[Biopython] IMGT/HLA DB Access

[Willis, Jordan R]

Hi Eyal,

The imgt database is not that dynamic to be honest. Will one download not suffice? You can get all the accession numbers from this table.

http://www.imgt.org/IMGTrepertoireMH/index.php?section=LocusGenes&repertoire=RepresentativeGenes#notes

I have been trying to get an IMGT api for years now. Unfortunately, you are just better off creating your own tools from scratch.



On Jan 28, 2014, at 4:00 PM, David Winter <djwinter at asu.edu<mailto:djwinter at asu.edu>> wrote:

Hi Eyal,

The Entrez module is specifically for the NCBI's entrez databases (the
likes of the nucleotide, refseq and pubmed), and won't work for others.

If the mgt/hla database has an API (a quick search around the site doesn't
find one) it might be possible to write your own code to access the
database programatically, but I don't think there in anything in Biopython
that will help you with actually querying the database or fetching records
from it.

David


On Tue, Jan 28, 2014 at 11:42 AM, Eyal Arian <eyalarian at gmail.com<mailto:eyalarian at gmail.com>> wrote:

Hello,
I would like to access data directly from the imgt/hla database into
BioPython: http://www.ebi.ac.uk/cgi-bin/ipd/imgt/hla/align.cgi

For example, the following doesn't work, but it may give you the idea of
what I am trying to do:
import Bio
from Bio import Entrez
Entrez.email = "eyalarian at gmail.com<mailto:eyalarian at gmail.com>"
handle = Entrez.esearch(db="x-imgt-hla", term="DPB1*01:01:01")
record = Entrez.read(handle)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "Bio/Entrez/__init__.py", line 372, in read
record = handler.read(handle)
File "Bio/Entrez/Parser.py", line 187, in read
self.parser.ParseFile(handle)
File "Bio/Entrez/Parser.py", line 325, in endElementHandler
raise RuntimeError(value)
RuntimeError: Invalid db name specified: x-imgt-hla

Thanks!
E. Arian
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David Winter
Postdoctoral Research Associate
Center for Evolutionary Medicine and Informatics
The Biodesign Institute
Arizona State University

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