orfdata 0.1.0__tar.gz

orfdata-0.1.0/LICENSE

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orfdata-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: orfdata
+Version: 0.1.0
+Summary: Reference open reading frames and experimental translation evidence on annotated transcripts
+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: 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"
+Dynamic: license-file
+
+# orfdata
+
+**An evidence layer over [PyEnsembl](https://github.com/openvax/pyensembl) for
+proteins beyond standard annotations.** orfdata tells you which open reading
+frames (ORFs) have experimental support for producing peptides or proteins.
+
+PyEnsembl supplies reference transcripts and annotated proteins. orfdata adds
+other ORFs, their sequences, and evidence to those same transcript objects.
+One RNA can have several ORFs, even when its annotation says it is noncoding.
+The original transcript's biotype and annotated protein stay intact.
+
+## Which ORFs?
+
+The bundled catalogue includes:
+
+- **Upstream ORFs (uORFs):** before the main protein-coding region.
+- **Overlapping ORFs:** extending into or out of the main coding region.
+- **Internal ORFs:** alternative reading frames within the main coding region.
+- **Downstream ORFs (dORFs):** after the main coding region.
+- **ORFs on noncoding RNAs:** including long noncoding RNAs (lncRNAs) and
+  processed transcripts without an annotated protein.
+
+These are additional possible protein sources that standard transcript protein
+annotations may omit. The catalogue currently contains **7,264 human GRCh38
+ORFs**, of which **2,186 have reported supporting mass-spectrometry observations**.
+It is a source-backed reference catalogue; it does not discover every possible
+ORF. [Data sources and current limits](docs/reference.md#data-and-limits).
+
+## What does the evidence mean?
+
+| Evidence | What it supports |
+| --- | --- |
+| Ribosome profiling | Translation of the ORF. |
+| Protease-digest mass spectrometry (MS) | Detection of peptides matching its protein sequence. |
+| MHC/HLA peptidomics | Detection of matching peptides presented by MHC molecules. |
+
+Peptide matches can be ambiguous, so orfdata keeps their source, mapping and
+quality information. These observations have different strengths: a translated
+ORF or detected peptide does not by itself establish a stable, functional protein.
+Missing evidence also does not establish that an ORF is never translated.
+[Evidence interpretation](docs/reference.md#evidence).
+
+## Use with PyEnsembl
+
+With the selected PyEnsembl annotation already downloaded and indexed:
+
+```python
+from pyensembl import EnsemblRelease
+from orfdata import load_catalog
+
+genome = EnsemblRelease(95, species="human")
+catalog = load_catalog()
+transcript = genome.transcript_by_id("ENST00000304842")  # TPST1
+
+for orf in catalog.for_transcript(transcript):
+    print(orf.model.orf_id, orf.protein_sequence)
+    print(orf.evidence.has_evidence("ms"))
+    assert orf.transcript is transcript
+```
+
+The same call works for a noncoding parent, such as NUTM2B-AS1
+(`ENST00000483080`). Each returned `ReferenceORF` keeps its model, evidence and
+original PyEnsembl transcript together, after checking its coordinates and
+sequence against that transcript.
+
+Varcode describes changes to this reference ORF; Isovar connects it to observed
+RNA products. Reference evidence stays separate from evidence for a variant or
+fusion. See the [API and integration guide](docs/reference.md).
+
+The catalogue API supports other species, with explicit species and assembly
+checks. **Bundled evidence is currently human-only**; mouse bindings use synthetic
+test data. [Adding another species](docs/reference.md#other-species).
+
+Install with `pip install orfdata[pyensembl]`. See the
+[quantitative, multispecies data roadmap](https://github.com/openvax/orfdata/issues/3)
+for planned RNA abundance, ribosome occupancy and protein measurements.

