[BioPython] import error

[James Swetnam]

Hi Peter, and subscribers:

The problem seems to vanish with the current CVS release of python. I  
was using the fink package (which I believe is 1.44?).  Thank you for  
your help.

James
On Mar 11, 2008, at 7:16 PM, Peter wrote:

> On Tue, Mar 11, 2008 at 10:21 PM, James Swetnam <jswetnam at gmail.com>  
> wrote:
>> Hello.
>>
>> First off, apologies if my problem has been resolved in a previous
>> mailing; the archives search on the OBF wiki is disabled.
>
> Hmm.  I don't know anything about that - I've always just used Google
> to search the mailing list.
>
>> Also, it's quite possible i'm doing something boneheaded, as I  
>> still consider
>> myself a fairly novice python programmer.  So apologies if I make you
>> read through this just to correct an indentation error or somethinig
>> similar!
>> ...
>
> I haven't tried to reproduce this (which would be tricky without the
> FASTA file), but my initial guess would be duplicate identifiers.
> i.e. perhaps Biopython is failing to add one of the records because
> its id clashes with an existing record in the database.  It should be
> fairly easy for you to check this...
>
> If I'm right, then the fix could be to assign the modified SeqRecord a
> new id, maybe some combination of the parent GenBank id and a unique
> count - or the sub string location?
>
> Keep in mind that our BioSQL code is currently a little bit fussy
> about the formatting of the record id - it expects it to end in a
> ".version", see bug 2425.
> http://bugzilla.open-bio.org/show_bug.cgi?id=2425
>
> Peter