pyVSV 0.3.0__tar.gz

pyvsv-0.3.0/.gitignore

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+# Python environments, caches, and distributions
+.venv*/
+__pycache__/
+*.py[cod]
+*.egg-info/
+build/
+dist/
+.pytest_cache/
+.mypy_cache/
+.ruff_cache/
+.coverage
+.coverage.*
+htmlcov/
+coverage.xml
+
+# Local configuration and editor state
+.env
+.env.*
+!.env.example
+.DS_Store
+.idea/
+.vscode/
+
+# Notebook checkpoints and generated research artifacts
+.ipynb_checkpoints/

pyvsv-0.3.0/.python-version

@@ -0,0 +1 @@
+3.12

pyvsv-0.3.0/CHANGELOG.md

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+# Changelog
+
+## 0.3.0
+
+Initial PyPI release of `pyVSV`, with the `vsv` Python package and command-line interface.
+
+- Requires Python 3.12 or later; CI checks Python 3.12, 3.13, and 3.14.
+- Includes inline type information, the ontology, and the reference SBOL resource in the wheel.
+- Includes tests, documentation, reference data, and curated designs in the source archive. The curated design library is supplied separately when using the installed wheel.
+- Publishes through PyPI Trusted Publishing after the release tag, tests, metadata, and isolated wheel and source installs pass validation.

pyvsv-0.3.0/CONTRIBUTING.md

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+# Development
+
+Install [uv](https://docs.astral.sh/uv/getting-started/installation/), then run `make setup` to create the local environment from `uv.lock`. The default interpreter is Python 3.12, pinned in `.python-version`.
+
+## Working on the code
+
+Genomes live in `vsv.genome`. Architectures, edits, evidence, and the design library live in `vsv.design`. The command-line interface lives in `src/vsv/cli/`. A default `uv sync` installs the library and the dev tools. Add a dependency when a feature needs it.
+
+Use type annotations for public interfaces. Keep file access, network access, and command-line argument handling separate from analysis code, so computations can be tested independently. Imports should not initiate downloads, write files, or run analyses.
+
+Put automated tests in `tests/`. Use small synthetic fixtures for sequence-related tests, and document their purpose. Tests must run offline without external services or large datasets. Test observable behavior, including error cases, when introducing functionality.
+
+Use notebooks for exploration and move reusable logic into the package. Clear notebook outputs before committing and keep generated artifacts in `results/`.
+
+## Dependencies
+
+```sh
+uv add <package>
+uv add --dev <development-tool>
+uv lock --upgrade-package <package>
+```
+
+Review and include both `pyproject.toml` and `uv.lock` whenever changing dependencies. Normal development and CI use `--locked` so stale dependency declarations fail instead of silently changing the lockfile.
+
+## Checks
+
+```sh
+make format       # Apply Ruff formatting
+make check        # Lint, formatting check, strict type checking, and tests
+make build        # Build a source distribution and wheel in dist/
+make check-dist   # Build and validate PyPI metadata and README
+```
+
+Individual checks are available through `make lint`, `make format-check`, `make typecheck`, and `make test`. These targets run tools through uv, so activating the virtual environment is optional.
+
+CI runs these checks on Python 3.12, 3.13, and 3.14, then builds and checks both distributions on Python 3.12. It installs each artifact into a fresh environment to verify metadata, packaged resources, and entry points, and runs the tests from the extracted source distribution. The distribution name is `pyVSV` and its version is defined in `pyproject.toml`. The Python API and CLI read that installed distribution metadata. The import package and the `vsv` command remain `vsv`.
+
+See [docs/releasing.md](docs/releasing.md) for PyPI setup, release validation, and publication.
+

pyvsv-0.3.0/LICENSE

@@ -0,0 +1,201 @@
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pyvsv-0.3.0/Makefile

