[Biopython-dev] NCBI Abuse activity with Biopython

Michiel de Hoon mjldehoon at yahoo.com
Thu Jun 26 23:20:49 UTC 2008

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

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.


--- On Thu, 6/26/08, Peter <biopython at maubp.freeserve.co.uk> wrote:
From: Peter <biopython at maubp.freeserve.co.uk>
Subject: Re: [Biopython-dev] NCBI Abuse activity with Biopython
To: "Biopython Developers Mailing List" <biopython-dev at biopython.org>
Cc: "Andrew Dalke" <dalke at dalkescientific.com>
Date: Thursday, June 26, 2008, 6:05 PM

On Thu, Jun 26, 2008 at 10:40 PM, Andrew Dalke
<dalke at dalkescientific.com> wrote:
> On Jun 26, 2008, at 7:04 PM, Peter wrote:
>> I started working on a patch to mark Bio.GenBank.search_for() etc as
>> deprecated, but on reflection I don't really like the longer code
>> needed with Bio.Entrez
>> One idea that might be worth discussing is having variations of the
>> Entrez.e* functions which will parse the XML and return the results.
>> i.e. something like this:
>> def esearch2(...) :
>>   """Calls ESearch and parses the returned
>>   return read(esearch(..., retmode="XML"))
> What about calling it "search"?  That is, the one that does
everything the
> default way as most people expect is the one which doesn't need the

I like that idea for the naming :)  What do you think Michiel, as this
is your module?

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