[Biopython] Primer3 for testing primers

Peter Saffrey pzs at dcs.gla.ac.uk
Tue Jul 7 12:41:14 EDT 2009


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...

Peter


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