[Biopython] eprimer3 and primer3 incompatibility

[Peter]

On Fri, Dec 31, 2010 at 11:33 PM, David Koppstein wrote:
> Hi,
>
> I noticed today, while trying to work with
> Bio.Emboss.Applications.Primer3CommandLine, that there is an incompatibility
> in the TAG format between the current version of Emboss's eprimer3 (6.3.1)
> and the current version of primer3_core (2.2.3).
>
> The EMBOSS developers apparently know about this:
>
> http://web.archiveorange.com/archive/v/yWYDQkVd25Rxx2EAVunh
>
> but haven't yet fixed it, unless you want to download a c program and
> recompile manually.

Oh yeah, it looks like it was me that reported this to them back in April 2010
(linked to in the thread you found):
http://www.mail-archive.com/emboss@lists.open-bio.org/msg01405.html

> If and when they do fix it, at some point the tag lists will probably have
> to be updated for the Biopython module.

Possibly - if EMBOSS change their command line arguments.

> In the meantime, I am using the old
> primer3_core (1.1.4) which should interface with eprimer3 just fine. Would
> it make sense, however, to have a Biopython module that interfaces directly
> with primer3_core, rather than going through eprimer3?

Maybe. I've not looked at the native command line API of primer3_core
to form an opinion.

> Happy New Year!
> David

You too,

Peter