[BioPython] Primer3Commandline

[Yair Benita]

Dear Larry,
There is actually an error in the ³Bio/Emboss/Applications.py² file. The
application in Emboss is not called Primer3 but rather eprimer3. So all you
have to do is to change line number 13 from:

    def __init__(self, cmd = "primer3"):

To:

    def __init__(self, cmd = "eprimer3"):

You should also notice that not all the options available in eprimer are
listed in the parameter list. So if one of the options is missing just add
it to the list.

Good luck,
Yair
-- 
Yair Benita
Pharmaceutical Proteomics
Utrecht University


on 25/4/2003 21:04, Larry at l.heisler at rogers.com wrote:

> but...when I run a script similar to that in Brad Thompsons lectures,
> something does not work
> http://open-bio.org/bosc2002/slides/2002-08-01-Chapman-Biopython.pdf
> 
> 
> -----relevant part of my script-----
> primer_cl=Primer3Commandline()
> primer_cl.set_parameter("-sequence","in.pr3")
> primer_cl.set_parameter("-outfile","out.pr3")
> print str(primer_cl)    # i added this to see the command line that was used
> result,r,e=generic_run(primer_cl)
> ---------