[BioPython] import error

[Peter]

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