DeepMutSim 1.0.0__tar.gz → 1.1.0__tar.gz

deepmutsim-1.1.0/PKG-INFO

@@ -0,0 +1,172 @@
+Metadata-Version: 2.4
+Name: DeepMutSim
+Version: 1.1.0
+Summary: Enumerate all possible SNVs for MANE transcripts using HGVS nomenclature.
+Author-email: Liu Sun <sunliu@yxnu.edu.cn>, Jian Yang <yangjian@yxnu.edu.cn>
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/liu-sun/DeepMutSim
+Project-URL: Issues, https://github.com/liu-sun/DeepMutSim/issues
+Project-URL: Repository, https://github.com/liu-sun/DeepMutSim
+Keywords: bioinformatics,hgvs,variant,mane,ncbi,entrez,mutation
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+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: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: biopython
+Provides-Extra: test
+Requires-Dist: pytest>=7.0; extra == "test"
+Requires-Dist: pytest-cov>=4.0; extra == "test"
+Dynamic: license-file
+
+# DeepMutSim
+
+Generate all possible single nucleotide variants (SNVs) for MANE transcripts
+using [HGVS nomenclature][hgvs].  DeepMutSim queries NCBI Entrez to fetch the
+MANE Select / MANE Plus Clinical transcript for any human gene and enumerates
+every possible substitution — coding, UTR, splice sites, and protein-level.
+
+[hgvs]: https://varnomen.hgvs.org/
+
+## Features
+
+| Function | Output | Description |
+|---|---|---|
+| `cds(gene)` | `list[tuple]` | All CDS SNVs with protein consequence (1-letter & 3-letter) |
+| `missense(gene)` | `list[tuple]` | Missense variants (codon substitutions that change the amino acid) |
+| `codon_sub(gene)` | `list[str]` | All codon substitutions (silent + missense, incl. multi-base `delins`) |
+| `aa_sub(gene)` | `list[tuple]` | All single amino-acid substitutions |
+| `utr5(gene)` | `list[str]` | All 5' UTR SNVs (negative HGVS numbering) |
+| `utr3(gene)` | `list[str]` | All 3' UTR SNVs (`c.*` numbering) |
+| `splice_site(gene)` | `list[str]` | Canonical splice donor/acceptor ±1, ±2 variants |
+
+## Installation
+
+```bash
+pip install deepmutsim
+```
+
+DeepMutSim requires Python ≥3.8 and [Biopython][biopython].
+
+[biopython]: https://biopython.org/
+
+## Configuration
+
+Two environment variables are **mandatory** for NCBI Entrez access:
+
+| Variable | Required | Description |
+|---|---|---|
+| `EMAIL` | Yes | Your email address (NCBI policy) |
+| `API_KEY` | Recommended | NCBI API key — raises the rate limit from 3 to 10 req/s |
+
+[Obtain an API key][ncbi-key] from your NCBI account settings.
+
+[ncbi-key]: https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/
+
+**Linux / macOS:**
+
+```bash
+export EMAIL="your.email@example.com"
