[BioPython] [Correction!] Emboss eprimer3-Product Size Range

[Stefanie Lück]

I'm sorry!
I prescribed me!

primer_cl.set_parameter("-productsizerange", "100-200 250-300")
Causes no output and not
primer_cl.set_parameter("-productsizerange", "100-200")
as I wrote!

>You don't seem to be using Bio.Fasta, and this module is now obsolete.
Sorry I just forgot to deleted. I showed only a part of the code.

The error print and on the command prompt gives:

Command line:
eprimer3 -sequence in.txt -outfile out.pr3 -target 50,100 -productsizerange 100-200 250-300 
Return code:
1
Errors:
Error: Argument '250-300' : Too many parameters 3/2
Messages:

But it's described in the eprimer3 help file:

"-productsizerange   range      [100-300] ...If one desires PCR
                                  products in either the range from 100 to 150
                                  bases or in the range from 200 to 250 bases
                                  then one would set this parameter to
                                  100-150 200-250.
                                  EPrimer3 favors ranges to the left side of
                                  the parameter string..."

My input file is a normal multiple fasta file.

Thanks and sorry for the mistake!






----- Original Message ----- 
From: "Peter" <biopython at maubp.freeserve.co.uk>
To: "Stefanie Lück" <lueck at ipk-gatersleben.de>
Cc: <biopython at biopython.org>
Sent: Monday, December 01, 2008 4:08 PM
Subject: Re: [BioPython] Emboss eprimer3-Product Size Range


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