@@ -0,0 +1,29 @@
+.PHONY: setup check lint format format-check typecheck test build check-dist
+
+DIST_DIR ?= dist
+
+setup:
+	uv sync --locked
+
+check: lint format-check typecheck test
+
+lint:
+	uv run --locked ruff check .
+
+format:
+	uv run --locked ruff format .
+
+format-check:
+	uv run --locked ruff format --check .
+
+typecheck:
+	uv run --locked mypy
+
+test:
+	uv run --locked pytest
+
+build:
+	uv build --no-sources --out-dir "$(DIST_DIR)"
+
+check-dist: build
+	uv run --locked twine check --strict "$(DIST_DIR)"/*.whl "$(DIST_DIR)"/*.tar.gz

pyvsv-0.3.0/PKG-INFO

@@ -0,0 +1,230 @@
+Metadata-Version: 2.4
+Name: pyVSV
+Version: 0.3.0
+Summary: Computational genetics tools for Vesicular Stomatitis Virus (VSV) research.
+Project-URL: Homepage, https://github.com/marpaia/pyVSV
+Project-URL: Documentation, https://github.com/marpaia/pyVSV#readme
+Project-URL: Repository, https://github.com/marpaia/pyVSV
+Project-URL: Issues, https://github.com/marpaia/pyVSV/issues
+License-Expression: Apache-2.0
+License-File: LICENSE
+Keywords: bioinformatics,sbol,vsv
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Typing :: Typed
+Requires-Python: >=3.12
+Requires-Dist: click>=8.5.0
+Requires-Dist: rdflib<7,>=6.1.1
+Requires-Dist: sbol3>=1.2.0.post0
+Description-Content-Type: text/markdown
+
+# pyVSV
+
+pyVSV is a Python library for assembling recombinant Vesicular Stomatitis Virus (VSV) vaccine plans on the Indiana antigenome.
+
+<p align="center">
+  <img src="https://www.arpaia.io/images/vsv/vsv-structure-genome.jpg" alt="VSV Structure and Genome">
+</p>
+<p align="center">
+  <em>Liu G, Cao W, Salawudeen A, et al. Vesicular Stomatitis Virus: From Agricultural Pathogen to Vaccine Vector. Pathogens. 2021;10(9):1092. Published 2021 Aug 27. doi:<a href="https://doi.org/10.3390/pathogens10091092">10.3390/pathogens10091092</a></em>
+</p>
+
+## Install
+
+```sh
+pip install pyVSV
+```
+
+The Python library is installed as `pyVSV` but the import package is `vsv`.
+
+## Quick start
+
+```python
+import vsv
+from vsv import Gene, GlycoproteinForm, Host, Replication, Timing
+
+outbreak = vsv.read_record("outbreak.gb")  # pathogen record: FASTA, GenBank, or SBOL
+glycoprotein = outbreak.cds(Gene.GLYCOPROTEIN)
+vaccine = vsv.indiana().replace(
+    glycoprotein,
+    identifier="rvsv_dg_outbreak_gp",
+    name="rVSV outbreak glycoprotein",
+    antigen_class="zaire-ebolavirus-glycoprotein",
+    strain="Kikwit-1995",
+    form=GlycoproteinForm.FULL_LENGTH,
+    replication=Replication.COMPETENT,
+)
+vaccine.check()
+
+# Gene order, the edit, its citation, and the foreign coding sequence.
+vaccine.write_plan("plan.ttl")
+
+# That coding sequence spliced into the Indiana reference, NC_001560.1.
+vaccine.write_antigenome("antigenome.ttl")
+```
+
+`read_record` reads the pathogen genome from FASTA, GenBank, or an SBOL genome document. `write_plan` stores the plan: ordered genes, the edit, the method citation, and the foreign coding sequence. `write_antigenome` stores the antigenome, the same coding sequence spliced into the Indiana reference NC_001560.1. `vsv.read` opens a plan and returns a `Vaccine`. `read_record` opens that antigenome and returns a `Genome`. Calling code does not handle SBOL objects.
+
+## The coding sequence
+
+`cds` returns the DNA string for one of the five VSV genes and raises when that gene has no coding sequence. Spans inside a `Genome` are zero-based and half-open. In an SBOL file those spans are one-based inclusive ranges.
+
+## Placing the gene
+
+`replace` removes the VSV glycoprotein and puts the coding sequence in its place. The new vaccine cites the 2004 glycoprotein-replacement method. The antigen id defaults to `Glycoprotein`.
+
+`replication` is `Replication.COMPETENT` when the antigen supplies entry, and `Replication.SINGLE_CYCLE` when it does not.