+export API_KEY="your_api_key_here"
+```
+
+**Windows (PowerShell):**
+
+```powershell
+$env:EMAIL = "your.email@example.com"
+$env:API_KEY = "your_api_key_here"
+```
+
+## Quick start
+
+```python
+import deepmutsim
+
+# All CDS single-nucleotide variants
+variants = deepmutsim.cds("INS")
+# [('NM_000207.3:c.1A>G', 'NP_000198.1:p.(M1?)', 'NP_000198.1:p.(Met1?)'), ...]
+
+# All missense variants
+missense = deepmutsim.missense("TP53")
+
+# All 5' UTR SNVs
+utr5_vars = deepmutsim.utr5("BRCA1")
+
+# All canonical splice site variants
+splice = deepmutsim.splice_site("CFTR")
+```
+
+## API reference
+
+### Query helpers
+
+- **`nm(gene)`** — Fetch the MANE nucleotide record (GenBank).
+- **`np(gene)`** — Fetch the MANE protein record (FASTA).
+- **`nc(gene)`** — Fetch the primary assembly RefSeq accession.
+
+### CDS variants
+
+- **`cds(gene)`** → `list[tuple[str, str, str]]`
+  Every possible single-nucleotide substitution across the coding sequence.
+  Each entry is `(c.HGVS, p.HGVS_1letter, p.HGVS_3letter)`.  The initiator
+  methionine is always reported as `M1?` / `Met1?`.
+
+- **`missense(gene)`** → `list[tuple[str, str, str]]`
+  Codon substitutions that change the encoded amino acid.  Includes multi-base
+  changes (reported as `delins`).  Same tuple format as `cds()`.
+
+- **`codon_sub(gene)`** → `list[str]`
+  All possible codon substitutions (silent + missense).  Single-base changes
+  use `X>Y` notation; multi-base changes use `delins`.
+
+### UTR variants
+
+- **`utr5(gene)`** → `list[str]`
+  All SNVs in the 5' untranslated region.  Positions use negative HGVS
+  numbering (`c.-59`, `c.-58`, …, `c.-1`).
+
+- **`utr3(gene)`** → `list[str]`
+  All SNVs in the 3' untranslated region.  Positions use `c.*` numbering
+  (`c.*1`, `c.*2`, …).
+
+### Splice site variants
+
+- **`splice_site(gene)`** → `list[str]`
+  Canonical donor (+1, +2) and acceptor (−2, −1) positions of every intron
+  within the CDS boundaries.  Prefixed with the genomic RefSeq accession.
+
+### Protein-level variants
+
+- **`aa_sub(gene)`** → `list[tuple[str, str]]`
+  All single amino-acid substitutions.  Each entry is
+  `(p.HGVS_1letter, p.HGVS_3letter)`.  The initiator methionine is reported
+  as `M1?` / `Met1?`.
+
+## Development
+
+```bash
+# Editable install with test dependencies
+pip install -e ".[test]"
+
+# Run tests (no network required — 38 tests)
+pytest tests/ -v
+
+# Run tests with coverage
+pytest --cov=deepmutsim --cov-report=term-missing
+
+# Build a distribution
+python -m build
+```
+
+## License
+
+MIT — see [LICENSE](LICENSE).