orfdata-0.1.0/README.md

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+# orfdata
+
+**An evidence layer over [PyEnsembl](https://github.com/openvax/pyensembl) for
+proteins beyond standard annotations.** orfdata tells you which open reading
+frames (ORFs) have experimental support for producing peptides or proteins.
+
+PyEnsembl supplies reference transcripts and annotated proteins. orfdata adds
+other ORFs, their sequences, and evidence to those same transcript objects.
+One RNA can have several ORFs, even when its annotation says it is noncoding.
+The original transcript's biotype and annotated protein stay intact.
+
+## Which ORFs?
+
+The bundled catalogue includes:
+
+- **Upstream ORFs (uORFs):** before the main protein-coding region.
+- **Overlapping ORFs:** extending into or out of the main coding region.
+- **Internal ORFs:** alternative reading frames within the main coding region.
+- **Downstream ORFs (dORFs):** after the main coding region.
+- **ORFs on noncoding RNAs:** including long noncoding RNAs (lncRNAs) and
+  processed transcripts without an annotated protein.
+
+These are additional possible protein sources that standard transcript protein
+annotations may omit. The catalogue currently contains **7,264 human GRCh38
+ORFs**, of which **2,186 have reported supporting mass-spectrometry observations**.
+It is a source-backed reference catalogue; it does not discover every possible
+ORF. [Data sources and current limits](docs/reference.md#data-and-limits).
+
+## What does the evidence mean?
+
+| Evidence | What it supports |
+| --- | --- |
+| Ribosome profiling | Translation of the ORF. |
+| Protease-digest mass spectrometry (MS) | Detection of peptides matching its protein sequence. |
+| MHC/HLA peptidomics | Detection of matching peptides presented by MHC molecules. |
+
+Peptide matches can be ambiguous, so orfdata keeps their source, mapping and
+quality information. These observations have different strengths: a translated
+ORF or detected peptide does not by itself establish a stable, functional protein.
+Missing evidence also does not establish that an ORF is never translated.
+[Evidence interpretation](docs/reference.md#evidence).
+
+## Use with PyEnsembl
+
+With the selected PyEnsembl annotation already downloaded and indexed:
+
+```python
+from pyensembl import EnsemblRelease
+from orfdata import load_catalog
+
+genome = EnsemblRelease(95, species="human")
+catalog = load_catalog()
+transcript = genome.transcript_by_id("ENST00000304842")  # TPST1
+
+for orf in catalog.for_transcript(transcript):
+    print(orf.model.orf_id, orf.protein_sequence)
+    print(orf.evidence.has_evidence("ms"))
+    assert orf.transcript is transcript
+```
+
+The same call works for a noncoding parent, such as NUTM2B-AS1
+(`ENST00000483080`). Each returned `ReferenceORF` keeps its model, evidence and
+original PyEnsembl transcript together, after checking its coordinates and
+sequence against that transcript.
+
+Varcode describes changes to this reference ORF; Isovar connects it to observed
+RNA products. Reference evidence stays separate from evidence for a variant or
+fusion. See the [API and integration guide](docs/reference.md).
+
+The catalogue API supports other species, with explicit species and assembly
+checks. **Bundled evidence is currently human-only**; mouse bindings use synthetic
+test data. [Adding another species](docs/reference.md#other-species).
+
+Install with `pip install orfdata[pyensembl]`. See the
+[quantitative, multispecies data roadmap](https://github.com/openvax/orfdata/issues/3)
+for planned RNA abundance, ribosome occupancy and protein measurements.

orfdata-0.1.0/orfdata/__init__.py

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+"""Reference ORFs and evidence, independent of disease and patient variants."""
+
+from .catalog import (
+    EVIDENCE_METHODS,
+    ORFCatalog,
+    ORFEvidence,
+    ORFRecord,
+    PeptideEvidence,
+    UORFCatalog,
+    UORFPeptide,
+    UORFRecord,
+    load_catalog,
+    load_uorf_catalog,
+)
+from .initiation_context import KOZAK_PREFERENCES, InitiationContext, annotate_initiation_context
+from .model import ORFModel, ReferenceORF
+from .version import __version__
+
+__all__ = [
+    "__version__",
+    "EVIDENCE_METHODS",
+    "ORFCatalog",
+    "ORFRecord",
+    "ORFEvidence",
+    "PeptideEvidence",
+    "ORFModel",
+    "ReferenceORF",
+    "load_catalog",
+    "UORFCatalog",
+    "UORFRecord",
+    "UORFPeptide",
+    "load_uorf_catalog",
+    "KOZAK_PREFERENCES",
+    "InitiationContext",
+    "annotate_initiation_context",
+]