| Name | gene-thesaurus JSON |
| Version |
3.1.0
JSON |
| download |
| home_page | None |
| Summary | GeneThesaurus is a Python package that translates gene aliases and old gene symbols to the current HGNC standard gene symbols. |
| upload_time | 2025-08-12 14:31:52 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.8 |
| license | MIT License Copyright (c) 2023 Uppsala University, Department of Medical Sciences, Molecular Precision Medicine Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. |
| keywords |
genomics
gene
hgnc
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
build
bumpver
certifi
charset-normalizer
click
colorama
exceptiongroup
flake8
freezegun
idna
importlib-metadata
iniconfig
lexid
mccabe
numpy
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pytz
requests
six
toml
tomli
typing-extensions
tzdata
urllib3
wheel
zipp
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# GeneThesaurus v3.1.0
GeneThesaurus is a Python package that translates between different gene standards using publicly available data from [HGNC](https://www.genenames.org/) 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'}
```
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"description": "# GeneThesaurus v3.1.0\n\nGeneThesaurus is a Python package that translates between different gene standards using publicly available data from [HGNC](https://www.genenames.org/) and NIH.\n\nPresently, GeneThesaurus supports translating:\n- gene aliases and old gene symbols to the current HGNC standard gene symbols\n- gene symbols to ensembl identifiers\n- ensembl identifiers to gene symbols\n- entrez (NCBI) identifiers to gene symbols or ensembl identifiers\n\nPlease get in touch (or consider submitting a pull request to this project) if you need translation between other formats.\n\n# Installation\n\nYou can install GeneThesaurus with:\n```\npip install gene-thesaurus\n```\n\n# Example usage\n```\nfrom gene_thesaurus import GeneThesaurus\ngt = GeneThesaurus(data_dir='/tmp')\n\noutdated_gene = 'TNFSF2'\nup_to_date_gene = 'ETV6'\nfake_gene = 'NOTAREALGENE'\ninput = [outdated_gene, up_to_date_gene, fake_gene]\n\n#############################\n### update_gene_symbols() ###\n#############################\n\nupdated_genes = gt.update_gene_symbols(input)\nprint(updated_genes)\n# {'TNFSF2': 'TNF'}\n\n#########################\n### translate_genes() ###\n#########################\n\n# Valid values for source and target are 'symbol', 'ensembl_id' and 'entrez_id'.\n\ntranslated_genes = gt.translate_genes(input, source='symbol', target='ensembl_id')\nprint(translated_genes)\n{'TNFSF2': 'ENSG00000232810', 'ETV6': 'ENSG00000139083'}\n\n```\n",
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