+
+Apache 2.0. Downloadable datasets keep their sources' own terms and
+attribution, recorded in each release manifest.

orfdata-0.28.0/README.md

@@ -0,0 +1,117 @@
+[![Tests](https://github.com/openvax/orfdata/actions/workflows/tests.yml/badge.svg)](https://github.com/openvax/orfdata/actions/workflows/tests.yml)
+[![PyPI](https://img.shields.io/pypi/v/orfdata.svg)](https://pypi.org/project/orfdata/)
+
+# orfdata
+
+orfdata builds the protein reference for a species: the proteins annotated in
+a [PyEnsembl](https://github.com/openvax/pyensembl) genome, plus open reading
+frames (ORFs) that ribosome-profiling studies found translated outside those
+annotations. These include upstream and downstream ORFs, ORFs in other reading
+frames of a coding sequence, and ORFs on RNAs annotated as noncoding. Each added
+ORF stays bound to its PyEnsembl transcript, with its source, category and
+evidence.
+
+## Installation
+
+Use Python 3.9 or later. Install orfdata and one PyEnsembl annotation:
+
+```sh
+python -m pip install 'orfdata[pyensembl]'
+pyensembl install --release 115 --species human
+```
+
+## Example
+
+```python
+from pyensembl import EnsemblRelease
+from orfdata import Proteome
+
+genome = EnsemblRelease(115, species="human")
+proteome = Proteome.from_genome(genome).with_extra_orfs(evidence="ms")
+proteome.write_fasta("human-e115.fasta")
+print(proteome.summary()["kinds"], len(proteome.excluded))
+```
+
+```text
+{'annotated': 245535, 'extra_orf': 2181} 5
+```
+
+This takes every protein in the Ensembl 115 annotation and adds the 2,181
+bundled human ORFs that have supporting mass-spectrometry peptides and are
+encoded by an Ensembl 115 transcript. Each entry lists every transcript encoding
+it; the other 5 selected ORFs are listed in `proteome.excluded` with the
+reason. Use `evidence="ribosome"` for all 7,239 encoded ribosome-profiling ORFs,
+or a rule such as `RiboSeq(min_studies=2) & MS()` to set Ribo-seq and MS
+stringency separately (1,293 encoded ORFs).
+`proteome.save(path)` writes a checksummed snapshot that `Proteome.load` reads
+offline. From the command line:
+
+```sh
+orfdata proteome --species human --release 115 --output human-e115.fasta
+```
+
+A translated ORF or a detected peptide does not by itself establish a stable,
+functional protein. Most MS support in the bundled human catalogue comes from
+immunopeptidomics: peptides eluted from HLA molecules.
+
+## Species
+
+The bundled noncanonical ORF catalogue is human GRCh38. Mouse has 48,805:
+Ribo-seq ORFs of Chang et al. 2025 and Yang et al. 2024, and 2,976 MS-supported
+ones from OpenProt 2.2;
+`pip install "orfdata[data,build-data]"` then `orfdata setup --species mouse`
+builds all three from their sources' own files. After `orfdata chains download` (add
+`--accept-terms` for UCSC's non-commercial mouse chains), older assemblies
+(GRCh37, NCBI36, GRCm38, NCBIM37) and T2T-CHM13 use these catalogues lifted
+to them; `orfdata genomes install t2t-chm13` installs a CHM13 annotation. Dog and yeast proteomes contain their
+PyEnsembl-annotated proteins. `load_catalog(species=...)` and
+`with_extra_orfs()` pick the catalogue for a species and raise when none is
+available or built.
+Human evidence is never transferred to another species. Viral proteomes can be added with
+`with_viral(...)`, but only to a proteome for one of the virus's recorded hosts.
+orfdata also provides [RNA, ribosome and protein measurements](https://openvax.github.io/orfdata/measurements/)
+for human, mouse, dog and yeast.
+
+## Measurement datasets
+
+RNA, ribosome and protein measurements are separate, downloadable datasets with
+the same species-scoped API. Install the `data` extra, then download and query
+one:
+
+```sh
+pip install 'orfdata[data]'
+orfdata datasets list
+orfdata datasets download ingolia-yeast-rna-ribo
+```
+
+| Guide | Species | Measurements |
+| --- | --- | --- |
+| [Protein abundance](https://openvax.github.io/orfdata/pfizer-protein/) | Human, mouse, dog | TMT protein groups (Oziolor et al.) |
+| [RNA abundance](https://openvax.github.io/orfdata/pfizer-rna/) | Dog, mouse | Native gene counts (Oziolor et al.) |
+| [Matched human tissues](https://openvax.github.io/orfdata/human-tissue/) | Human | RNA and protein from adjacent cryosections (Wang et al.) |
+| [Yeast protein and RNA](https://openvax.github.io/orfdata/copy-yeast/) | Budding yeast | Calibrated protein and RNA abundance (CoPY) |
+| [Yeast RNA and ribosome occupancy](https://openvax.github.io/orfdata/ingolia-yeast/) | Budding yeast | Source regions, including UTR and ncRNA labels (Ingolia et al.) |
+
+Gene RNA and canonical protein measurements do not establish noncanonical ORF
+abundance. See [released data and gaps](https://openvax.github.io/orfdata/coverage/).
+
+## Documentation
+
+The [documentation](https://openvax.github.io/orfdata/) covers:
+
+| Task | Guide |
+| --- | --- |
+| Build a proteome: evidence levels, exclusions, contigs, viral proteins | [Build a reference proteome](https://openvax.github.io/orfdata/proteome/) |
+| ORF classes, evidence definitions, Varcode and Isovar integration | [ORFs and evidence](https://openvax.github.io/orfdata/reference/) |
+| Species and reference identity, mitochondrial genetic codes | [Species, references and genetic codes](https://openvax.github.io/orfdata/species/) |
+| Versioned ORF catalogues managed through DataCache | [Optional ORF catalogues](https://openvax.github.io/orfdata/catalogs/) |
+| Quantitative datasets and what has been released | [Measurements](https://openvax.github.io/orfdata/measurements/), [released data and gaps](https://openvax.github.io/orfdata/coverage/) |
+
+The [data roadmap](https://github.com/openvax/orfdata/issues/3) tracks further
+species and sources. Every PR includes a version bump, lint and tests;
+maintainers publish with `./deploy.sh` from clean `main`.
+
+## License
+
+Apache 2.0. Downloadable datasets keep their sources' own terms and
+attribution, recorded in each release manifest.