[Biopython] Primer3 for testing primers
Peter Saffrey
pzs at dcs.gla.ac.uk
Tue Jul 7 16:41:14 UTC 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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