+
+To keep the VSV glycoprotein, or to place the gene first, use `insert`. It keeps the parent's replication class, so it takes no `replication` argument. The published sites are `"g"` and `"leader"`.
+
+```python
+# Keep the VSV glycoprotein and add the gene after it. Cites the 1997 method.
+vaccine = vsv.indiana().insert(
+    coding,
+    after="g",
+    identifier="rvsv_gl_outbreak_gp",
+    name="rVSV outbreak glycoprotein",
+    antigen_class="zaire-ebolavirus-glycoprotein",
+    module="outbreak_gp",
+    form=GlycoproteinForm.FULL_LENGTH,
+    strain="Kikwit-1995",
+)
+
+# Place the gene first, after the leader. Cites the 2014 method.
+vaccine = vsv.indiana().insert(
+    coding,
+    after="leader",
+    identifier="rvsv_leader_outbreak_gp",
+    name="rVSV outbreak glycoprotein",
+    antigen_class="zaire-ebolavirus-glycoprotein",
+    module="outbreak_gp",
+    form=GlycoproteinForm.FULL_LENGTH,
+    strain="Kikwit-1995",
+)
+```
+
+`vsv.indiana()` is nucleoprotein, phosphoprotein, matrix protein, glycoprotein, and large polymerase, with realization `NC_001560`.
+
+## Checking a vaccine
+
+`check()` is true only when `violations` is empty. A knowledge gap is a violation: unknown replication, or an unknown parent. `vsv check` exits 0 when every violation is a gap and exits 1 on any other rule.
+
+When the edited antigen has a coding sequence, `check()` also rejects:
+
+- an unclosed reading frame
+- a gene-end inside the transcription unit
+- a gene-end joined directly to a gene-start
+- a soluble glycoprotein used as a replication-competent glycoprotein replacement
+- a full-length or tail-chimera competent glycoprotein replacement with no hydrophobic anchor in its last 60 residues
+- a Zaire glycoprotein whose editing site is not eight A's when full-length, or seven A's when soluble
+
+```python
+result = vaccine.check()
+if not result:
+    for violation in result.violations:
+        print(violation.rule, violation.message)
+```
+
+`vaccine.observations` is empty until a result is recorded. `write_plan` stores the coding sequence when one is set. The curated shelf cards have none.
+
+## Finding precedents
+
+`precedents` returns published vaccines with the same arrangement: the glycoprotein replaced, one gene after the glycoprotein, or one gene after the leader. `vsv.library()` reads the curated shelf.
+
+```python
+for precedent in vaccine.precedents(vsv.library()):
+    print(precedent.id)
+```
+
+`antigen_class` keeps vaccines whose antigen is that class or a subclass of it. `phenotype`, `host`, and `timing` keep vaccines with a matching observation. A filovirus query includes the species glycoproteins. A Zaire query does not include Sudan or Marburg. A nonhuman-primate query includes cynomolgus and rhesus.
+
+```python
+from vsv import Phenotype
+
+vaccine.precedents(
+    vsv.library(),
+    antigen_class="filovirus-glycoprotein",
+    phenotype=Phenotype.PROTECTION,
+    host=Host.NONHUMAN_PRIMATE,
+)
+```
+
+A vaccine with any number of non-viral genes other than one is not compared.
+
+`data/designs/` holds the Indiana chassis and one directory per published filovirus vaccine. Each directory has `design.ttl` and `PROVENANCE.md`. The Turtle describes the ordered genome and the papers. A nucleotide sequence is present only when the antigen feature has an `sbol:Sequence`. The shelf cards have none.
+
+The curated library lives in the repository, not in the wheel. `vsv.library()` finds it from a checkout. From an installed package, pass the directory:
+
+```python
+from pathlib import Path
+
+shelf = vsv.library(Path("path/to/pyVSV/data/designs"))
+```
+
+## Antigenome
+
