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

Brad Chapman chapmanb at 50mail.com
Thu Dec 9 12:59:59 UTC 2010


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



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