deepmutsim-1.1.0/README.md

@@ -0,0 +1,142 @@
+# DeepMutSim
+
+Generate all possible single nucleotide variants (SNVs) for MANE transcripts
+using [HGVS nomenclature][hgvs].  DeepMutSim queries NCBI Entrez to fetch the
+MANE Select / MANE Plus Clinical transcript for any human gene and enumerates
+every possible substitution — coding, UTR, splice sites, and protein-level.
+
+[hgvs]: https://varnomen.hgvs.org/
+
+## Features
+
+| Function | Output | Description |
+|---|---|---|
+| `cds(gene)` | `list[tuple]` | All CDS SNVs with protein consequence (1-letter & 3-letter) |
+| `missense(gene)` | `list[tuple]` | Missense variants (codon substitutions that change the amino acid) |
+| `codon_sub(gene)` | `list[str]` | All codon substitutions (silent + missense, incl. multi-base `delins`) |
+| `aa_sub(gene)` | `list[tuple]` | All single amino-acid substitutions |
+| `utr5(gene)` | `list[str]` | All 5' UTR SNVs (negative HGVS numbering) |
+| `utr3(gene)` | `list[str]` | All 3' UTR SNVs (`c.*` numbering) |
+| `splice_site(gene)` | `list[str]` | Canonical splice donor/acceptor ±1, ±2 variants |
+
+## Installation
+
+```bash
+pip install deepmutsim
+```
+
+DeepMutSim requires Python ≥3.8 and [Biopython][biopython].
+
+[biopython]: https://biopython.org/
+
+## Configuration
+
+Two environment variables are **mandatory** for NCBI Entrez access:
+
+| Variable | Required | Description |
+|---|---|---|
+| `EMAIL` | Yes | Your email address (NCBI policy) |
+| `API_KEY` | Recommended | NCBI API key — raises the rate limit from 3 to 10 req/s |
+
+[Obtain an API key][ncbi-key] from your NCBI account settings.
+
+[ncbi-key]: https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/
+
+**Linux / macOS:**
+
+```bash
+export EMAIL="your.email@example.com"
+export API_KEY="your_api_key_here"
+```
+
+**Windows (PowerShell):**
+
+```powershell
+$env:EMAIL = "your.email@example.com"
+$env:API_KEY = "your_api_key_here"
+```
+
+## Quick start
+
+```python
+import deepmutsim
+
+# All CDS single-nucleotide variants
+variants = deepmutsim.cds("INS")
+# [('NM_000207.3:c.1A>G', 'NP_000198.1:p.(M1?)', 'NP_000198.1:p.(Met1?)'), ...]
+
+# All missense variants
+missense = deepmutsim.missense("TP53")
+
+# All 5' UTR SNVs
+utr5_vars = deepmutsim.utr5("BRCA1")
+
+# All canonical splice site variants
+splice = deepmutsim.splice_site("CFTR")
+```
+
+## API reference
+
+### Query helpers
+
+- **`nm(gene)`** — Fetch the MANE nucleotide record (GenBank).
+- **`np(gene)`** — Fetch the MANE protein record (FASTA).
+- **`nc(gene)`** — Fetch the primary assembly RefSeq accession.
+
+### CDS variants
+
+- **`cds(gene)`** → `list[tuple[str, str, str]]`
+  Every possible single-nucleotide substitution across the coding sequence.