+`vaccine.antigenome()` splices the coding sequence into NC_001560.1 and returns a `Genome`. The chassis sequence is the SBOL document `NC_001560.ttl`. A glycoprotein replacement has five named genes, so `cds` returns the inserted glycoprotein. The backbone is `https://vsv.bio/backbone/VSV-Indiana`. The reference accession is NC_001560.1. The papers' infectious clones stay on `Implementation.plasmid`.
+
+A glycoprotein replacement keeps both flanking intergenic dinucleotides on the backbone. An insert between the glycoprotein and the large polymerase prefixes `CT`. An insert after the leader suffixes `CT`, so a gene-end is not joined directly to the next gene-start.
+
+A shelf card has no coding sequence, so `antigenome()` and `write_antigenome` raise for those files.
+
+## Command line
+
+```bash
+vsv genes data/raw/NC_001560.fasta
+vsv genes data/raw/NC_001560.ttl
+vsv extract -g g --kind protein data/raw/NC_001560.gb
+vsv designs
+vsv show rvsv_dg_zebov_kikwit_gp
+vsv check data/designs/vsv_indiana
+vsv precedents rvsv_dg_zebov_kikwit_gp --locus 3
+vsv precedents data/designs/rvsv_gl_zebov_sgp
+vsv antigenome kikwit.ttl
+```
+
+On the command line the genes are `n` (nucleoprotein), `p` (phosphoprotein), `m` (matrix protein), `g` (glycoprotein), and `l` (large polymerase). The full command reference (every subcommand, its filters, and what an empty `precedents` answer means) is in [docs/cli.md](https://github.com/marpaia/pyVSV/blob/master/docs/cli.md).
+
+## Literature
+
+### Methods the library cites
+
+`replace` and `insert` record the citation for the method they implement, so a written plan carries the paper its arrangement came from.
+
+| Arrangement | Call | Method paper |
+|---|---|---|
+| Glycoprotein replacement | `replace(...)` | Garbutt et al., *Journal of Virology*, May 2004, [10.1128/jvi.78.10.5458-5465.2004](https://doi.org/10.1128/jvi.78.10.5458-5465.2004) |
+| Gene after the glycoprotein | `insert(..., after="g")` | [10.1128/jvi.71.8.5982-5989.1997](https://doi.org/10.1128/jvi.71.8.5982-5989.1997) |
+| Gene after the leader | `insert(..., after="leader")` | [10.1128/jvi.00019-14](https://doi.org/10.1128/jvi.00019-14) |
+
+Each curated design carries its own citations and quoted evidence in its `PROVENANCE.md`.
+
+### Vector design and recovery
+
+- [Vesicular stomatitis virus (VSV) as a vaccine vector for immunization against viral infections](https://pubmed.ncbi.nlm.nih.gov/24379275/) - Jan 2013
+- [An efficient plasmid-based system for the recovery of recombinant vesicular stomatitis virus encoding foreign glycoproteins](https://www.nature.com/articles/s41598-024-65384-8) - Jun 2024
+- [Leveraging Synthetic Virology for the Rapid Engineering of Vesicular Stomatitis Virus (VSV)](https://pubmed.ncbi.nlm.nih.gov/39459973/) - Oct 2024
+- [Low-dose VSV-EBOV vaccination provides rapid protection from lethal Ebola virus challenge](https://pubmed.ncbi.nlm.nih.gov/41727071/) - Feb 2026
+
+### Reference genomes
+
+- [Complete Genome Sequences of Two Vesicular Stomatitis Virus Isolates Collected in Mexico](https://pmc.ncbi.nlm.nih.gov/articles/PMC5597772/) - Sep 2017 ([VSV Isolate 1](https://www.ncbi.nlm.nih.gov/nuccore/MF196237), [VSV Isolate 2](https://www.ncbi.nlm.nih.gov/nuccore/MF196238))
+
+## Data
+
+- [VSV Genome Sequence](https://www.ncbi.nlm.nih.gov/nuccore/NC_001560) - Complete genome sequence of Vesicular Stomatitis Virus (VSV)
+- [VSV Protein Structures](https://www.rcsb.org/structure/6VSV) - 3D structures of VSV proteins available in the Protein Data Bank (PDB)
+- [Vesiculovirus on ViralZone](https://viralzone.expasy.org/21) - Information on the Vesiculovirus genus, including VSV, on ViralZone
+
+## Resources
+
+- [VSV Gene Expression Vector on VectorBuilder](https://en.vectorbuilder.com/resources/vector-system/pVSV_Exp.html)
+
+## License
+
+Apache-2.0. See [LICENSE](https://github.com/marpaia/pyVSV/blob/master/LICENSE).