rpg-conv 0.2.0

Robust protein marker to gene symbol resolution backed by SQLite.

rpg_conv

rpg_conv resolves protein marker aliases (for example ki67, SMA, CD57) to canonical gene symbols using a local SQLite database populated from a bundled merged Ensembl reference table (human + mouse aliases together).

Install

pip install rpg_conv

For development:

pip install -e ".[dev]"

Quick Start

from rpg_conv import GeneResolver

resolver = GeneResolver()  # creates/loads a local SQLite DB in ~/.rpg_conv

print(resolver.resolve_one("ki67"))    # MKI67
print(resolver.resolve_one("a-sma", return_top=False)) # contains ACTA2 among merged aliases
print(resolver.resolve_one("CD57", return_top=False))  # contains B3GAT1 among merged aliases
print(resolver.resolve_one("PDCD1"))   # PDCD1

CLI

rpg-conv "ki--67"
rpg-conv "ki--67" --no-only-return-confident
rpg-conv "CD57" --return-ensembl-id
rpg-conv "hox1" --no-return-top --sep "|"
rpg-conv "hox1" --return-df --verbose

Data model

The SQLite database stores one merged alias table with:

• Ensembl gene ID
• canonical gene symbols
• aliases/synonyms
• normalized alias keys used for robust lookup
• bundled Ensembl reference rows loaded on first initialization

Matching behavior

• Direct normalized DB match is tried first.
• If no direct match, fuzzy search uses rapidfuzz.distance.Levenshtein.
• only_return_confident=True means only exact or strict fuzzy (distance < confidence_distance_lt) matches are accepted.
• If only_return_confident=False, worst-case fallback returns the original query string.