[BioPython] Primer3Commandline

[Larry Heisler]

Thanks for the help Yair.  Actually found this myself (pat myself on the
back).  Took a while though because when I installed biopython did not
realize that it copied the files to a directory under python, so I was
trying to make changes to the wrong file (still figuring out linux).   Had
some help from Brad Thompson as well.
Larry

----- Original Message -----
From: "Yair Benita" <Y.Benita at pharm.uu.nl>
To: "Larry" <l.heisler at rogers.com>; <biopython at biopython.org>
Sent: Monday, April 28, 2003 7:24 AM
Subject: Re: [BioPython] Primer3Commandline


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)
> ---------