GeneThesaurus v3.2.0

GeneThesaurus is a Python package that translates between different gene standards using publicly available data from HGNC and NIH.

Presently, GeneThesaurus supports translating:

• gene aliases and old gene symbols to the current HGNC standard gene symbols
• gene symbols to ensembl identifiers
• ensembl identifiers to gene symbols
• entrez (NCBI) identifiers to gene symbols or ensembl identifiers

Please get in touch (or consider submitting a pull request to this project) if you need translation between other formats.

Installation

You can install GeneThesaurus with:

pip install gene-thesaurus

Example usage

from gene_thesaurus import GeneThesaurus
gt = GeneThesaurus(data_dir='/tmp')

outdated_gene = 'TNFSF2'
up_to_date_gene = 'ETV6'
fake_gene = 'NOTAREALGENE'
input = [outdated_gene, up_to_date_gene, fake_gene]

#############################
### update_gene_symbols() ###
#############################

updated_genes = gt.update_gene_symbols(input)
print(updated_genes)
# {'TNFSF2': 'TNF'}

#########################
### translate_genes() ###
#########################

# Valid values for source and target are 'symbol', 'ensembl_id' and 'entrez_id'.

translated_genes = gt.translate_genes(input, source='symbol', target='ensembl_id')
print(translated_genes)
{'TNFSF2': 'ENSG00000232810', 'ETV6': 'ENSG00000139083'}