+  Each entry is `(c.HGVS, p.HGVS_1letter, p.HGVS_3letter)`.  The initiator
+  methionine is always reported as `M1?` / `Met1?`.
+
+- **`missense(gene)`** → `list[tuple[str, str, str]]`
+  Codon substitutions that change the encoded amino acid.  Includes multi-base
+  changes (reported as `delins`).  Same tuple format as `cds()`.
+
+- **`codon_sub(gene)`** → `list[str]`
+  All possible codon substitutions (silent + missense).  Single-base changes
+  use `X>Y` notation; multi-base changes use `delins`.
+
+### UTR variants
+
+- **`utr5(gene)`** → `list[str]`
+  All SNVs in the 5' untranslated region.  Positions use negative HGVS
+  numbering (`c.-59`, `c.-58`, …, `c.-1`).
+
+- **`utr3(gene)`** → `list[str]`
+  All SNVs in the 3' untranslated region.  Positions use `c.*` numbering
+  (`c.*1`, `c.*2`, …).
+
+### Splice site variants
+
+- **`splice_site(gene)`** → `list[str]`
+  Canonical donor (+1, +2) and acceptor (−2, −1) positions of every intron
+  within the CDS boundaries.  Prefixed with the genomic RefSeq accession.
+
+### Protein-level variants
+
+- **`aa_sub(gene)`** → `list[tuple[str, str]]`
+  All single amino-acid substitutions.  Each entry is
+  `(p.HGVS_1letter, p.HGVS_3letter)`.  The initiator methionine is reported
+  as `M1?` / `Met1?`.
+
+## Development
+
+```bash
+# Editable install with test dependencies
+pip install -e ".[test]"
+
+# Run tests (no network required — 38 tests)
+pytest tests/ -v
+
+# Run tests with coverage
+pytest --cov=deepmutsim --cov-report=term-missing
+
+# Build a distribution
+python -m build
+```
+
+## License
+
+MIT — see [LICENSE](LICENSE).

deepmutsim-1.1.0/pyproject.toml

@@ -0,0 +1,51 @@
+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "DeepMutSim"
+version = "1.1.0"
+authors = [
+  { name="Liu Sun", email="sunliu@yxnu.edu.cn" },
+  { name="Jian Yang", email="yangjian@yxnu.edu.cn" },
+]
+description = "Enumerate all possible SNVs for MANE transcripts using HGVS nomenclature."
+readme = "README.md"
+license = "MIT"
+requires-python = ">=3.8"
+keywords = ["bioinformatics", "hgvs", "variant", "mane", "ncbi", "entrez", "mutation"]
+dependencies = [
+  "biopython",
+]
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Intended Audience :: Science/Research",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+
+[project.optional-dependencies]
+test = [
+    "pytest>=7.0",
+    "pytest-cov>=4.0",
+]
+
+[project.urls]
+Homepage = "https://github.com/liu-sun/DeepMutSim"
+Issues = "https://github.com/liu-sun/DeepMutSim/issues"
+Repository = "https://github.com/liu-sun/DeepMutSim"
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+pythonpath = ["src"]
+addopts = [
+    "--doctest-modules",
+    "-v",
+]

