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pybiomart 사용법

A simple and pythonic biomart interface for Python. The intent of pybiomart is to provide a simple interface to biomart, which can be used to easily query biomart databases from Python. In this sense, pybiomart aims to provide functionality similar to packages such as biomaRt (which provides access to biomart from R).

https://pypi.org/project/pybiomart/

Documentation

PyBiomart - pybiomart 0.2.0 documentation

The intent of pybiomart is to provide a simple interface to biomart, which can be used to easily query biomart databases from Python. In this sense, pybiomart aims to provide functionality similar to packages such as biomaRt (which provides access to biomart from R).

https://jrderuiter.github.io/pybiomart/

Install

conda install -c bioconda pybiomart
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Quickstart

from pybiomart import Dataset
dataset = Dataset(name='hsapiens_gene_ensembl', host='http://www.ensembl.org')

res = dataset.query(attributes=['ensembl_gene_id', 'external_gene_name'])

server = Server(host='http://www.ensembl.org')
server.list_marts()

mart = server['ENSEMBL_MART_ENSEMBL']
mart.list_datasets()

dataset = mart['hsapiens_gene_ensembl']

# Datset의 attribute를 얻습니다.
dataset.list_attributes()
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Mapping from ensg to symbol (Protein-coding gene only)

from pybiomart import Dataset
dataset = Dataset(name='hsapiens_gene_ensembl', host='http://www.ensembl.org')
res = dataset.query(attributes=['ensembl_gene_id', 'external_gene_name', 'gene_biotype'])

ensg2symbol = {r['Gene stable ID']:r['Gene name'] for r in res[res['Gene type'] == 'protein_coding'].to_records()}
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Mapping from ensg to symbol

from pybiomart import Dataset
dataset = Dataset(name='hsapiens_gene_ensembl', host='http://www.ensembl.org')
res = dataset.query(attributes=['ensembl_gene_id', 'external_gene_name', 'gene_biotype'])

ensg2symbol = {r['Gene stable ID']:r['Gene name'] for r in res.to_records()}
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Mapping from ensg to symbol (mouse)

from pybiomart import Dataset
dataset = Dataset(name='mmusculus_gene_ensembl', host='http://www.ensembl.org')
res = dataset.query(attributes=['ensembl_gene_id', 'external_gene_name', 'gene_biotype'])

ensg2symbol = {r['Gene stable ID']:r['Gene name'] for r in res.to_records()}
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Entrez ID to symbol

dataset = Dataset(name='hsapiens_gene_ensembl', host='http://www.ensembl.org')
res = dataset.query(attributes=['external_gene_name', 'entrezgene_id']).dropna()

entrez2symbol = {str(int(r['NCBI gene (formerly Entrezgene) ID'])):r['Gene name'] for r in res.to_records()}
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