[Biopython-dev] NCBI Abuse activity with Biopython

Peter biopython at maubp.freeserve.co.uk
Thu Jun 26 23:45:50 UTC 2008

On Fri, Jun 27, 2008 at 12:20 AM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
> There are some other possibilities, for example to use the retout parameter.
> This parameter lets you choose between XML, HTML, plain text, ... format for
> the results.

I'm not sure if its rettype, retmode or retout - but something like that.

> We could make the rule that without an explicit value for this
> parameter, the Bio.Entrez.e* functions return the parsed results.

You suggestion to automatically do the parsing when XML format is
requested would prevent the user from parsing the XML themselves (e.g.
using SAX or DOM).  It would also spoil my plan to include some of the
Entrez sequence XML formats in Bio.SeqIO as this would need
Bio.efetch(...) to return a handle with XML in it.

> If we're not sure what to do, I suggest we keep the search_for function in
> Bio.GenBank for the upcoming release, and take this issue up later.

That would be expedient.


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