[Biopython] eprimer3 and primer3 incompatibility

[David Koppstein]

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.

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

Happy New Year!
David

-- 
David Koppstein
MIT Biology
Graduate Student, Bartel Lab
Whitehead Institute, Room 621
9 Cambridge Center
Cambridge, MA 02142
Cell: (609) 933-3952