[Biopython] Primer3 for testing primers

[Peter]

On Tue, Jul 7, 2009 at 5:41 PM, Peter Saffrey<pzs at dcs.gla.ac.uk> wrote:
> Has anybody done this through Biopython? I found this posting:
>
> http://portal.open-bio.org/pipermail/biopython/2003-October/001673.html
>
> but it generates a primer3 input file, rather than using the set_parameter()
> method provided by Bio.Emboss.Applications.Primer3Commandline.
>
> The problem is that by running primer3 from the command line, I can't get it
> to report problems with (for example) temperature or GC content without
> using the PRIMER_EXPLAIN_FLAG option, and Primer3Commandline
> doesn't seem to support that option.
>
> This also makes me wonder whether Biopython's primer3 output parsing knows
> how to read the primer3 "explain" syntax:
>
> PRIMER_LEFT_EXPLAIN=considered 1, ok 1
> PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
>
> Does anybody know?
>
> I'm not finding the primer3 documentation all that helpful either :( There
> is no mailing list or contact email address...

Are you sure you are using the EMBOSS version of primer3? i.e.
the command line tool called eprimer3 (with an "e" at the start).

EMBOSS mailing list:
http://emboss.sourceforge.net/support/#usermail
http://emboss.open-bio.org/mailman/listinfo/emboss

EMBOSS docs:
http://emboss.sourceforge.net/apps/cvs/emboss/apps/eprimer3.html

This does specifically list the "-explainflag" argument, which should be
set to a boolean value. This is supported in the Primer3Commandline
wrapper in Biopython. I'm not sure about the parser off hand.

Peter