[Biopython-dev] NCBI Abuse activity with Biopython

Peter biopython at maubp.freeserve.co.uk
Thu Jun 26 22:05:45 UTC 2008

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 XML."""
>>   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 prefix?

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


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