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jrderuiter / pybiomart

A simple pythonic interface to biomart.
MIT License
55 stars 11 forks source link

Problem with working old assemblies #20

Open himanshusingh2018 opened 3 years ago

himanshusingh2018 commented 3 years ago

Hi The tool is not working with old assembly. I want to find Ensembl Transcript ID and Gene Symbol conversion for mm9. My code is below:

dataset = Dataset(name='mmusculus_gene_ensembl', host='http://www.ensembl.org')# working with latest assembly

dataset = Dataset(name='mmusculus_gene_ensembl',host='https://may2012.archive.ensembl.org/')# NOT WORKING WITH MM9 ASSEMBLY

annot = dataset.query(attributes=['ensembl_transcript_id','external_gene_name'])

ConnectionError: HTTPConnectionPool(host='https', port=80): Max retries exceeded with url: //may2012.archive.ensembl.org:80/biomart/martservice?dataset=mmusculus_gene_ensembl&type=configuration (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0x7f8c0f480af0>: Failed to establish a new connection: [Errno -3] Temporary failure in name resolution'))

Thanks Himanshu

mcjmigdal commented 1 month ago

If someone else experience this issue, for me it is actually working just not every time.

from pybiomart import Server

server = Server(host='http://feb2021.archive.ensembl.org')

dataset = (server.marts['ENSEMBL_MART_ENSEMBL'].datasets['hsapiens_gene_ensembl'])
dataset.query(attributes=['ensembl_gene_id', 'external_gene_name'])