Hi,
I have been trying to find a uniform way of extracting exon sequences for
specific Ensembl transcript IDs using BIOMart SOAP service Python (+ suds).
The documentation is somewhat vague on this point, and I haven't been able
to make the provided example work.
(I am not able to use the Ensembl Perl API, in case you're wondering why
this detour.)
This is what I have come up with:
"""
biomartclient.py
"""
from suds.client import Client
client = Client("http://www.biomart.org/biomart/martwsdl";)
datasets = client.service.getDatasets('ensembl')
attribs = client.service.getAttributes(datasets[0].name)
wanted =
attribs[4].attributeGroup[0].attributeCollection[0].attributeInfo[8] #
this is the exon sequence attribute info
res = client.service.query('default', 0, 0, 0, datasets[0], wanted)
# I am aware that attributeInfo is not the same as Attribute, but
still not sure how to use this knowledge.
But the query is not working.
'print client' tells me just this about the query method:
query(xs:string virtualSchemaName, xs:int header, xs:int count, xs:int
uniqueRows, Dataset[] Dataset, )
I do not know how to make use of this information, and have already tried
many different ways.
I would be very glad if somebody would provide me with some useful insights
about this.
Thank you,
Ana Bulovic
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