[Biopython] ASN.1 and Entrez SNP
biopython at maubp.freeserve.co.uk
Tue Apr 13 08:22:42 UTC 2010
2010/4/13 Tiago Antão <tiagoantao at gmail.com>:
> Just a simple question:
> Entrez SNP seems to return ASN.1 format only.
> Is there any way to parse this in biopython? I've looked at SeqIO and
> found nothing...
> I can think of tools to process this outside, but I am just curious if
> this is processed natively with Biopython (being an exposed NCBI
> Many thanks,
> PS - You can easily try this with:
> hdl = Entrez.efetch(db="snp", id="3739022")
> print hdl.read()
No, we don't support ASN.1, and I don't see any good reason to - I
think it would only be NCBI ASN.1 we'd we interested in, and I think
that all their resources are available in other easier to use formats
like XML these days.
See also http://en.wikipedia.org/wiki/Abstract_Syntax_Notation_One
Instead ask Entrez to give you the SNP data as XML:
Entrez.efetch(db="snp", id="3739022", retmode="xml")
Hopefully the SNP XML file has everything in it.
You have a choice of Python XML parsers to use. However, the
Bio.Entrez parser doesn't like this XML. This appears to be related
(or caused by) a known NCBI bug. See
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