[Biopython] Access Entrez gene DB using rettype 'gb'

Chris Fields cjfields at illinois.edu
Thu Dec 9 13:49:04 UTC 2010


On Dec 9, 2010, at 6:59 AM, Brad Chapman wrote:

> Peter;
> 
>> What's wrong with the current Entrez XML parser for the gene
>> database? Is this one of the corner cases where the NCBI are
>> not currently returning "proper" XML with a DTD?
> 
> That's right. The gene database doesn't give back the "native" XML
> format which Entrez.read deals with. Instead it's got custom XML
> output:
> 
> http://www.ncbi.nlm.nih.gov/entrez/query/static/efetchseq_help.html#gene
> 
> Brad

Looks like it's just a straight conversion of their ASN.1 data.  Ick.

chris




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