deepmutsim-1.1.0/src/DeepMutSim.egg-info/PKG-INFO

@@ -0,0 +1,172 @@
+Metadata-Version: 2.4
+Name: DeepMutSim
+Version: 1.1.0
+Summary: Enumerate all possible SNVs for MANE transcripts using HGVS nomenclature.
+Author-email: Liu Sun <sunliu@yxnu.edu.cn>, Jian Yang <yangjian@yxnu.edu.cn>
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/liu-sun/DeepMutSim
+Project-URL: Issues, https://github.com/liu-sun/DeepMutSim/issues
+Project-URL: Repository, https://github.com/liu-sun/DeepMutSim
+Keywords: bioinformatics,hgvs,variant,mane,ncbi,entrez,mutation
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+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: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: biopython
+Provides-Extra: test
+Requires-Dist: pytest>=7.0; extra == "test"
+Requires-Dist: pytest-cov>=4.0; extra == "test"
+Dynamic: license-file
+
+# DeepMutSim
+
+Generate all possible single nucleotide variants (SNVs) for MANE transcripts
+using [HGVS nomenclature][hgvs].  DeepMutSim queries NCBI Entrez to fetch the
+MANE Select / MANE Plus Clinical transcript for any human gene and enumerates
+every possible substitution — coding, UTR, splice sites, and protein-level.
+
+[hgvs]: https://varnomen.hgvs.org/
+
+## Features
+
+| Function | Output | Description |
+|---|---|---|
+| `cds(gene)` | `list[tuple]` | All CDS SNVs with protein consequence (1-letter & 3-letter) |
+| `missense(gene)` | `list[tuple]` | Missense variants (codon substitutions that change the amino acid) |
+| `codon_sub(gene)` | `list[str]` | All codon substitutions (silent + missense, incl. multi-base `delins`) |
+| `aa_sub(gene)` | `list[tuple]` | All single amino-acid substitutions |
+| `utr5(gene)` | `list[str]` | All 5' UTR SNVs (negative HGVS numbering) |
+| `utr3(gene)` | `list[str]` | All 3' UTR SNVs (`c.*` numbering) |
+| `splice_site(gene)` | `list[str]` | Canonical splice donor/acceptor ±1, ±2 variants |
+
+## Installation
+
+```bash
+pip install deepmutsim
+```
+
+DeepMutSim requires Python ≥3.8 and [Biopython][biopython].
+
+[biopython]: https://biopython.org/
+
+## Configuration
+
+Two environment variables are **mandatory** for NCBI Entrez access:
+
+| Variable | Required | Description |
+|---|---|---|
+| `EMAIL` | Yes | Your email address (NCBI policy) |
+| `API_KEY` | Recommended | NCBI API key — raises the rate limit from 3 to 10 req/s |
+
+[Obtain an API key][ncbi-key] from your NCBI account settings.
+
+[ncbi-key]: https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/
+
+**Linux / macOS:**
+
+```bash
+export EMAIL="your.email@example.com"
+export API_KEY="your_api_key_here"
+```
+
+**Windows (PowerShell):**
+
+```powershell
+$env:EMAIL = "your.email@example.com"
+$env:API_KEY = "your_api_key_here"
+```
+
+## Quick start
+
+```python
+import deepmutsim
+
+# All CDS single-nucleotide variants
+variants = deepmutsim.cds("INS")
+# [('NM_000207.3:c.1A>G', 'NP_000198.1:p.(M1?)', 'NP_000198.1:p.(Met1?)'), ...]
+
+# All missense variants
+missense = deepmutsim.missense("TP53")
+
+# All 5' UTR SNVs
+utr5_vars = deepmutsim.utr5("BRCA1")
+
+# All canonical splice site variants
+splice = deepmutsim.splice_site("CFTR")
+```
+
+## API reference
+
+### Query helpers
+
+- **`nm(gene)`** — Fetch the MANE nucleotide record (GenBank).
+- **`np(gene)`** — Fetch the MANE protein record (FASTA).
+- **`nc(gene)`** — Fetch the primary assembly RefSeq accession.
+
+### CDS variants
+
+- **`cds(gene)`** → `list[tuple[str, str, str]]`
+  Every possible single-nucleotide substitution across the coding sequence.
+  Each entry is `(c.HGVS, p.HGVS_1letter, p.HGVS_3letter)`.  The initiator
+  methionine is always reported as `M1?` / `Met1?`.
+
+- **`missense(gene)`** → `list[tuple[str, str, str]]`
+  Codon substitutions that change the encoded amino acid.  Includes multi-base
+  changes (reported as `delins`).  Same tuple format as `cds()`.
+
+- **`codon_sub(gene)`** → `list[str]`
+  All possible codon substitutions (silent + missense).  Single-base changes
+  use `X>Y` notation; multi-base changes use `delins`.
+
+### UTR variants
+
+- **`utr5(gene)`** → `list[str]`
+  All SNVs in the 5' untranslated region.  Positions use negative HGVS
+  numbering (`c.-59`, `c.-58`, …, `c.-1`).
+
+- **`utr3(gene)`** → `list[str]`
+  All SNVs in the 3' untranslated region.  Positions use `c.*` numbering
+  (`c.*1`, `c.*2`, …).
+
+### Splice site variants
+
+- **`splice_site(gene)`** → `list[str]`
+  Canonical donor (+1, +2) and acceptor (−2, −1) positions of every intron
+  within the CDS boundaries.  Prefixed with the genomic RefSeq accession.
+
+### Protein-level variants
+
+- **`aa_sub(gene)`** → `list[tuple[str, str]]`
+  All single amino-acid substitutions.  Each entry is
+  `(p.HGVS_1letter, p.HGVS_3letter)`.  The initiator methionine is reported
+  as `M1?` / `Met1?`.
+
+## Development
+
+```bash
+# Editable install with test dependencies
+pip install -e ".[test]"
+
+# Run tests (no network required — 38 tests)
+pytest tests/ -v
+
+# Run tests with coverage
+pytest --cov=deepmutsim --cov-report=term-missing
+
+# Build a distribution
+python -m build
+```
+
+## License
+
+MIT — see [LICENSE](LICENSE).

