[BioPython] Emboss eprimer3-Product Size Range

[Peter]

On Mon, Dec 1, 2008 at 1:13 PM, Stefanie Lück <lueck at ipk-gatersleben.de> wrote:
> Hi!
>
> I'm working with Emboss eprimer3 and I have a short question:
>
> How can I enter the paramter "product size range"? Usually it's
> something like 500-1000 450-500 etc.

According the the eprimer3 tool itself (try "eprimer3 --help" at the
command line) you seem to be using productsizerange correctly in the
following code snippet.

> from Bio import Fasta

You don't seem to be using Bio.Fasta, and this module is now obsolete.

> from Bio.Emboss.Applications import Primer3Commandline
> from Bio.Application import generic_run
> from Bio.Emboss import Primer3
>
> primer_cl = Primer3Commandline()
> primer_cl.set_parameter("-sequence", "in.txt")
> primer_cl.set_parameter("-outfile", "out.pr3")
> primer_cl.set_parameter("-productsizerange", "100-200")
> primer_cl.set_parameter("-target", "%s,%s" % (50, 100))
> result, messages, errors = generic_run(primer_cl)

So this fails - what what exactly goes wrong  i.e. what does this give:

print "Command line:"
print primer_cl
print "Return code:"
print result.return_code
print "Errors:"
print errors.read()
print "Messages":
print messages.read()

And my usual question in this sort of situation: what happens if you
run this command by hand at the command prompt?

If you email me your input file (in.txt) then I can try running this
on my machine (don't send it to the mailing list unless its very small
and you don't mind sharing it with the world).

Peter