[Biopython] Issues with BioSQL and BioPython--can't access features and annotation

[Peter Cock]

On Mon, Mar 4, 2013 at 9:37 PM, Dan Tomso <dtomso at agbiome.com> wrote:
> Gents--
> Updating to the github version of BioPython has solved the problem, although
> I am not greatly enlightened.  If you are in debug mode, let me know if
> there is anything I can do to help, otherwise I will proceed w/ some crazy
> science . . .
>
> Many thanks!!
>
> Dan T.

Hi Dan,

I'm pretty sure this was an int/long issue (Python 2 specific, this distinction
goes away in Python 3), with your database binding giving you longs
rather than ints - in which case this was the fix:
https://github.com/biopython/biopython/commit/4a67d851d1eda0a138b604c8aeffc151d331a29b

That was included in Biopython 1.61 onwards, so you were just a bit
unlucky with Biopython 1.60 to run into this.

If you want to make absolutely sure, you could test with Biopython 1.61
and/or edit those lines in Bio/SeqFeature.py just to check.

Thanks for helping diagnose this,

Peter