hugo-unifier 0.1.1

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hugo-unifier

This python package can unify gene symbols based on the HUGO database.

Installation

The package can be installed via pip, or any other Python package manager.

pip install hugo-unifier

Usage

The package can be used both as a command line tool and as a library.

Command Line Tool

Currently, the command line tool only supports unifying the entries of a column in an AnnData objects var attribute. The input file and column name must be passed as an argument. The tool will update the column in place and save the AnnData object to a new file.

Check the help message for more information:

hugo-unifier --help

Library

The package can be used as a library to unify gene symbols in a pandas DataFrame. The unify function takes a list of gene symbols and returns a list of unified gene symbols. The function can be used as follows:

from hugo_unifier import unify
gene_symbols = ["TP53", "BRCA1", "EGFR"]
unified_symbols = unify(gene_symbols)
print(unified_symbols)

How it works

Different datasets sometimes use different gene symbols for the same gene. Sometimes, the same gene symbol occurs with slight modifications, such as dashes, underscores, or other characters. The hugo-unifier iteratively applies attempts to manipulate the gene symbols and check them against the HUGO database.

The following manipulations are applied in the following order:

1. identity: Use the gene symbol as is.
2. dot-to-dash: Replace dots with dashes.
3. discard-after-dot: Discard everything after the first dot.

More conservative manipulations are applied first. The first manipulation that returns a valid gene symbol is used.

Resolution of aliases

Documentation for this will be added soon.