A small example for how to create XML queries for biomart using python

querybiomartexample.py

import requests

def main():
    exampleTaxonomy = "mmusculus_gene_ensembl"
    exampleGene = "ENSMUSG00000086981"

    urlTemplate = \
        '''http://ensembl.org/biomart/martservice?query=''' \
        '''<?xml version="1.0" encoding="UTF-8"?>''' \
        '''<!DOCTYPE Query>''' \
        '''<Query virtualSchemaName="default" formatter="CSV" header="0" uniqueRows="0" count="" datasetConfigVersion="0.6">''' \
        '''<Dataset name="%s" interface="default"><Filter name="ensembl_gene_id" value="%s"/>''' \
        '''<Attribute name="ensembl_gene_id"/><Attribute name="ensembl_transcript_id"/>''' \
        '''<Attribute name="transcript_start"/><Attribute name="transcript_end"/>''' \
        '''<Attribute name="exon_chrom_start"/><Attribute name="exon_chrom_end"/>''' \
        '''</Dataset>''' \
        '''</Query>'''

    exampleURL = urlTemplate % (exampleTaxonomy, exampleGene)
    req = requests.get(exampleURL, stream=True)
    for line in req.iter_lines():
        print line

if __name__ == '__main__':
    main()