[Biopython-dev] Error in Bio.Entrez.__init__

Peter Cock p.j.a.cock at googlemail.com
Thu Nov 29 14:49:42 UTC 2012

On Thu, Nov 29, 2012 at 2:33 PM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
> --- On Mon, 11/26/12, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>> In general the NCBI identifiers are arbitrary strings,
>> although perhaps the pubmed identifiers could be treated as
>> integers.
>> This is perhaps worth changing in the Bio.Entrez code...
>> What do you think Michael?
> If we change this in the Bio.Entrez code, we should put str(..) around
> all NCBI identifiers, not just the pubmed ones. Otherwise we'd have
> special treatment for one of the Entrez databases, which may cause
> problems in the future.

Yes, after all there are other Entrez database with 'numerical' identifiers.

> I'm OK if somebody else adds the calls to str(..), but I wouldn't champion
> it myself.

I don't mind doing the commit (and a unit test), but do you have any
specific concern in mind?


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