DeepMutSim 1.1.0

Enumerate all possible SNVs for MANE transcripts using HGVS nomenclature.

DeepMutSim

Generate all possible single nucleotide variants (SNVs) for MANE transcripts using HGVS nomenclature. 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.

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

pip install deepmutsim

DeepMutSim requires Python ≥3.8 and Biopython.

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 from your NCBI account settings.

Linux / macOS:

export EMAIL="[e-mail]"
export API_KEY="your_api_key_here"

Windows (PowerShell):

$env:EMAIL = "[e-mail]"
$env:API_KEY = "your_api_key_here"

Quick start

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

# 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.