BiomartException: Query ERROR for existing dataset in BioMart
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0
Entering edit mode
5 weeks ago
Luqman • 0

I am trying to fetch protein sequences for a list of gene IDs using from BioMart API using the Python code:

def fetch_protein_sequences(gene_ids):
    dataset = Dataset(name='taestivum_eg_gene', host='http://plants.ensembl.org')
    # Fetch protein sequences
    response = dataset.query(
        attributes=[
            'ensembl_gene_id', 
            'peptide'
        ],
        filters={'gene_id': gene_ids}
    )
    return response

# Read gene IDs from file
with open('gene_ids.txt') as f:
    gene_ids = [line.strip() for line in f]

# Fetch protein sequences
protein_sequences = fetch_protein_sequences(gene_ids)

Bu keep getting the error message:

BiomartException: Query ERROR: caught BioMart::Exception::Usage: WITHIN Virtual Schema : default, Dataset taestivum_eg_gene NOT FOUND

Verified the existence of data taestivum_eg_gene, attributes and filter using:

server = Server(host='http://plants.ensembl.org')
for dataset in server.marts['plants_mart'].datasets:
    print(dataset)

Could someone please help me understand why I am seeing this error?

Thank you in advance!

biomart ensembl wheat python pybiomart • 408 views
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0
Entering edit mode

The dataset you want (taestivum_eg_gene) exists within the "plants_mart" schema, not the default schema. Your current code assumes the default schema.

The most straightforward fix is to explicitly tell the Dataset object to use the "plants_mart" schema

from biomart import BiomartServer, Dataset

def fetch_protein_sequences(gene_ids):
    server = BiomartServer("http://plants.ensembl.org")  # Connect to server
    # Specify the correct mart
    dataset = server.marts["plants_mart"].datasets["taestivum_eg_gene"]
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0
Entering edit mode

I am using pybiomart which has Server inplace of BiomartServer, I used that as per above but still getting the same error. Also, when I am checking filters for the dataset it works and prints available filters, same for when checking attributes. Somehow the fetching function returns error.

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0
Entering edit mode

Could share some examples for gene_ids?

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0
Entering edit mode

Yes please see below:

TraesCS2B02G372900
TraesCS2B02G375100
TraesCS2B02G374700
TraesCS2B02G382000
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