{deepmutsim-1.0.0 → deepmutsim-1.1.0}/src/DeepMutSim.egg-info/SOURCES.txt

@@ -6,4 +6,8 @@ src/DeepMutSim.egg-info/SOURCES.txt
 src/DeepMutSim.egg-info/dependency_links.txt
 src/DeepMutSim.egg-info/requires.txt
 src/DeepMutSim.egg-info/top_level.txt
-src/deepmutsim/__init__.py
+src/deepmutsim/__init__.py
+src/deepmutsim/_fetch.py
+src/deepmutsim/_variants.py
+tests/test_fetch.py
+tests/test_variants.py

deepmutsim-1.1.0/src/DeepMutSim.egg-info/requires.txt

@@ -0,0 +1,5 @@
+biopython
+
+[test]
+pytest>=7.0
+pytest-cov>=4.0

deepmutsim-1.1.0/src/deepmutsim/__init__.py

@@ -0,0 +1,34 @@
+"""DeepMutSim — generate all possible SNVs for MANE transcripts in HGVS notation.
+
+Usage::
+
+    import deepmutsim
+    deepmutsim.cds("INS")       # all CDS single-nucleotide variants
+    deepmutsim.missense("INS")  # all missense variants
+    deepmutsim.aa_sub("INS")    # all amino-acid substitutions
+    deepmutsim.utr5("INS")      # all 5'UTR SNVs
+    deepmutsim.utr3("INS")      # all 3'UTR SNVs
+    deepmutsim.splice_site("INS")  # canonical splice-site SNVs
+    deepmutsim.codon_sub("INS")    # all codon substitutions
+
+Requires ``EMAIL`` and ``API_KEY`` environment variables for NCBI Entrez access.
+"""
+
+from ._fetch import _configure_entrez, nm, np, nc
+from ._variants import aa_sub, cds, codon_sub, missense, splice_site, utr3, utr5
+
+# Configure NCBI Entrez credentials on first import.
+_configure_entrez()
+
+__all__ = [
+    "nm",
+    "np",
+    "nc",
+    "cds",
+    "utr5",
+    "utr3",
+    "splice_site",
+    "aa_sub",
+    "codon_sub",
+    "missense",
+]

deepmutsim-1.1.0/src/deepmutsim/_fetch.py

@@ -0,0 +1,92 @@
+"""NCBI Entrez query helpers for fetching MANE transcript records.
+
+All functions require ``EMAIL`` and ``API_KEY`` environment variables to be set
+before use.  Call :func:`_configure_entrez` once, or set them through
+``Bio.Entrez.email`` / ``Bio.Entrez.api_key`` directly.
+"""
+
+import os
+
+from Bio import Entrez, SeqIO
+
+
+def _configure_entrez():
+    """Set NCBI Entrez credentials from environment variables.
+
+    Reads ``EMAIL`` (mandatory) and ``API_KEY`` (recommended) and configures
+    Biopython's Entrez module accordingly.
+    """
+    Entrez.email = os.environ["EMAIL"]
+    Entrez.api_key = os.environ.get("API_KEY", "")
+
+
+def nm(gene: str):
+    """Fetch the MANE Select / MANE Plus Clinical nucleotide record for *gene*.
+
+    Parameters
+    ----------
+    gene : str
+        Gene symbol (e.g. ``"INS"``, ``"TP53"``).
+
+    Returns
+    -------
+    Bio.SeqRecord.SeqRecord
+        GenBank record of the MANE transcript.
+    """
+    stream = Entrez.esearch(
+        db="nucleotide",
+        term=f'{gene}[Gene Name] AND ("MANE Select"[Keyword] OR "MANE Plus Clinical"[keyword])',
+    )
+    record = Entrez.read(stream)
+    stream = Entrez.efetch(
+        db="nucleotide", id=record["IdList"], rettype="gb", retmode="text"
+    )
+    return SeqIO.read(stream, "genbank")
+
+
+def np(gene: str):
+    """Fetch the MANE Select / MANE Plus Clinical protein record for *gene*.
+
+    Parameters
+    ----------
+    gene : str
+        Gene symbol (e.g. ``"INS"``, ``"TP53"``).
+
+    Returns
+    -------
+    Bio.SeqRecord.SeqRecord
+        FASTA record of the MANE protein.
+    """
+    stream = Entrez.esearch(
+        db="protein",
+        term=f'{gene}[Gene Name] AND ("MANE Select"[Keyword] OR "MANE Plus Clinical"[keyword])',
+    )
+    record = Entrez.read(stream)
+    stream = Entrez.efetch(
+        db="protein", id=record["IdList"], rettype="fasta", retmode="text"
+    )
+    return SeqIO.read(stream, "fasta")
+
+
+def nc(gene: str) -> str:
+    """Fetch the primary assembly RefSeq accession for *gene*.
+
+    Parameters
+    ----------
+    gene : str
+        Gene symbol (e.g. ``"INS"``, ``"TP53"``).
+
+    Returns
+    -------
+    str
+        RefSeq accession of the primary assembly (e.g. ``"NC_000011.10"``).
+    """
+    stream = Entrez.esearch(
+        db="nucleotide",
+        term=f'{gene}[Gene Name] AND "Primary Assembly"[Title] AND human[Organism]',
+    )
+    record = Entrez.read(stream)
+    stream = Entrez.efetch(
+        db="nucleotide", id=record["IdList"], rettype="acc", retmode="text"
+    )
+    return stream.read().strip()